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TY - JOUR
TI - Genome of a songbird unveiled
AU - Pinaud, Raphael
PY - 2011
T2 - Journal of Biology
J2 - J Biol
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2871510/
VL - 9
IS - 3
SP - 19-19
DO - 10.1186/jbiol222
C2 - 2871510
N2 - An international collaborative effort has recently uncovered the genome of the zebra finch, a songbird model that has provided unique insights into an array of biological phenomena. See research articles , , and
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Reprogramming of the non-coding transcriptome during brain development
AU - Valadkhan, Saba
AU - Nilsen, Timothy W
PY - 2011
T2 - Journal of Biology
J2 - J Biol
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2871522/
VL - 9
IS - 1
SP - 5-5
DO - 10.1186/jbiol197
C2 - 2871522
N2 - A recent global analysis of gene expression during the differentiation of neuronal stem cells to neurons and oligodendrocytes indicates a complex pattern of changes in the expression of both protein-coding transcripts and long non-protein-coding RNAs. See research article .
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - LINE-1 Retrotransposition Activity in Human Genomes
AU - Beck, Christine R
AU - Collier, Pamela
AU - Macfarlane, Catriona
AU - Malig, Maika
AU - Kidd, Jeffrey M
AU - Eichler, Evan E
AU - Badge, Richard M
AU - Moran, John V
PY - 2011
T2 - Cell
J2 - Cell
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013285/
VL - 141
IS - 7
SP - 1159-1170
DO - 10.1016/j.cell.2010.05.021
C2 - 3013285
N2 - Summary: Long Interspersed Element-1 (LINE-1 or L1) sequences comprise the bulk of retrotransposition activity in the human genome; however, the abundance of highly active or ‘hot’ L1s in the human population remains largely unexplored. Here, we used a fosmid-based, paired-end DNA sequencing strategy to identify 68 full-length L1s which are differentially present among individuals but are absent from the human genome reference sequence. The majority of these L1s were highly active in a cultured cell retrotransposition assay. Genotyping 26 elements revealed that two L1s are only found in Africa and that two more are absent from the H952 subset of the Human Genome Diversity Panel. Therefore, these results suggest that ‘hot’ L1s are more abundant in the human population than previously appreciated, and that ongoing L1 retrotransposition continues to be a major source of inter-individual genetic variation.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Lrp12/Mig13a Reveals Changing Patterns of Preplate Neuronal Polarity during Corticogenesis that Are Absent in Reeler Mutant Mice
AU - Schneider, Stephanie
AU - Gulacsi, Alexandra
AU - Hatten, Mary E
PY - 2011
T2 - Cerebral Cortex (New York, NY)
J2 - Cereb Cortex
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000567/
VL - 21
IS - 1
SP - 134-144
DO - 10.1093/cercor/bhq070
C2 - 3000567
N2 - During corticogenesis, the earliest generated neurons form the preplate, which evolves into the marginal zone and subplate. Lrp12/Mig13a, a mammalian gene related to the Caenorhabditis elegans neuroblast migration gene mig-13, is expressed in a subpopulation of preplate neurons that undergo ventrally directed tangential migrations in the preplate layer and pioneer axon projections to the anterior commissure. As the preplate separates, Lrp12/Mig13a-positive neurons polarize in the radial plane and form a pseudocolumnar pattern, prior to moving to a deeper position within the emerging subplate layer. These changes in neuronal polarity do not occur in reeler mutant mice, revealing the earliest known defect in reeler cortical patterning and suggesting that the alignment of preplate neurons into a pseudolayer facilitates the movement of later-born radially migrating neurons into the emerging cortical plate.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - ENCODE whole-genome data in the UCSC genome browser (2011 update)
AU - Raney, Brian J
AU - Cline, Melissa S
AU - Rosenbloom, Kate R
AU - Dreszer, Timothy R
AU - Learned, Katrina
AU - Barber, Galt P
AU - Meyer, Laurence R
AU - Sloan, Cricket A
AU - Malladi, Venkat S
AU - Roskin, Krishna M
AU - Suh, Bernard B
AU - Hinrichs, Angie S
AU - Clawson, Hiram
AU - Zweig, Ann S
AU - Kirkup, Vanessa
AU - Fujita, Pauline A
AU - Rhead, Brooke
AU - Smith, Kayla E
AU - Pohl, Andy
AU - Kuhn, Robert M
AU - Karolchik, Donna
AU - Haussler, David
AU - Kent, W James
PY - 2011
T2 - Nucleic Acids Research
J2 - Nucleic Acids Res
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013645/
VL - 39
IS - Database issue
SP - D871-D875
DO - 10.1093/nar/gkq1017
C2 - 3013645
N2 - The ENCODE project is an international consortium with a goal of cataloguing all the functional elements in the human genome. The ENCODE Data Coordination Center (DCC) at the University of California, Santa Cruz serves as the central repository for ENCODE data. In this role, the DCC offers a collection of high-throughput, genome-wide data generated with technologies such as ChIP-Seq, RNA-Seq, DNA digestion and others. This data helps illuminate transcription factor-binding sites, histone marks, chromatin accessibility, DNA methylation, RNA expression, RNA binding and other cell-state indicators. It includes sequences with quality scores, alignments, signals calculated from the alignments, and in most cases, element or peak calls calculated from the signal data. Each data set is available for visualization and download via the UCSC Genome Browser (). ENCODE data can also be retrieved using a metadata system that captures the experimental parameters of each assay. The ENCODE web portal at UCSC () provides information about the ENCODE data and links for access.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - BACs as Tools for the Study of Genomic Imprinting
AU - Tunster, S J
AU - Van De Pette, M
AU - John, R M
PY - 2011
T2 - Journal of Biomedicine and Biotechnology
J2 - J Biomed Biotechnol
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3010669/
VL - 2011
DO - 10.1155/2011/283013
C2 - 3010669
N2 - Genomic imprinting in mammals results in the expression of genes from only one parental allele. Imprinting occurs as a consequence of epigenetic marks set down either in the father's or the mother's germ line and affects a very specific category of mammalian gene. A greater understanding of this distinctive phenomenon can be gained from studies using large genomic clones, called bacterial artificial chromosomes (BACs). Here, we review the important applications of BACs to imprinting research, covering physical mapping studies and the use of BACs as transgenes in mice to study gene expression patterns, to identify imprinting centres, and to isolate the consequences of altered gene dosage. We also highlight the significant and unique advantages that rapid BAC engineering brings to genomic imprinting research.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera
AU - Munoz-Torres, Monica C
AU - Reese, Justin T
AU - Childers, Christopher P
AU - Bennett, Anna K
AU - Sundaram, Jaideep P
AU - Childs, Kevin L
AU - Anzola, Juan M
AU - Milshina, Natalia
AU - Elsik, Christine G
PY - 2011
T2 - Nucleic Acids Research
J2 - Nucleic Acids Res
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013718/
VL - 39
IS - Database issue
SP - D658-D662
DO - 10.1093/nar/gkq1145
C2 - 3013718
N2 - The Hymenoptera Genome Database (HGD) is a comprehensive model organism database that caters to the needs of scientists working on insect species of the order Hymenoptera. This system implements open-source software and relational databases providing access to curated data contributed by an extensive, active research community. HGD contains data from 9 different species across ∼200 million years in the phylogeny of Hymenoptera, allowing researchers to leverage genetic, genome sequence and gene expression data, as well as the biological knowledge of related model organisms. The availability of resources across an order greatly facilitates comparative genomics and enhances our understanding of the biology of agriculturally important Hymenoptera species through genomics. Curated data at HGD includes predicted and annotated gene sets supported with evidence tracks such as ESTs/cDNAs, small RNA sequences and GC composition domains. Data at HGD can be queried using genome browsers and/or BLAST/PSI-BLAST servers, and it may also be downloaded to perform local searches. We encourage the public to access and contribute data to HGD at: .
