Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells.

ABSTRACT: Single-cell RNA sequencing studies on gene co-expression patterns could yield important regulatory and functional insights, but have so far been limited by the confounding effects of differentiation and cell cycle. We apply a tailored experimental design that eliminates these confounders, and report thousands of intrinsically covarying gene pairs in mouse embryonic stem cells. These covariations form a network with biological properties, outlining known and novel gene interactions. We provide the first evidence that miRNAs naturally induce transcriptome-wide covariations and compare the relative importance of nuclear organization, transcriptional and post-transcriptional regulation in defining covariations. We find that nuclear organization has the greatest impact, and that genes encoding

SUBMITTER: Tarbier M 

PROVIDER: S-EPMC7595044 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature