小柯机器人

英国剑桥大学John C. Marioni、Rebecca V. Berrens等研究人员合作利用CELLO-seq检测单细胞中转座元件的特定位置表达。2021年11月15日，《自然—生物技术》杂志在线发表了这项成果。

CELLO-seq（Single CELl LOng-read RNA-sequencing）将长读单细胞测序与与计算分析相结合，可用于测量可转座元件（TE）在独特位点的表达。研究人员使用CELLO-seq来评估了TE在二细胞小鼠卵裂球以及人类诱导多能干细胞中的广泛表达。在这两个物种中，老的和年轻的TE都显示了基因座特异性表达的证据，模拟显示只有小鼠中的少数非常年轻的元件不能以高置信度映射到参照上。单个元件的表达和潜在调节因子之间的关系显示出巨大的异质性，一类中TE显示了不同的相关模式，并表明了不同的调节机制。

据介绍，TE调节着从早期发育到癌症的各种生物过程。年轻的TE表达很难用第二代单细胞测序技术来测量，因为它们的高度重复性意味着短的互补DNA读数不能明确地映射到一个特定的基因座。

附：英文原文

Title: Locus-specific expression of transposable elements in single cells with CELLO-seq

Author: Berrens, Rebecca V., Yang, Andrian, Laumer, Christopher E., Lun, Aaron T. L., Bieberich, Florian, Law, Cheuk-Ting, Lan, Guocheng, Imaz, Maria, Bowness, Joseph S., Brockdorff, Neil, Gaffney, Daniel J., Marioni, John C.

Issue&Volume: 2021-11-15

Abstract: Transposable elements (TEs) regulate diverse biological processes, from early development to cancer. Expression of young TEs is difficult to measure with next-generation, single-cell sequencing technologies because their highly repetitive nature means that short complementary DNA reads cannot be unambiguously mapped to a specific locus. Single CELl LOng-read RNA-sequencing (CELLO-seq) combines long-read single cell RNA-sequencing with computational analyses to measure TE expression at unique loci. We used CELLO-seq to assess the widespread expression of TEs in two-cell mouse blastomeres as well as in human induced pluripotent stem cells. Across both species, old and young TEs showed evidence of locus-specific expression with simulations demonstrating that only a small number of very young elements in the mouse could not be mapped back to the reference with high confidence. Exploring the relationship between the expression of individual elements and putative regulators revealed large heterogeneity, with TEs within a class showing different patterns of correlation and suggesting distinct regulatory mechanisms. Expression of transposable elements is mapped to unique genomic loci with CELLO-seq.

DOI: 10.1038/s41587-021-01093-1

Source: https://www.nature.com/articles/s41587-021-01093-1

Nature Biotechnology：《自然—生物技术》，创刊于1996年。隶属于施普林格·自然出版集团，最新IF：68.164
官方网址：https://www.nature.com/nbt/
投稿链接：https://mts-nbt.nature.com/cgi-bin/main.plex