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing
AU - Martelli, Pier L
AU - D'Antonio, Mattia
AU - Bonizzoni, Paola
AU - Castrignanò, Tiziana
AU - D'Erchia, Anna M
AU - D'Onorio De Meo, Paolo
AU - Fariselli, Piero
AU - Finelli, Michele
AU - Licciulli, Flavio
AU - Mangiulli, Marina
AU - Mignone, Flavio
AU - Pavesi, Giulio
AU - Picardi, Ernesto
AU - Rizzi, Raffaella
AU - Rossi, Ivan
AU - Valletti, Alessio
AU - Zauli, Andrea
AU - Zambelli, Federico
AU - Casadio, Rita
AU - Pesole, Graziano
PY - 2011
T2 - Nucleic Acids Research
J2 - Nucleic Acids Res
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013677/
VL - 39
IS - Database issue
SP - D80-D85
DO - 10.1093/nar/gkq1073
C2 - 3013677
N2 - Alternative splicing is emerging as a major mechanism for the expansion of the transcriptome and proteome diversity, particularly in human and other vertebrates. However, the proportion of alternative transcripts and proteins actually endowed with functional activity is currently highly debated. We present here a new release of ASPicDB which now provides a unique annotation resource of human protein variants generated by alternative splicing. A total of 256 939 protein variants from 17 191 multi-exon genes have been extensively annotated through state of the art machine learning tools providing information of the protein type (globular and transmembrane), localization, presence of PFAM domains, signal peptides, GPI-anchor propeptides, transmembrane and coiled-coil segments. Furthermore, full-length variants can be now specifically selected based on the annotation of CAGE-tags and polyA signal and/or polyA sites, marking transcription initiation and termination sites, respectively. The retrieval can be carried out at gene, transcript, exon, protein or splice site level allowing the selection of data sets fulfilling one or more features settled by the user. The retrieval interface also enables the selection of protein variants showing specific differences in the annotated features. ASPicDB is available at .
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - TIARA: a database for accurate analysis of multiple personal genomes based on cross-technology
AU - Hong, Dongwan
AU - Park, Sung-Soo
AU - Ju, Young Seok
AU - Kim, Sheehyun
AU - Shin, Jong-Yeon
AU - Kim, Sujung
AU - Yu, Saet-Byeol
AU - Lee, Won-Chul
AU - Lee, Seungbok
AU - Park, Hansoo
AU - Kim, Jong-Il
AU - Seo, Jeong-Sun
PY - 2011
T2 - Nucleic Acids Research
J2 - Nucleic Acids Res
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013693/
VL - 39
IS - Database issue
SP - D883-D888
DO - 10.1093/nar/gkq1101
C2 - 3013693
N2 - High-throughput genomic technologies have been used to explore personal human genomes for the past few years. Although the integration of technologies is important for high-accuracy detection of personal genomic variations, no databases have been prepared to systematically archive genomes and to facilitate the comparison of personal genomic data sets prepared using a variety of experimental platforms. We describe here the Total Integrated Archive of Short-Read and Array (TIARA; ) database, which contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs). At present, 36 individual genomes have been archived and may be displayed in the database. TIARA supports a user-friendly genome browser, which retrieves read-depths (RDs) and log2 ratios from NGS and CGH arrays, respectively. In addition, this database provides information on all genomic variants and the raw data, including short reads and feature-level CGH data, through anonymous file transfer protocol. More personal genomes will be archived as more individuals are analyzed by NGS or CGH array. TIARA provides a new approach to the accurate interpretation of personal genomes for genome research.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Primate and Rodent Specific Intron Gains and the Origin of Retrogenes with Splice Variants
AU - Szcze?niak, Micha? W
AU - Ciomborowska, Joanna
AU - Nowak, Witold
AU - Rogozin, Igor B
AU - Maka?owska, Izabela
PY - 2011
T2 - Molecular biology and evolution
J2 - Mol Biol Evol
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3002245/
VL - 28
IS - 1
SP - 33-37
DO - 10.1093/molbev/msq260
C2 - 3002245
N2 - Retroposition, a leading mechanism for gene duplication, is an important process shaping the evolution of genomes. Retrogenes are also involved in the gene structure evolution as a major player in the process of intron deletion. Here, we demonstrate the role of retrogenes in intron gain in mammals. We identified one case of “intronization,” the transformation of exonic sequences into an intron, in the primate specific retrogene RNF113B and two independent “intronization” events in the retrogene DCAF12L2, one in the common ancestor of primates and rodents and another one in the rodent lineage. Intron gain resulted from the origin of new splice variants, and both genes have two transcript forms, one with retained intron and one with the intron spliced out. Evolution of these genes, especially RNF113B, has been very dynamic and has been accompanied by several additional events including parental gene loss, secondary retroposition, and exaptation of transposable elements.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Structural insights and ab initio sequencing within the DING proteins family
AU - Elias, Mikael
AU - Liebschner, Dorothee
AU - Gotthard, Guillaume
AU - Chabriere, Eric
PY - 2011
T2 - Journal of Synchrotron Radiation
J2 - J Synchrotron Radiat
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3004253/
VL - 18
IS - Pt 1
SP - 45-49
DO - 10.1107/S0909049510036009
C2 - 3004253
N2 - DING proteins constitute an intriguing family of phosphate-binding proteins that was identified in a wide range of organisms, from prokaryotes and archae to eukaryotes. Despite their seemingly ubiquitous occurrence in eukaryotes, their encoding genes are missing from sequenced genomes. Such a lack has considerably hampered functional studies. In humans, these proteins have been related to several diseases, like atherosclerosis, kidney stones, inflammation processes and HIV inhibition. The human phosphate binding protein is a human representative of the DING family that was serendipitously discovered from human plasma. An original approach was developed to determine ab initio the complete and exact sequence of this 38?kDa protein by utilizing mass spectrometry and X-ray data in tandem. Taking advantage of this first complete eukaryotic DING sequence, a immunohistochemistry study was undertaken to check the presence of DING proteins in various mice tissues, revealing that these proteins are widely expressed. Finally, the structure of a bacterial representative from Pseudomonas fluorescens was solved at sub-angstrom resolution, allowing the molecular mechanism of the phosphate binding in these high-affinity proteins to be elucidated.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - dbDNV: a resource of duplicated gene nucleotide variants in human genome
AU - Ho, Meng-Ru
AU - Tsai, Kuo-Wang
AU - Chen, Chun-Houh
AU - Lin, Wen-Chang
PY - 2011
T2 - Nucleic Acids Research
J2 - Nucleic Acids Res
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013738/
VL - 39
IS - Database issue
SP - D920-D925
DO - 10.1093/nar/gkq1197
C2 - 3013738
N2 - Gene duplications are scattered widely throughout the human genome. A single-base difference located in nearly identical duplicated segments may be misjudged as a single nucleotide polymorphism (SNP) from individuals. This imperfection is undistinguishable in current genotyping methods. As the next-generation sequencing technologies become more popular for sequence-based association studies, numerous ambiguous SNPs are rapidly accumulated. Thus, analyzing duplication variations in the reference genome to assist in preventing false positive SNPs is imperative. We have identified >10% of human genes associated with duplicated gene loci (DGL). Through meticulous sequence alignments of DGL, we systematically designated 1 236 956 variations as duplicated gene nucleotide variants (DNVs). The DNV database (dbDNV) () has been established to promote more accurate variation annotation. Aside from the flat file download, users can explore the gene-related duplications and the associated DNVs by DGL and DNV searches, respectively. In addition, the dbDNV contains 304 110 DNV-coupled SNPs. From DNV-coupled SNP search, users observe which SNP records are also variants among duplicates. This is useful while ∼58% of exonic SNPs in DGL are DNV-coupled. Because of high accumulation of ambiguous SNPs, we suggest that annotating SNPs with DNVs possibilities should improve association studies of these variants with human diseases.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Database resources of the National Center for Biotechnology Information
AU - Sayers, Eric W
AU - Barrett, Tanya
AU - Benson, Dennis A
AU - Bolton, Evan
AU - Bryant, Stephen H
AU - Canese, Kathi
AU - Chetvernin, Vyacheslav
AU - Church, Deanna M
AU - Dicuccio, Michael
AU - Federhen, Scott
AU - Feolo, Michael
AU - Fingerman, Ian M
AU - Geer, Lewis Y
AU - Helmberg, Wolfgang
AU - Kapustin, Yuri
AU - Landsman, David
AU - Lipman, David J
AU - Lu, Zhiyong
AU - Madden, Thomas L
AU - Madej, Tom
AU - Maglott, Donna R
AU - Marchler-Bauer, Aron
AU - Miller, Vadim
AU - Mizrachi, Ilene
AU - Ostell, James
AU - Panchenko, Anna
AU - Phan, Lon
AU - Pruitt, Kim D
AU - Schuler, Gregory D
AU - Sequeira, Edwin
AU - Sherry, Stephen T
AU - Shumway, Martin
AU - Sirotkin, Karl
AU - Slotta, Douglas
AU - Souvorov, Alexandre
AU - Starchenko, Grigory
AU - Tatusova, Tatiana A
AU - Wagner, Lukas
AU - Wang, Yanli
AU - Wilbur, W John
AU - Yaschenko, Eugene
AU - Ye, Jian
PY - 2011
T2 - Nucleic Acids Research
J2 - Nucleic Acids Res
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013733/
VL - 39
IS - Database issue
SP - D38-D51
DO - 10.1093/nar/gkq1172
C2 - 3013733
N2 - In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Electronic PCR, OrfFinder, Splign, ProSplign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), IBIS, Biosystems, Peptidome, OMSSA, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at .
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Isolation of Specific Clones from Nonarrayed BAC Libraries through Homologous Recombination
AU - Nefedov, Mikhail
AU - Carbone, Lucia
AU - Field, Matthew
AU - Schein, Jacquie
AU - de Jong, Pieter J
PY - 2011
T2 - Journal of Biomedicine and Biotechnology
J2 - J Biomed Biotechnol
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2957146/
VL - 2011
DO - 10.1155/2011/560124
C2 - 2957146
N2 - We have developed a new approach to screen bacterial artificial chromosome (BAC) libraries by recombination selection. To test this method, we constructed an orangutan BAC library using an E. coli strain (DY380) with temperature inducible homologous recombination (HR) capability. We amplified one library segment, induced HR at 42°C to make it recombination proficient, and prepared electrocompetent cells for transformation with a kanamycin cassette to target sequences in the orangutan genome through terminal recombineering homologies. Kanamycin-resistant colonies were tested for the presence of BACs containing the targeted genes by the use of a PCR-assay to confirm the presence of the kanamycin insertion. The results indicate that this is an effective approach for screening clones. The advantage of recombination screening is that it avoids the high costs associated with the preparation, screening, and archival storage of arrayed BAC libraries. In addition, the screening can be conceivably combined with genetic engineering to create knockout and reporter constructs for functional studies.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - DBASS3 and DBASS5: databases of aberrant 3′- and 5′-splice sites
AU - Buratti, Emanuele
AU - Chivers, Martin
AU - Hwang, Gyulin
AU - Vorechovsky, Igor
PY - 2011
T2 - Nucleic Acids Research
J2 - Nucleic Acids Res
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013770/
VL - 39
IS - Database issue
SP - D86-D91
DO - 10.1093/nar/gkq887
C2 - 3013770
N2 - DBASS3 and DBASS5 provide comprehensive repositories of new exon boundaries that were induced by pathogenic mutations in human disease genes. Aberrant 5′- and 3′-splice sites were activated either by mutations in the consensus sequences of natural exon–intron junctions (cryptic sites) or elsewhere (‘de novo’ sites). DBASS3 and DBASS5 currently contain approximately 900 records of cryptic and de novo 3′- and 5′-splice sites that were produced by over a thousand different mutations in approximately 360 genes. DBASS3 and DBASS5 data can be searched by disease phenotype, gene, mutation, location of aberrant splice sites in introns and exons and their distance from authentic counterparts, by bibliographic references and by the splice-site strength estimated with several prediction algorithms. The user can also retrieve reference sequences of both aberrant and authentic splice sites with the underlying mutation. These data will facilitate identification of introns or exons frequently involved in aberrant splicing, mutation analysis of human disease genes and study of germline or somatic mutations that impair RNA processing. Finally, this resource will be useful for fine-tuning splice-site prediction algorithms, better definition of auxiliary splicing signals and design of new reporter assays. DBASS3 and DBASS5 are freely available at .
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Identification of causal sequence variants of disease in the next generation sequencing era.
AU - Kingsley, Christopher B
PY - 2011
T2 - Methods in molecular biology (Clifton, N.J.)
J2 - Methods Mol Biol
UR - http://www.ncbi.nlm.nih.gov/pubmed/21204025
VL - 700
SP - 37-46
N2 - Over the last decade, genetic studies have identified numerous associations between single nucleotide polymorphism (SNP) alleles in the human genome and important human diseases. Unfortunately, extending these initial associative findings to identification of the true causal variants that underlie disease susceptibility is usually not a straightforward task. Causal variant identification typically involves searching through sizable regions of genomic DNA in the vicinity of disease-associated SNPs for sequence variants in functional elements including protein coding, regulatory, and structural sequences. Prioritization of these searches is greatly aided by knowledge of the location of functional sequences in the human genome. This chapter briefly reviews several of the common approaches used to functionally annotate the human genome and discusses how this information can be used in concert with the emerging technology of next generation high-throughput sequencing to identify causal variants of human disease.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Cell-Based Co-transfection Microarrays for Use with HEK293T Cells on a Poly D: -Lysine-Coated Polystyrene Microplate.
AU - Soni, Meenal
AU - Lai, Fang
PY - 2011
T2 - Methods in molecular biology (Clifton, N.J.)
J2 - Methods Mol Biol
UR - http://www.ncbi.nlm.nih.gov/pubmed/21104051
VL - 706
SP - 13-25
N2 - Analysis of the human genome sequence has identified thousands of putative genes with unknown function; therefore, a new tool allowing for rapid identification of gene functions is needed. Reverse transfection microarray technology, which turns a DNA microarray into a cell-based microarray, has emerged for simultaneously studying the function of many genes. Since the initial demonstration in 2001, many variations have surfaced, making the technology more versatile for a broad range of applications. We have developed a protocol to make ready-to-transfect DNA microarrays in a 96-well microplate for co-transfection of two plasmids into HEK293T cells. This cell-based microarray in a microplate may be used for screening hundreds of analytes against multiple protein targets in parallel, providing a powerful tool for functional genomics and drug discovery.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Bovine Genome Database: integrated tools for genome annotation and discovery
AU - Childers, Christopher P
AU - Reese, Justin T
AU - Sundaram, Jaideep P
AU - Vile, Donald C
AU - Dickens, C Michael
AU - Childs, Kevin L
AU - Salih, Hanni
AU - Bennett, Anna K
AU - Hagen, Darren E
AU - Adelson, David L
AU - Elsik, Christine G
PY - 2011
T2 - Nucleic Acids Research
J2 - Nucleic Acids Res
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013744/
VL - 39
IS - Database issue
SP - D830-D834
DO - 10.1093/nar/gkq1235
C2 - 3013744
N2 - The Bovine Genome Database (BGD; ) strives to improve annotation of the bovine genome and to integrate the genome sequence with other genomics data. BGD includes GBrowse genome browsers, the Apollo Annotation Editor, a quantitative trait loci (QTL) viewer, BLAST databases and gene pages. Genome browsers, available for both scaffold and chromosome coordinate systems, display the bovine Official Gene Set (OGS), RefSeq and Ensembl gene models, non-coding RNA, repeats, pseudogenes, single-nucleotide polymorphism, markers, QTL and alignments to complementary DNAs, ESTs and protein homologs. The Bovine QTL viewer is connected to the BGD Chromosome GBrowse, allowing for the identification of candidate genes underlying QTL. The Apollo Annotation Editor connects directly to the BGD Chado database to provide researchers with remote access to gene evidence in a graphical interface that allows editing and creating new gene models. Researchers may upload their annotations to the BGD server for review and integration into the subsequent release of the OGS. Gene pages display information for individual OGS gene models, including gene structure, transcript variants, functional descriptions, gene symbols, Gene Ontology terms, annotator comments and links to National Center for Biotechnology Information and Ensembl. Each gene page is linked to a wiki page to allow input from the research community.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Characterization of New Otic Enhancers of the Pou3f4 Gene Reveal Distinct Signaling Pathway Regulation and Spatio-Temporal Patterns
AU - Robert-Moreno, Àlex
AU - Naranjo, Silvia
AU - de la Calle-Mustienes, Elisa
AU - Gómez-Skarmeta, José Luis
AU - Alsina, Berta
PY - 2010
T2 - PLoS ONE
J2 - PLoS One
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013142/
VL - 5
IS - 12
DO - 10.1371/journal.pone.0015907
C2 - 3013142
N2 - POU3F4 is a member of the POU-homedomain transcription factor family with a prominent role in inner ear development. Mutations in the human POU3F4 coding unit leads to X-linked deafness type 3 (DFN3), characterized by conductive hearing loss and progressive sensorineural deafness. Microdeletions found 1 Mb 5′ upstream of the coding region also displayed the same phenotype, suggesting that cis-regulatory elements might be present in that region. Indeed, we and others have recently identified several enhancers at the 1 Mb 5′ upstream interval of the pou3f4 locus. Here we characterize the spatio-temporal patterns of these regulatory elements in zebrafish transgenic lines. We show that the most distal enhancer (HCNR 81675) is activated earlier and drives GFP reporter expression initially to a broad ear domain to progressively restrict to the sensory patches. The proximal enhancer (HCNR 82478) is switched later during development and promotes expression, among in other tissues, in sensory patches from its onset. The third enhancer (HCNR 81728) is also active at later stages in the otic mesenchyme and in the otic epithelium. We also characterize the signaling pathways regulating these enhancers. While HCNR 81675 is regulated by very early signals of retinoic acid, HCNR 82478 is regulated by Fgf activity at a later stage and the HCNR 81728 enhancer is under the control of Hh signaling. Finally, we show that Sox2 and Pax2 transcription factors are bound to HCNR 81675 genomic region during otic development and specific mutations to these transcription factor binding sites abrogates HCNR 81675 enhancer activity. Altogether, our results suggest that pou3f4 expression in inner ear might be under the control of distinct regulatory elements that fine-tune the spatio-temporal activity of this gene and provides novel data on the signaling mechanisms controlling pou3f4 function.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Activation of Pluripotency Genes in Human Fibroblast Cells by a Novel mRNA Based Approach
AU - Plews, Jordan R.
