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单细胞ATAC-seq | 果蝇ATAC-seq数据和文章都在这里
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作者：小丫 来源：嘉因
今天汇总果蝇的ATAC-seq数据和文章。
果蝇的ATAC-seq文章有8篇已发表，2套数据的文章未发表，还有1个biorxiv预印本。
想看单细胞ATAC-seq？直接拖到结尾看这篇预印本。
SRA上有166套果蝇ATAC-seq，比上个月增加了40多套！！！
出自10个项目：
No.1 Davie K, Jacobs J, Atkins M, Potier D et al. Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling. PLoS Genet 2015 Feb;11(2):e1004994. PMID: 25679813. 影响因子：6.1
摩尔根的年代，果蝇仗着体型小，占据了模式生物的榜首；
二代测序的年代，果蝇仗着基因组小，新技术出来总是先在果蝇上练手。
作为2015年的No.1，想知道开放染色质是否能够用来鉴定正常发育状态和肿瘤发生中驱动基因表达的活跃promoter和enhancer。
先跟以前的技术做对比，发现ATAC-seq和FAIRE都能找到promoter、enhancer和insulator。
还找到了AP1和Stat92E的motif
结论：FAIRE-seq和ATAC-seq结合motif，是鉴定功能性基因组调控区、重要调控因子和控制复杂体内过程的调控网络的直接方法。
We show that FAIRE-seq and ATAC-seq based open chromatin profiling, combined withmotif discovery, is a straightforward approach to identify functional genomic regulatory regions, master regulators, and gene regulatory networks controlling complex in vivo processes.
GSE59078，7套ATAC-seq + 4 FAIRE-seq + H1 ChIP-seq
L3, Eye-Antennal disc
No. 2 Iwasaki YW, Murano K, Ishizu H, Shibuya A et al. Piwi Modulates Chromatin Accessibility by Regulating Multiple Factors Including Histone H1 to Repress Transposons. Mol Cell 2016 Aug 4;63(3):408-19. PMID: 27425411. 影响因子：14.714
GSE81434，10套ATAC-seq + 24 RNA-seq, ChIP-seq
Ovarian Somatic Cells
No. 3 Koenecke N, Johnston J, Gaertner B, Natarajan M et al. Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis. Genome Biol 2016 Sep 27;17(1):196. PMID: 27678375. 影响因子：11.908
借助果蝇背腹形态建成这一过程，建立了de novo找组织特异性enhancer的方法。
目的：找新的组织特异性enhancer。
解决方案：
不能用H3K27ac找enhancer，为什么？虽然H3K27ac出现在enhancer附近，经常用来标active enhancer，但它太宽，不能精确标出enhancer的具体位置。
分别用H3K27ac的乙酰转移酶CBP的ChIP-seq和ATAC-seq找enhancer，结果相似。
结论：Taken together, our analysis suggests that CBP regions are more likely to be enhancers and are less sequencebiased compared to ATAC-seq regions. We therefore present the results from using CBP regions as the starting point for our analysis. However, we have also performed the same analysis for ATAC-seq regions and found similar
results suggesting that ATAC-seq regions are a useful alternative to CBP regions.
GSE68983，2套ATAC-seq + 45 RNA-seq, H3K4me1, H3K27ac, H3K27me3 ChIP-seq
2-4h embryo
No. 4 Blythe SA, Wieschaus EF. Establishment and maintenance of heritable chromatin structure during early Drosophila embryogenesis. Elife 2016 Nov 23;5. PMID: 27879204. 影响因子：7.725
借助果蝇系统，研究胚胎早期染色质结构的建成和维持。
每3分钟取一次胚胎做ATAC-seq，两个基因型，各3个核质比，各3-6个时间点。
结论：In general, acquisition of promoter accessibility is controlled by the biological timer that measures the nucleo-cytoplasmic (N:C) ratio, whereas timing of enhancer accessibility is regulated independently of the N:C ratio. These different timing classes each associate with binding sites for two transcription factors, GAGA-factor and Zelda, previously implicated in controlling chromatin accessibility at ZGA.
