Persistent chromatin states, pervasive transcription, and sharedcis-regulatory sequences have shaped theC. elegansgenome

Abstract

Despite highly conserved chromatin states and cis-regulatory elements, studies of metazoan genomes reveal that gene organization and the strategies to control mRNA expression can vary widely among animal species. C. elegans gene regulation is often assumed to be similar to that of other model organisms, yet evidence suggests the existence of distinct molecular mechanisms to pattern the developmental transcriptome, including extensive post-transcriptional RNA control pathways, widespread splice leader (SL) trans-splicing of pre-mRNAs, and the organization of genes into operons. Here, we performed ChIP-seq for histone modifications in highly synchronized embryos cohorts representing three major developmental stages, with the goal of better characterizing whether the dynamic changes in embryonic mRNA expression are accompanied by changes to the chromatin state. We were surprised to find that thousands of promoters are persistently marked by active histone modifications, despite a fundamental restructuring of the transcriptome. We employed global run-on sequencing using a long-read nanopore format to map nascent RNA transcription across embryogenesis, finding that the invariant open chromatin regions are persistently transcribed by Pol II at all stages of embryo development, even though the mature mRNA is not produced. By annotating our nascent RNA sequencing reads into directional transcription units, we find extensive evidence of polycistronic RNA transcription genome-wide, suggesting that nearby genes in C. elegans are linked by shared transcriptional regulatory mechanisms. We present data indicating that the sharing of cisregulatory sequences has constrained C. elegans gene positioning and likely explains the remarkable retention of syntenic gene pairs over long evolutionary timescales.

Rapid generation ofC. eleganssingle copy transgenes combining RMCE and drug selection

“…The C. elegans genome lacks the classic insulator protein CTCF (Heger et al, 2009) and studies have argued that the main influence on gene expression specificity in C. elegans is the distance between enhancers and promoter (Quintero-Cadena and Sternberg, 2016). Operons are also common in C. elegans (Blumenthal and Gleason, 2003) and recent work suggests that polycistronic transcription is more prevalent than previously thought (Bellush and Whitehouse, 2019). The crosstalk observed in rRMCE transgenes could in most cases logically be explained either by polycistronic transcription resulting from failure of RNA polymerase II termination or by enhancer sharing.…”