AU - Li, JianLiang
AU - Jones, Mark
AU - Moore, Harry D.
AU - Mason, Chris
AU - Andrews, Peter W.
AU - Na, Jie
PY - 2010
T2  - PLoS ONE
J2 - PLoS One
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3012685/
VL - 5
IS - 12
DO - 10.1371/journal.pone.0014397
C2 - 3012685
N2 - Background: Several methods have been used to induce somatic cells to re-enter the pluripotent state. Viral transduction of reprogramming genes yields higher efficiency but involves random insertions of viral sequences into the human genome. Although induced pluripotent stem (iPS) cells can be obtained with the removable PiggyBac transposon system or an episomal system, both approaches still use DNA constructs so that resulting cell lines need to be thoroughly analyzed to confirm they are free of harmful genetic modification. Thus a method to change cell fate without using DNA will be very useful in regenerative medicine. Methodology/Principal Findings: In this study, we synthesized mRNAs encoding OCT4, SOX2, cMYC, KLF4 and SV40 large T (LT) and electroporated them into human fibroblast cells. Upon transfection, fibroblasts expressed these factors at levels comparable to, or higher than those in human embryonic stem (ES) cells. Ectopically expressed OCT4 localized to the cell nucleus within 4 hours after mRNA introduction. Transfecting fibroblasts with a mixture of mRNAs encoding all five factors significantly increased the expression of endogenous OCT4, NANOG, DNMT3β, REX1 and SALL4. When such transfected fibroblasts were also exposed to several small molecules (valproic acid, BIX01294 and 5′-aza-2′-deoxycytidine) and cultured in human embryonic stem cell (ES) medium they formed small aggregates positive for alkaline phosphatase activity and OCT4 protein within 30 days. Conclusion/Significance: Our results demonstrate that mRNA transfection can be a useful approach to precisely control the protein expression level and short-term expression of reprogramming factors is sufficient to activate pluripotency genes in differentiated cells.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence.
AU - Trost, Eva
AU - Ott, Lisa
AU - Schneider, Jessica
AU - Schroder, Jasmin
AU - Jaenicke, Sebastian
AU - Goesmann, Alexander
AU - Husemann, Peter
AU - Stoye, Jens
AU - Alves Dorella, Fernanda
AU - Souza Rocha, Flavia
AU - de Castro Soares, Siomar
AU - D'Afonseca, Vivian
AU - Miyoshi, Anderson
AU - Ruiz, Jeronimo
AU - Silva, Artur
AU - Azevedo, Vasco
AU - Burkovski, Andreas
AU - Guiso, Nicole
AU - Join-Lambert, Olivier F
AU - Kayal, Samer
AU - Tauch, Andreas
PY - 2010
T2 - BMC genomics
J2 - BMC Genomics
UR - http://www.ncbi.nlm.nih.gov/pubmed/21192786
VL - 11
IS - 1
SP - 728
N2 - ABSTRACT: BACKGROUND: Corynebacterium pseudotuberculosis is generally regarded as an important animal pathogen that rarely infects humans. Clinical strains are occasionally recovered from human cases of lymphadenitis, such as C. pseudotuberculosis FRC41 that was isolated from the inguinal lymph node of a 12-year-old girl with necrotizing lymphadenitis. To detect potential virulence factors and corresponding gene-regulatory networks in this human isolate, the genome sequence of C. pseudotuberculosis FCR41 was determined by pyrosequencing and functionally annotated. RESULTS: Sequencing and assembly of the C. pseudotuberculosis FRC41 genome yielded a circular chromosome with a size of 2,337,913 bp and a mean G+C content of 52.2%. Specific gene sets associated with iron and zinc homeostasis were detected among the 2,110 predicted protein-coding regions and integrated into a gene-regulatory network that is linked with both the central metabolism and the oxidative stress response of FRC41. Two gene clusters encode proteins involved in the sortase-mediated polymerization of adhesive pili that can probably mediate the adherence to host tissue to facilitate additional ligand-receptor interactions and the delivery of virulence factors. The prominent virulence factors phospholipase D (Pld) and corynebacterial protease CP40 are encoded in the genome of this human isolate. The genome annotation revealed additional serine proteases, neuraminidase H, nitric oxide reductase, an invasion-associated protein, and acyl-CoA carboxylase subunits involved in mycolic acid biosynthesis as potential virulence factors. The cAMP-sensing transcription regulator GlxR plays a key role in controlling the expression of several genes contributing to virulence. CONCLUSION: The functional data deduced from the genome sequencing and the extended knowledge of virulence factors indicate that the human isolate C. pseudotuberculosis FRC41 is equipped with a distinct gene set promoting its survival under unfavorable environmental conditions encountered in the mammalian host.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Analysis of MicroRNA Expression in the Prepubertal Testis
AU - Buchold, Gregory M
AU - Coarfa, Cristian
AU - Kim, Jong
AU - Milosavljevic, Aleksandar
AU - Gunaratne, Preethi H
AU - Matzuk, Martin M
PY - 2010
T2 - PLoS ONE
J2 - PLoS One
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3012074/
VL - 5
IS - 12
DO - 10.1371/journal.pone.0015317
C2 - 3012074
N2 - Only thirteen microRNAs are conserved between D. melanogaster and the mouse; however, conditional loss of miRNA function through mutation of Dicer causes defects in proliferation of premeiotic germ cells in both species. This highlights the potentially important, but uncharacterized, role of miRNAs during early spermatogenesis. The goal of this study was to characterize on postnatal day 7, 10, and 14 the content and editing of murine testicular miRNAs, which predominantly arise from spermatogonia and spermatocytes, in contrast to prior descriptions of miRNAs in the adult mouse testis which largely reflects the content of spermatids. Previous studies have shown miRNAs to be abundant in the mouse testis by postnatal day 14; however, through Next Generation Sequencing of testes from a B6;129 background we found abundant earlier expression of miRNAs and describe shifts in the miRNA signature during this period. We detected robust expression of miRNAs encoded on the X chromosome in postnatal day 14 testes, consistent with prior studies showing their resistance to meiotic sex chromosome inactivation. Unexpectedly, we also found a similar positional enrichment for most miRNAs on chromosome 2 at postnatal day 14 and for those on chromosome 12 at postnatal day 7. We quantified in vivo developmental changes in three types of miRNA variation including 5′ heterogeneity, editing, and 3′ nucleotide addition. We identified eleven putative novel pubertal testis miRNAs whose developmental expression suggests a possible role in early male germ cell development. These studies provide a foundation for interpretation of miRNA changes associated with testicular pathology and identification of novel components of the miRNA editing machinery in the testis.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Primate-specific evolution of noncoding element insertion into PLA2G4C and human preterm birth
AU - Plunkett, Jevon
AU - Doniger, Scott
AU - Morgan, Thomas
AU - Haataja, Ritva
AU - Hallman, Mikko
AU - Puttonen, Hilkka
AU - Menon, Ramkumar
AU - Kuczynski, Edward
AU - Norwitz, Errol
AU - Snegovskikh, Victoria
AU - Palotie, Aarno
AU - Peltonen, Leena
AU - Fellman, Vineta
AU - Defranco, Emily A
AU - Chaudhari, Bimal P
AU - Oates, John
AU - Boutaud, Olivier
AU - McGregor, Tracy L
AU - McElroy, Jude J
AU - Teramo, Kari
AU - Borecki, Ingrid
AU - Fay, Justin C
AU - Muglia, Louis J
PY - 2010
T2 - BMC Medical Genomics
J2 - BMC Medical Genomics
UR - http://www.biomedcentral.com/1755-8794/3/62
VL - 3
IS - 1
SP - 62
DO - 10.1186/1755-8794-3-62
N2 - Abstract Background: The onset of birth in humans, like other apes, differs from non-primate mammals in its endocrine physiology. We hypothesize that higher primate-specific gene evolution may lead to these differences and target genes involved in human preterm birth, an area of global health significance. Methods: We performed a comparative genomics screen of highly conserved noncoding elements and identified PLA2G4C, a phospholipase A isoform involved in prostaglandin biosynthesis as human accelerated. To examine whether this gene demonstrating primate-specific evolution was associated with birth timing, we genotyped and analyzed 8 common single nucleotide polymorphisms (SNPs) in PLA2G4C in US Hispanic (n = 73 preterm, 292 control), US White (n = 147 preterm, 157 control) and US Black (n = 79 preterm, 166 control) mothers. Results: Detailed structural and phylogenic analysis of PLA2G4C suggested a short genomic element within the gene duplicated from a paralogous highly conserved element on chromosome 1 specifically in primates. SNPs rs8110925 and rs2307276 in US Hispanics and rs11564620 in US Whites were significant after correcting for multiple tests (p < 0.006). Additionally, rs11564620 (Thr360Pro) was associated with increased metabolite levels of the prostaglandin thromboxane in healthy individuals (p = 0.02), suggesting this variant may affect PLA2G4C activity. Conclusions: Our findings suggest that variation in PLA2G4C may influence preterm birth risk by increasing levels of prostaglandins, which are known to regulate labor.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Complete genome sequence of the zoonotic pathogen Chlamydophila psittaci.
