+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans



Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans



Genome Research 27(12): 2096-2107



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.

Please choose payment method:






(PDF emailed within 0-6 h: $19.90)

Accession: 059498766

Download citation: RISBibTeXText

PMID: 29141961

DOI: 10.1101/gr.226233.117


Related references

Chromatin accessibility dynamics across C. elegans development and ageing. Elife 7:, 2018

Genetic screens for enhancers of brahma reveal functional interactions between the BRM chromatin-remodeling complex and the delta-notch signal transduction pathway in Drosophila. Genetics 170(4): 1761-1774, 2005

Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers. Nucleic Acids Research 46(21): 11184-11201, 2018

Analysis of chromatin accessibility in human epidermis identifies putative barrier dysfunction-sensing enhancers. Plos one 12(9): E0184500, 2017

Distributed probing of chromatin structure in vivo reveals pervasive chromatin accessibility for expressed and non-expressed genes during tissue differentiation in C. elegans. Bmc Genomics 11: 465, 2010

The Chromatin Accessibility Complex: Chromatin Dynamics through Nucleosome Sliding. 2004

The chromatin accessibility complex: chromatin dynamics through nucleosome sliding. Cold Spring Harbor Symposia on Quantitative Biology 69: 281-287, 2004

Chromatin signatures at Notch-regulated enhancers reveal large-scale changes in H3K56ac upon activation. Embo Journal 34(14): 1889-1904, 2015

Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility. Plos Computational Biology 13(1): E1005311, 2017

Direct and quantitative analysis of chromatin accessibility by MIRECAL--a Micrococcus nuclease/real-time PCR chromatin accessibility assay with locus specificity. Analytical Biochemistry 354(2): 308-310, 2006

Micromanipulation studies of chromatin fibers in Xenopus egg extracts reveal ATP-dependent chromatin assembly dynamics. Molecular Biology of the Cell 18(2): 464-474, 2007

Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex. Elife 6:, 2017

Alternative polyadenylation sites reveal distinct chromatin accessibility and histone modification in human cell lines. Bioinformatics 29(14): 1713-1717, 2013

Chromatin Accessibility Dynamics during iPSC Reprogramming. Cell Stem Cell 21(6): 819-833.E6, 2017

Chromatin Accessibility Dynamics during Chemical Induction of Pluripotency. Cell Stem Cell 22(4): 529-542.E5, 2018