Chromatin accessibility dynamics reveal novel functional enhancers inC. elegans

Abstract

Chromatin accessibility, a crucial component of genome regulation, has primarily been studied in homogeneous and simple systems, such as isolated cell populations or early-development models. Whether chromatin accessibility can be assessed in complex, dynamic systems in vivo with high sensitivity remains largely unexplored. In this study, we use ATAC-seq to identify chromatin accessibility changes in a whole animal, the model organism Caenorhabditis elegans, from embryogenesis to adulthood. Chromatin accessibility changes between developmental stages are highly reproducible, recapitulate histone modification changes, and reveal key regulatory aspects of the epigenomic landscape throughout organismal development. We find that over 5000 distal noncoding regions exhibit dynamic changes in chromatin accessibility between developmental stages and could thereby represent putative enhancers. When tested in vivo, several of these putative enhancers indeed drive novel cell-type-and temporal-specific patterns of expression. Finally, by integrating transcription factor binding motifs in a machine learning framework, we identify EOR-1 as a unique transcription factor that may regulate chromatin dynamics during development. Our study provides a unique resource for C. elegans, a system in which the prevalence and importance of enhancers remains poorly characterized, and demonstrates the power of using whole organism chromatin accessibility to identify novel regulatory regions in complex systems.

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

“…hypodermal, muscle, neuronal) which proliferate after hatching (Sulston and Horvitz 1977). However, the select inactivation of highly-transcribed early gene promoters would lead to an expected decrease in nascent RNA levels (Tome et al 2018)-instead, we find consistent nascent RNA transcription, a readout shown to positively correlate with chromatin accessibility at multiple stages of C. elegans development (Daugherty et al 2017).…”

“…In addition, we considered the possibility that the stable H3K27ac and H3K4me2 ChIP-seq profiles generated from synchronized embryos may be disproportionately biased by the crosslinking and immunoprecipitation procedure (Teytelman et al 2013). We compared embryo H3K27ac peak positions relative to accessible chromatin sites identified by a cross-linking independent assay, ATAC-seq (Daugherty et al 2017). We found that the vast majority of transposase accessible sites identified in a mixed population of embryos to directly overlap (~60%), or lie within 5 kb (~70%) of our early embryo H3K27ac peaks ( Figure 1C).…”

“…Although the genetic pathways and cellular events responsible for patterning the C. elegans embryo are well-documented (Sulston and Horvitz 1977;Sulston et al 1983), a clear understanding of how the landscape of chromatin modifications and active Pol II transcription changes through early development is not known. Techniques sampling mRNA from whole embryos (Hashimshony et al 2015;Boeck et al 2016), individual tissues (Meissner et al 2009;Tzur et al 2018), and single-cells (Cao et al 2017;Packer et al 2019a) have revealed the dynamic expression of thousands of genes, but the gene regulatory context remains incomplete without integrating annotations of the chromatin architecture and Pol II transcription landscape at distinct developmental milestones (Gerstein et al 2010;Levin et al 2012;Kruesi et al 2013;Ho et al 2014;Pourkarimi et al 2016;Daugherty et al 2017).…”

“…Given the importance of promoters and enhancers in the context of cellular development and disease (Sur and Taipale 2016;Furlong and Levine 2018), recent high-throughput sequencing efforts have sought to annotate the genomic features of cis-regulatory regions across eukaryotes (Harbison et al 2004;Gehrig et al 2009;Negre et al 2011;Shen et al 2012;Daugherty et al 2017). It is evident that certain "active" histone modifications like histone H3 lysine 4 methylation (H3K4me) and lysine 27 acetylation (H3K27ac) generally mark regions of chromatin accessibility and correlate with sites of transcriptional activity, allowing the approximate locations of most promoters and enhancers to be mapped (Heintzman et al 2007).…”

“…However, despite the lack of conserved TAD structures to regulate transcription, the chromatin landscape in C. elegans is decorated with the same patterns of patterns modifications found in other metazoa, including active marks: H3K27ac and H3K4me and repressive marks, H3K9me and H3K27me (Gerstein et al 2010). Guided by the association between active histone marks and Pol II transcription initiation, recent chromatin profiling studies have revealed many thousands of putative gene promoters and enhancers across worm development (Chen et al 2013;Daugherty et al 2017;Ho et al 2017). Yet, beyond basic characterization, we have a limited understanding of how chromatin may control the differential mRNA expression patterns during C. elegans development.…”