AU - Seth-Smith, Helena M B
AU - Harris, Simon R
AU - Rance, Richard
AU - West, Anthony P
AU - Severin, Juliette A
AU - Ossewaarde, Jacobus M
AU - Cutcliffe, Lesley T
AU - Skilton, Rachel J
AU - Marsh, Pete
AU - Parkhill, Julian
AU - Clarke, Ian N
AU - Thomson, Nicholas R
PY - 2010
T2 - Journal of bacteriology
J2 - J Bacteriol
UR - http://www.ncbi.nlm.nih.gov/pubmed/21183672
N2 - We present the first genome sequence of Chlamydophila psittaci, an intracellular pathogen of birds, and a human zoonotic pathogen. A comparison with previously sequenced Chlamydophila genomes shows that, like other chlamydiae, most of the genome diversity is restricted to the plasticity zone. The Cp. psittaci plasmid was also sequenced.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Cancer and Neurodegeneration: Between the Devil and the Deep Blue Sea
AU - Plun-Favreau, Hélène
AU - Lewis, Patrick A
AU - Hardy, John
AU - Martins, L Miguel
AU - Wood, Nicholas W
PY - 2010
T2 - PLoS Genetics
J2 - PLoS Genet
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009676/
VL - 6
IS - 12
DO - 10.1371/journal.pgen.1001257
C2 - 3009676
N2 - Cancer and neurodegeneration are often thought of as disease mechanisms at opposite ends of a spectrum; one due to enhanced resistance to cell death and the other due to premature cell death. There is now accumulating evidence to link these two disparate processes. An increasing number of genetic studies add weight to epidemiological evidence suggesting that sufferers of a neurodegenerative disorder have a reduced incidence for most cancers, but an increased risk for other cancers. Many of the genes associated with either cancer and/or neurodegeneration play a central role in cell cycle control, DNA repair, and kinase signalling. However, the links between these two families of diseases remain to be proven. In this review, we discuss recent and sometimes as yet incomplete genetic discoveries that highlight the overlap of molecular pathways implicated in cancer and neurodegeneration.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - A Novel HMM-Based Method for Detecting Enriched Transcription Factor Binding Sites Reveals RUNX3 as a Potential Target in Pancreatic Cancer Biology
AU - Levkovitz, Liron
AU - Yosef, Nir
AU - Gershengorn, Marvin C
AU - Ruppin, Eytan
AU - Sharan, Roded
AU - Oron, Yoram
PY - 2010
T2 - PLoS ONE
J2 - PLoS One
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008686/
VL - 5
IS - 12
DO - 10.1371/journal.pone.0014423
C2 - 3008686
N2 - Background: Pancreatic adenocarcinoma (PAC) is one of the most intractable malignancies. In order to search for potential new therapeutic targets, we relied on computational methods aimed at identifying transcription factor binding sites (TFBSs) over-represented in the promoter regions of genes differentially expressed in PAC. Though many computational methods have been implemented to accomplish this, none has gained overall acceptance or produced proven novel targets in PAC. To this end we have developed DEMON, a novel method for motif detection. Methodology: DEMON relies on a hidden Markov model to score the appearance of sequence motifs, taking into account all potential sites in a promoter of potentially varying binding affinities. We demonstrate DEMON's accuracy on simulated and real data sets. Applying DEMON to PAC-related data sets identifies the RUNX family as highly enriched in PAC-related genes. Using a novel experimental paradigm to distinguish between normal and PAC cells, we find that RUNX3 mRNA (but not RUNX1 or RUNX2 mRNAs) exhibits time-dependent increases in normal but not in PAC cells. These increases are accompanied by changes in mRNA levels of putative RUNX gene targets. Conclusions: The integrated application of DEMON and a novel differentiation system led to the identification of a single family member, RUNX3, which together with four of its putative targets showed a robust response to a differentiation stimulus in healthy cells, whereas this regulatory mechanism was absent in PAC cells, emphasizing RUNX3 as a promising target for further studies.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Nicotinic Receptor Gene CHRNA4 Interacts with Processing Load in Attention
AU - Espeseth, Thomas
AU - Sneve, Markus Handal
AU - Rootwelt, Helge
AU - Laeng, Bruno
PY - 2010
T2 - PLoS ONE
J2 - PLoS One
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008676/
VL - 5
IS - 12
DO - 10.1371/journal.pone.0014407
C2 - 3008676
N2 - Background: Pharmacological studies suggest that cholinergic neurotransmission mediates increases in attentional effort in response to high processing load during attention demanding tasks . Methodology/Principal Findings: In the present study we tested whether individual variation in CHRNA4, a gene coding for a subcomponent in α4β2 nicotinic receptors in the human brain, interacted with processing load in multiple-object tracking (MOT) and visual search (VS). We hypothesized that the impact of genotype would increase with greater processing load in the MOT task. Similarly, we predicted that genotype would influence performance under high but not low load in the VS task. Two hundred and two healthy persons (age range?=?39–77, Mean?=?57.5, SD?=?9.4) performed the MOT task in which twelve identical circular objects moved about the display in an independent and unpredictable manner. Two to six objects were designated as targets and the remaining objects were distracters. The same observers also performed a visual search for a target letter (i.e. X or Z) presented together with five non-targets while ignoring centrally presented distracters (i.e. X, Z, or L). Targets differed from non-targets by a unique feature in the low load condition, whereas they shared features in the high load condition. CHRNA4 genotype interacted with processing load in both tasks. Homozygotes for the T allele (N?=?62) had better tracking capacity in the MOT task and identified targets faster in the high load trials of the VS task. Conclusion: The results support the hypothesis that the cholinergic system modulates attentional effort, and that common genetic variation can be used to study the molecular biology of cognition.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Somatic Mutation Profiles of MSI and MSS Colorectal Cancer Identified by Whole Exome Next Generation Sequencing and Bioinformatics Analysis
AU - Timmermann, Bernd
AU - Kerick, Martin
AU - Roehr, Christina
AU - Fischer, Axel
AU - Isau, Melanie
AU - Boerno, Stefan T
AU - Wunderlich, Andrea
AU - Barmeyer, Christian
AU - Seemann, Petra
AU - Koenig, Jana
AU - Lappe, Michael
AU - Kuss, Andreas W
AU - Garshasbi, Masoud
AU - Bertram, Lars
AU - Trappe, Kathrin
AU - Werber, Martin
AU - Herrmann, Bernhard G
AU - Zatloukal, Kurt
AU - Lehrach, Hans
AU - Schweiger, Michal R
PY - 2010
T2 - PLoS ONE
J2 - PLoS One
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008745/
VL - 5
IS - 12
DO - 10.1371/journal.pone.0015661
C2 - 3008745
N2 - Background: Colorectal cancer (CRC) is with approximately 1 million cases the third most common cancer worldwide. Extensive research is ongoing to decipher the underlying genetic patterns with the hope to improve early cancer diagnosis and treatment. In this direction, the recent progress in next generation sequencing technologies has revolutionized the field of cancer genomics. However, one caveat of these studies remains the large amount of genetic variations identified and their interpretation. Methodology/Principal Findings: Here we present the first work on whole exome NGS of primary colon cancers. We performed 454 whole exome pyrosequencing of tumor as well as adjacent not affected normal colonic tissue from microsatellite stable (MSS) and microsatellite instable (MSI) colon cancer patients and identified more than 50,000 small nucleotide variations for each tissue. According to predictions based on MSS and MSI pathomechanisms we identified eight times more somatic non-synonymous variations in MSI cancers than in MSS and we were able to reproduce the result in four additional CRCs. Our bioinformatics filtering approach narrowed down the rate of most significant mutations to 359 for MSI and 45 for MSS CRCs with predicted altered protein functions. In both CRCs, MSI and MSS, we found somatic mutations in the intracellular kinase domain of bone morphogenetic protein receptor 1A, BMPR1A, a gene where so far germline mutations are associated with juvenile polyposis syndrome, and show that the mutations functionally impair the protein function. Conclusions/Significance: We conclude that with deep sequencing of tumor exomes one may be able to predict the microsatellite status of CRC and in addition identify potentially clinically relevant mutations.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - High-Definition Mapping of Retroviral Integration Sites Defines the Fate of Allogeneic T Cells After Donor Lymphocyte Infusion