GSE83851，81套ATAC-seq，3-4次生物学重复
w ssm[185b]; His2Av-GFP和野生型
Embryos were collected in a three minute time course spanning three cell cycles
No. 5 Chen X, Rahman R, Guo F, Rosbash M. Genome-wide identification of neuronal activity-regulated genes in Drosophila. Elife 2016 Dec 9;5. PMID: 27936378. 影响因子：7.725
结论：Chromatin assays using ATAC-sequencing show that the transcription start sites (TSS) of ARGs do not change with neural firing but are already accessible prior to stimulation.
Lastly based on binding site enrichment in ARGs, we identified transcription factor mediators of firing and created neuronal activity reporters.
GSE83975，4套ATAC-seq + 85 RNA-seq
Elav-GAL4;UAS-TrpA1 or Elav-GAL4 flies
No. 6 Mueller B, Mieczkowski J, Kundu S, Wang P et al. Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction. Genes Dev 2017 Mar 1;31(5):451-462. PMID: 28356342. 影响因子：9.413
结论：There was an increase in the accessibility of nucleosomes, as measured by MNase digestion and ATAC-seq, that did not result fromremoval of the nucleosome.
Thus, changes in nucleosome accessibility predominate over changes in nucleosome occupancy during rapid transcriptional induction during the UPR.
MACC：MNase accessibility
GSE95689，6套ATAC-seq + 58 MNase-seq, H3K27ac, RNAseq and Pol2 profiles
UPR-induced S2 cells
No. 7 Meers MP, Henriques T, Lavender CA, McKay DJ et al. Histone gene replacement reveals a post-transcriptional role for H3K36 in maintaining metazoan transcriptome fidelity. Elife 2017 Mar 27;6. PMID: 28346137. 影响因子：7.725
We posit a model whereby H3K36 methylation contributes to transcript fitness in order to maintain global transcriptome fidelity.
GSE96922，6套ATAC-seq + 46 poly-A RNA-seq, total nuclear RNA-seq, Start-seq
HWT and K36R rescue larvae
No. 8 Rowley MJ, Nichols MH, Lyu X, Ando-Kuri M et al. Evolutionarily Conserved Principles Predict 3D Chromatin Organization. Mol Cell 2017 Sep 7;67(5):837-852.e7. PMID: 28826674. 影响因子：14.714
GSE96922，2套ATAC-seq + 16 ChIP-seq, HiChIP, ChIAPET
Kc167
No. 9 GSE86966，41套ATAC-seq + 22 ChIP-seq。9月提交到GEO，文章未发表。
single embryos staged at 12 minutes into nuclear cycle 14 in seven genotypes:
wild-type, bcd[E1], zelda[294], bcd[E1] nos[L7] tsl[4], and three transgenic lines expressing uniform bicoid.
No. 10 GSE104957，7套ATAC-seq。10月30日刚提交GEO，文章未发表。
20 anterior and 20 posterior stage 5 embryos
No. 11 2017年7月biorxiv预印本：
The cis-regulatory dynamics of embryonic development at single cell resolution
建立了一个单细胞ATAC-seq方法，single cell combinatorial indexing assay for transposase accessible chromatin(sci-ATAC-seq)。获得了多个发育阶段的开放染色质图谱。
结果：Our data reveal heterogeneity in the regulatory landscape prior to gastrulation that
reflects anatomical position, a feature that aligns with future cell fate. During mid embryogenesis, tissue granularity emerges such that cell types can be inferred by their chromatin accessibility, while maintaining a signature of their germ layer of origin.
We identify over 30,000 distal elements with tissue-specific accessibility. Using transgenic embryos, we tested the germ layer specificity of a subset of predicted enhancers, achieving near-perfect accuracy.
Overall, these data demonstrate the power of shotgun single cell profiling of embryos to resolve dynamic changes in open chromatin during development, and to uncover the cis-regulatory programs of germ layers and cell types.
相关文章
https://wap.sciencenet.cn/blog-3372875-1093024.html
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