AU - Cattoglio, Claudia
AU - Maruggi, Giulietta
AU - Bartholomae, Cynthia
AU - Malani, Nirav
AU - Pellin, Danilo
AU - Cocchiarella, Fabienne
AU - Magnani, Zulma
AU - Ciceri, Fabio
AU - Ambrosi, Alessandro
AU - von Kalle, Christof
AU - Bushman, Frederic D
AU - Bonini, Chiara
AU - Schmidt, Manfred
AU - Mavilio, Fulvio
AU - Recchia, Alessandra
PY - 2010
T2 - PLoS ONE
J2 - PLoS One
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008730/
VL - 5
IS - 12
DO - 10.1371/journal.pone.0015688
C2 - 3008730
N2 - The infusion of donor lymphocytes transduced with a retroviral vector expressing the HSV-TK suicide gene in patients undergoing hematopoietic stem cell transplantation for leukemia/lymphoma promotes immune reconstitution and prevents infections and graft-versus-host disease. Analysis of the clonal dynamics of genetically modified lymphocytes in vivo is of crucial importance to understand the potential genotoxic risk of this therapeutic approach. We used linear amplification-mediated PCR and pyrosequencing to build a genome-wide, high-definition map of retroviral integration sites in the genome of peripheral blood T cells from two different donors and used gene expression profiling and bioinformatics to associate integration clusters to transcriptional activity and to genetic and epigenetic features of the T cell genome. Comparison with matched random controls and with integrations obtained from CD34+ hematopoietic stem/progenitor cells showed that integration clusters occur within chromatin regions bearing epigenetic marks associated with active promoters and regulatory elements in a cell-specific fashion. Analysis of integration sites in T cells obtained ex vivo two months after infusion showed no evidence of integration-related clonal expansion or dominance, but rather loss of cells harboring integration events interfering with RNA post-transcriptional processing. The study shows that high-definition maps of retroviral integration sites are a powerful tool to analyze the fate of genetically modified T cells in patients and the biological consequences of retroviral transduction.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - In silico prediction of drug targets in Vibrio cholerae.
AU - Katara, Pramod
AU - Grover, Atul
AU - Kuntal, Himani
AU - Sharma, Vinay
PY - 2010
T2 - Protoplasma
J2 - Protoplasma
UR - http://www.ncbi.nlm.nih.gov/pubmed/21174131
N2 - Identification of potential drug targets is the first step in the process of modern drug discovery, subjected to their validation and drug development. Whole genome sequences of a number of organisms allow prediction of potential drug targets using sequence comparison approaches. Here, we present a subtractive approach exploiting the knowledge of global gene expression along with sequence comparisons to predict the potential drug targets more efficiently. Based on the knowledge of 155 known virulence and their coexpressed genes mined from microarray database in the public domain, 357 coexpressed probable virulence genes for Vibrio cholerae were predicted. Based on screening of Database of Essential Genes using blastn, a total of 102 genes out of these 357 were enlisted as vitally essential genes, and hence good putative drug targets. As the effective drug target is a protein which is only present in the pathogen, similarity search of these 102 essential genes against human genome sequence led to subtraction of 66 genes, thus leaving behind a subset of 36 genes whose products have been called as potential drug targets. The gene ontology analysis using Blast2GO of these 36 genes revealed their roles in important metabolic pathways of V. cholerae or on the surface of the pathogen. Thus, we propose that the products of these genes be evaluated as target sites of drugs against V. cholerae in future investigations.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Gene processing control loops suggested by sequencing, splicing, and RNA folding
AU - Jeffries, Clark D
AU - Perkins, Diana O
AU - Guan, Xiaojun
PY - 2010
T2 - BMC bioinformatics
J2 - BMC Bioinformatics
UR - http://www.biomedcentral.com/1471-2105/11/602
VL - 11
IS - 1
SP - 602
DO - 10.1186/1471-2105-11-602
N2 - Abstract Background: Small RNAs are known to regulate diverse gene expression processes including translation, transcription, and splicing. Among small RNAs, the microRNAs (miRNAs) of 17 to 27 nucleotides (nts) undergo biogeneses including primary transcription, RNA excision and folding, nuclear export, cytoplasmic processing, and then bioactivity as regulatory agents. We propose that analogous hairpins from RNA molecules that function as part of the spliceosome might also be the source of small, regulatory RNAs (somewhat smaller than miRNAs). Results: Deep sequencing technology has enabled discovery of a novel 16-nt RNA sequence in total RNA from human brain that we propose is derived from RNU1, an RNA component of spliceosome assembly. Bioinformatic alignments compel inquiring whether the novel 16-nt sequence or its precursor have a regulatory function as well as determining aspects of how processing intersects with the miRNA biogenesis pathway. Specifically, our preliminary in silico investigations reveal the sequence could regulate splicing factor Arg/Ser rich 1 (SFRS1), a gene coding an essential protein component of the spliceosome. All 16-base source sequences in the UCSC Human Genome Browser are within the 14 instances of RNU1 genes listed in wgEncodeGencodeAutoV3. Furthermore, 10 of the 14 instances of the sequence are also within a common 28-nt hairpin-forming subsequence of RNU1. Conclusions: An abundant 16-nt RNA sequence is sourced from a spliceosomal RNA, lies in a stem of a predicted RNA hairpin, and includes reverse complements of subsequences of the 3'UTR of a gene coding for a spliceosome protein. Thus RNU1 could function both as a component of spliceosome assembly and as inhibitor of production of the essential, spliceosome protein coded by SFRS1. Beyond this example, a general procedure is needed for systematic discovery of multiple alignments of sequencing, splicing, and RNA folding data.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Aromatase Is a Direct Target of FOXL2: C134W in Granulosa Cell Tumors via a Single Highly Conserved Binding Site in the Ovarian Specific Promoter
AU - Fleming, Nicholas I
AU - Knower, Kevin C
AU - Lazarus, Kyren A
AU - Fuller, Peter J
AU - Simpson, Evan R
AU - Clyne, Colin D
PY - 2010
T2 - PLoS ONE
J2 - PLoS One
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3004790/
VL - 5
IS - 12
DO - 10.1371/journal.pone.0014389
C2 - 3004790
N2 - Background: Granulosa cell tumors (GCT) of the ovary often express aromatase and synthesize estrogen, which in turn may influence their progression. Recently a specific point mutation (C134W) in the FOXL2 protein was identified in >94% of adult-type GCT and it is likely to contribute to their development. A number of genes are known to be regulated by FOXL2, including aromatase/CYP19A1, but it is unclear which are direct targets and whether the C134W mutation alters their regulation. Recently, it has been reported that FOXL2 forms a complex with steroidogenic factor 1 (SF-1) which is a known regulator of aromatase in granulosa cells. Methodology/Principal Findings: In this work, the human GCT-derived cell lines KGN and COV434 were heterozygous and wildtype for the FOXL2:C134W mutation, respectively. KGN had abundant FOXL2 mRNA expression but it was not expressed in COV434. Expression of exogenous FOXL2:C134W in COV434 cells induced higher expression of a luciferase reporter for the ovarian specific aromatase promoter, promoter II (PII) (−516bp) than expression of wildtype FOXL2, but did not alter induction of a similar reporter for the steroidogenic acute regulatory protein (StAR) promoter (−1300bp). Co-immunoprecipitation confirmed that FOXL2 bound SF-1 and that it also bound its homologue, liver receptor homologue 1 (LRH-1), however, the C134W mutation did not alter these interactions or induce a selective binding of the proteins. A highly conserved putative binding site for FOXL2 was identified in PII. FOXL2 was demonstrated to bind the site by electrophoretic mobility shift assays (EMSA) and site-directed mutagenesis of this element blocked its differential induction by wildtype FOXL2 and FOXL2:C134W. Conclusions/Significance: These findings suggest that aromatase is a direct target of FOXL2:C134W in adult-type GCT via a single distinctive and highly conserved binding site in PII and therefore provide insight into the pathogenic mechanism of this mutation.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Evidences showing wide presence of small genomic aberrations in chronic lymphocytic leukemia
AU - Kim, Yeong C
AU - Jung, Yong-Chul
AU - Chen, Jun
AU - Alhasan, Ali H
AU - Kaewsaard, Parawee
AU - Zhang, Yanming
AU - Ma, Shuo
AU - Rosen, Steve
AU - Wang, San Ming
PY - 2010
T2 - BMC research notes
J2 - BMC Res Notes
UR - http://www.biomedcentral.com/1756-0500/3/341
VL - 3
IS - 1
SP - 341
DO - 10.1186/1756-0500-3-341
C2 - 3016268
N2 - Abstract Background: Chronic lymphocytic leukemia (CLL) is the most common adult leukemia in the western population. Although genetic factors are considered to contribute to CLL etiology, at present genomic aberrations identified in CLL are limited compared with those identified in other types of leukemia, which raises the question of the degree of genetic influence on CLL. We performed a high-resolution genome scanning study to address this issue. Findings: Using the restriction paired-end-based Ditag Genome Scanning technique, we analyzed three primary CLL samples at a kilobase resolution, and further validated the results in eight primary CLL samples including the two used for ditag collection. From 51,632 paired-end tags commonly detected in the three CLL samples representing 5% of the HindIII restriction fragments in the genomes, we identified 230 paired-end tags that were present in all three CLL genomes but not in multiple normal human genome reference sequences. Mapping the full-length sequences of the fragments detected by these unmapped tags in seven additional CLL samples confirmed that these are the genomic aberrations caused by small insertions and deletions, and base changes spreading across coding and non-coding regions. Conclusions: Our study identified hundreds of loci with insertion, deletion, base change, and restriction site polymorphism present in both coding and non-coding regions in CLL genomes, indicating the wide presence of small genomic aberrations in chronic lymphocytic leukemia. Our study supports the use of a whole genome sequencing approach for comprehensively decoding the CLL genome for better understanding of the genetic defects in CLL.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - A Rare Myelin Protein Zero (MPZ) Variant Alters Enhancer Activity In Vitro and In Vivo
AU - Antonellis, Anthony
AU - Dennis, Megan Y
AU - Burzynski, Grzegorz
AU - Huynh, Jimmy
AU - Maduro, Valerie
AU - Hodonsky, Chani J
AU - Khajavi, Mehrdad
AU - Szigeti, Kinga
AU - Mukkamala, Sandeep
AU - Bessling, Seneca L
AU - NISC Comparative Sequencing Program
AU - Pavan, William J
AU - McCallion, Andrew S
AU - Lupski, James R
AU - Green, Eric D
PY - 2010
T2 - PLoS ONE
J2 - PLoS One
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3002941/
VL - 5
IS - 12
DO - 10.1371/journal.pone.0014346
C2 - 3002941
N2 - Background: Myelin protein zero (MPZ) is a critical structural component of myelin in the peripheral nervous system. The MPZ gene is regulated, in part, by the transcription factors SOX10 and EGR2. Mutations in MPZ, SOX10, and EGR2 have been implicated in demyelinating peripheral neuropathies, suggesting that components of this transcriptional network are candidates for harboring disease-causing mutations (or otherwise functional variants) that affect MPZ expression. Methodology: We utilized a combination of multi-species sequence comparisons, transcription factor-binding site predictions, targeted human DNA re-sequencing, and in vitro and in vivo enhancer assays to study human non-coding MPZ variants. Principal Findings: Our efforts revealed a variant within the first intron of MPZ that resides within a previously described SOX10 binding site is associated with decreased enhancer activity, and alters binding of nuclear proteins. Additionally, the genomic segment harboring this variant directs tissue-relevant reporter gene expression in zebrafish. Conclusions: This is the first reported MPZ variant within a cis-acting transcriptional regulatory element. While we were unable to implicate this variant in disease onset, our data suggests that similar non-coding sequences should be screened for mutations in patients with neurological disease. Furthermore, our multi-faceted approach for examining the functional significance of non-coding variants can be readily generalized to study other loci important for myelin structure and function.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Recombinant expression, purification and copper-binding characteristics of the amino terminus of a Plasmodium falciparum copper transport protein
AU - Choveaux, David
AU - Goldring, JP Dean
PY - 2010
T2 - Malaria journal
J2 - Malar J
UR - http://www.malariajournal.com/content/9/S2/-P62
VL - 9
IS - Suppl 2
SP - P62
DO - 10.1186/1475-2875-9-S2-P62
N2 -
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Concurrent genetic alterations in DNA polymerase proofreading and mismatch repair in human colorectal cancer.
AU - Yoshida, Rintaro
AU - Miyashita, Kaname
AU - Inoue, Mayuko
AU - Shimamoto, Akiyoshi
AU - Yan, Zhao
AU - Egashira, Akinori
AU - Oki, Eiji
AU - Kakeji, Yoshishiro
AU - Oda, Shinya
AU - Maehara, Yoshihiko
PY - 2010
T2 - European journal of human genetics : EJHG
J2 - Eur J Hum Genet
UR - http://www.ncbi.nlm.nih.gov/pubmed/21157497
N2 - Genomic sequences encoding the 3' exonuclease (proofreading) domains of both replicative DNA polymerases, pol delta and pol epsilon, were explored simultaneously in human colorectal carcinomas including six established cell lines. Three unequivocal sequence alterations, including one previously reported, were found, and all these were considered as dysfunctional mutations in light of the local amino-acid sequences. In particular, the F367S mutation found in the POLE gene encoding the pol epsilon catalytic subunit, which includes the proofreading domain, is the first found in human diseases. Surprisingly, the tumours carrying these proofreading domain mutations were all defective in DNA mismatch repair (MMR). In addition to the two cell lines with acknowledged MMR gene mutations, the third tumour was also demonstrated to harbour a distinct mutation in MLH1, and indeed exhibited a microsatellite-unstable phenotype. These findings suggest that, in concert with MMR deficiency, defective polymerase proofreading may also contribute to the mutator phenotype observed in human colorectal cancer. Our observations may suggest previously unrecognised complexities in the molecular abnormalities underlying the mutator phenotype in human neoplasms.European Journal of Human Genetics advance online publication, 15 December 2010; doi:10.1038/ejhg.2010.216.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Evolution of MicroRNAs and the Diversification of Species.
AU - Loh, Yong-Hwee E
AU - Yi, Soojin V
AU - Streelman, J Todd
PY - 2010
T2 - Genome Biology and Evolution
J2 - Genome Biol Evol
UR - http://www.ncbi.nlm.nih.gov/pubmed/21169229
N2 - MicroRNAs (miRNAs) are ancient, short, non-coding RNA molecules that regulate the transcriptome through post-transcriptional mechanisms. miRNA riboregulation is involved in a diverse range of biological processes and mis-regulation is implicated in disease. It is generally thought that miRNAs function to canalize cellular outputs, for instance as 'fail-safe' repressors of gene mis-expression. Genomic surveys in humans have revealed reduced genetic polymorphism and the signature of negative selection for both miRNAs themselves and the target sequences to which they are predicted to bind. We investigated the evolution of miRNAs and their binding sites across cichlid fishes from Lake Malawi (East Africa), where hundreds of diverse species have evolved in the last million years. Using low-coverage genome sequence data, we identified 100 cichlid miRNA genes with mature regions that are highly conserved in other animal species. We computationally predicted target sites on the 3'-UTRs of cichlid genes to which miRNAs may bind, and found that these sites possessed elevated single nucleotide polymorphism (SNP) densities. Furthermore, polymorphic sites in predicted miRNA targets showed higher minor allele frequencies on average and greater genetic differentiation between Malawi lineages when compared to a neutral expectation and non-target 3' UTR SNPs. Our data suggest that divergent selection on miRNA riboregulation may have contributed to the diversification of cichlid species, and may similarly play a role in rapid phenotypic evolution of other natural systems.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - A unique chromatin signature uncovers early developmental enhancers in humans.
AU - Rada-Iglesias, Alvaro
AU - Bajpai, Ruchi
AU - Swigut, Tomek
AU - Brugmann, Samantha A
AU - Flynn, Ryan A
AU - Wysocka, Joanna
PY - 2010
T2 - Nature
J2 - Nature
UR - http://www.ncbi.nlm.nih.gov/pubmed/21160473
N2 - Cell-fate transitions involve the integration of genomic information encoded by regulatory elements, such as enhancers, with the cellular environment. However, identification of genomic sequences that control human embryonic development represents a formidable challenge. Here we show that in human embryonic stem cells (hESCs), unique chromatin signatures identify two distinct classes of genomic elements, both of which are marked by the presence of chromatin regulators p300 and BRG1, monomethylation of histone H3 at lysine 4 (H3K4me1), and low nucleosomal density. In addition, elements of the first class are distinguished by the acetylation of histone H3 at lysine 27 (H3K27ac), overlap with previously characterized hESC enhancers, and are located proximally to genes expressed in hESCs and the epiblast. In contrast, elements of the second class, which we term 'poised enhancers', are distinguished by the absence of H3K27ac, enrichment of histone H3 lysine 27 trimethylation (H3K27me3), and are linked to genes inactive in hESCs and instead are involved in orchestrating early steps in embryogenesis, such as gastrulation, mesoderm formation and neurulation. Consistent with the poised identity, during differentiation of hESCs to neuroepithelium, a neuroectoderm-specific subset of poised enhancers acquires a chromatin signature associated with active enhancers. When assayed in zebrafish embryos, poised enhancers are able to direct cell-type and stage-specific expression characteristic of their proximal developmental gene, even in the absence of sequence conservation in the fish genome. Our data demonstrate that early developmental enhancers are epigenetically pre-marked in hESCs and indicate an unappreciated role of H3K27me3 at distal regulatory elements. Moreover, the wealth of new regulatory sequences identified here provides an invaluable resource for studies and isolation of transient, rare cell populations representing early stages of human embryogenesis.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Next generation sequencing and analysis of a conserved transcriptome of New Zealand's kiwi
AU - Subramanian, Sankar
AU - Huynen, Leon
AU - Millar, Craig D
AU - Lambert, David M
PY - 2010
T2 - BMC evolutionary biology
J2 - BMC Evol Biol
UR - http://www.biomedcentral.com/1471-2148/10/387
VL - 10
IS - 1
SP - 387
DO - 10.1186/1471-2148-10-387
C2 - 3009673
N2 - Abstract Background: Kiwi is a highly distinctive, flightless and endangered ratite bird endemic to New Zealand. To understand the patterns of molecular evolution of the nuclear protein-coding genes in brown kiwi (Apteryx australis mantelli) and to determine the timescale of avian history we sequenced a transcriptome obtained from a kiwi embryo using next generation sequencing methods. We then assembled the conserved protein-coding regions using the chicken proteome as a scaffold. Results: Using 1,543 conserved protein coding genes we estimated the neutral evolutionary divergence between the kiwi and chicken to be ~45%, which is approximately equal to the divergence computed for the human-mouse pair using the same set of genes. A large fraction of genes was found to be under high selective constraint, as most of the expressed genes appeared to be involved in developmental gene regulation. Our study suggests a significant relationship between gene expression levels and protein evolution. Using sequences from over 700 nuclear genes we estimated the divergence between the two basal avian groups, Palaeognathae and Neognathae to be 132 million years, which is consistent with previous studies using mitochondrial genes. Conclusions: The results of this investigation revealed patterns of mutation and purifying selection in conserved protein coding regions in birds. Furthermore this study suggests a relatively cost-effective way of obtaining a glimpse into the fundamental molecular evolutionary attributes of a genome, particularly when no closely related genomic sequence is available.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Transcriptional Activation of REST by Sp1 in Huntington's Disease Models
AU - Ravache, Myriam
AU - Weber, Chantal
AU - Mérienne, Karine
AU - Trottier, Yvon
PY - 2010
T2 - PLoS ONE
J2 - PLoS One
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3001865/
VL - 5
IS - 12
DO - 10.1371/journal.pone.0014311
C2 - 3001865
N2 - In Huntington's disease (HD), mutant huntingtin (mHtt) disrupts the normal transcriptional program of disease neurons by altering the function of several gene expression regulators such as Sp1. REST (Repressor Element-1 Silencing Transcription Factor), a key regulator of neuronal differentiation, is also aberrantly activated in HD by a mechanism that remains unclear. Here, we show that the level of REST mRNA is increased in HD mice and in NG108 cells differentiated into neuronal-like cells and expressing a toxic mHtt fragment. Using luciferase reporter gene assay, we delimited the REST promoter regions essential for mHtt-mediated REST upregulation and found that they contain Sp factor binding sites. We provide evidence that Sp1 and Sp3 bind REST promoter and interplay to fine-tune REST transcription. In undifferentiated NG108 cells, Sp1 and Sp3 have antagonistic effect, Sp1 acting as an activator and Sp3 as a repressor. Upon neuronal differentiation, we show that the amount and ratio of Sp1/Sp3 proteins decline, as does REST expression, and that the transcriptional role of Sp3 shifts toward a weak activator. Therefore, our results provide new molecular information to the transcriptional regulation of REST during neuronal differentiation. Importantly, specific knockdown of Sp1 abolishes REST upregulation in NG108 neuronal-like cells expressing mHtt. Our data together with earlier reports suggest that mHtt triggers a pathogenic cascade involving Sp1 activation, which leads to REST upregulation and repression of neuronal genes.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Personalized medicine - The promised land are we there yet?
AU - Li, Chumei
PY - 2010
T2 - Clinical genetics
J2 - Clin Genet
UR - http://www.ncbi.nlm.nih.gov/pubmed/21204795
N2 - The delivery of personalized genomic medicine (see box1 for a comparison of genomic vs. genetic medicine and box2 for glossary) hinges on obtaining personal genomic data through genome-wide association studies (GWAS) or whole genome sequencing. After the completion of the human genome project (see box 3 for human genome projects and its derivative projects) in 2003, there appeared to be a period of euphoric optimism that as soon as the cost of sequencing the whole human genome could be brought down to an affordable range, the promise of personalized medicine would become a reality. However, inasmuch as the miraculous technological advancements are making whole genome data acquisition an inexpensive reality, we are also starting to appreciate that making sense of the enormous amount of genomic data is a far bigger hurdle. Issues, both scientific and ethico-legal, will have to be addressed as genomic data are been pushed for clinical and direct-to-consumer utilization.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -

TY - JOUR
TI - Mining human genome for novel purinergic P2Y receptors: a sequence analysis and molecular modeling approach.
AU - Bhatnagar, Sonika
AU - Mishra, Shubhi
AU - Pathak, Ravi
PY - 2010
T2 - Journal of receptor and signal transduction research
J2 - J Recept Signal Transduct Res
UR - http://www.ncbi.nlm.nih.gov/pubmed/21142848
N2 - The purinergic P2Y receptors are G-protein coupled receptors (GPCRs) that control many physiological processes by mediating cellular responses to purines, pyrimidines and their analogues. They can be used as potential therapeutic targets in a variety of disease conditions. Therefore, it is critical to identify new members of this family of receptors from the human genome and characterize them for their role in health and disease. In the present work, molecular modeling was carried out for the 21 known P2Y receptors. Binding site analysis was done on the basis of docking and site-directed mutagenesis data. Thus, conserved features of P2Y receptors could be formulated. These features can be used to determine the purinergic nature of potential P2Y receptors in the human genome. We applied this knowledge to human genome GPCR sequences found by sensitive sequence search techniques and identified two orphan receptors, namely GPR34 and GP171 that have all the necessary conserved features of P2Y receptors.
N1 - Exported from www.Quertle.info. Search query: Genome-sequencing .
ER -