Chromatin accessibility dynamics across C. elegans development and ageing
- University of Cambridge, United Kingdom
- Max Delbrück Center for Molecular Medicine, Germany
Abstract
An essential step for understanding the transcriptional circuits that control development and physiology is the global identification and characterization of regulatory elements. Here we present the first map of regulatory elements across the development and ageing of an animal, identifying 42,245 elements accessible in at least one C. elegans stage. Based on nuclear transcription profiles, we define 15,714 protein-coding promoters and 19,231 putative enhancers, and find that both types of element can drive orientation-independent transcription. Additionally, more than 1000 promoters produce transcripts antisense to protein coding genes, suggesting involvement in a widespread regulatory mechanism. We find that the accessibility of most elements changes during development and/or ageing and that patterns of accessibility change are linked to specific developmental or physiological processes. The map and characterization of regulatory elements across C. elegans life provides a platform for understanding how transcription controls development and ageing.
Data availability
Sequencing data have been deposited in GEO under accession code GSE114494.
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Chromatin accessibility dynamics across C. elegans development and ageingPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE114494).
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The landscape of RNA polymerase II transcription initiation in C. elegans reveals a novel regulatory architecturePublicly available at the NCBI Gene Expression Omnibus (accession no: GSE42819).
Article and author information
Author details
Przemyslaw Stempor
Funding
Wellcome (101863)
- Jürgen Jänes
- Yan Dong
- Alex Appert
- Chiara Cerrato
- Ron Chen
- Carolina Gemma
- Ni Huang
- Przemyslaw Stempor
- Annette Steward
- Eva Zeiser
- Julie Ahringer
Medical Research Council
- Jacques Serizay
European Commission (FP7/2007-2013)
- Sascha Sauer
- Julie Ahringer
Wellcome (97679)
- Jürgen Jänes
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2018, Jänes et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Chromatin accessibility dynamics across C. elegans development and ageing
eLife 7:e37344.
https://doi.org/10.7554/eLife.37344
Further reading
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- Chromosomes and Gene Expression
The association between late replication timing and low transcription rates in eukaryotic heterochromatin is well known, yet the specific mechanisms underlying this link remain uncertain. In Saccharomyces cerevisiae, the histone deacetylase Sir2 is required for both transcriptional silencing and late replication at the repetitive ribosomal DNA (rDNA) arrays. We have previously reported that in the absence of SIR2, a de-repressed RNA PolII repositions MCM replicative helicases from their loading site at the ribosomal origin, where they abut well-positioned, high-occupancy nucleosomes, to an adjacent region with lower nucleosome occupancy. By developing a method that can distinguish activation of closely spaced MCM complexes, here we show that the displaced MCMs at rDNA origins have increased firing propensity compared to the nondisplaced MCMs. Furthermore, we found that both activation of the repositioned MCMs and low occupancy of the adjacent nucleosomes critically depend on the chromatin remodeling activity of FUN30. Our study elucidates the mechanism by which Sir2 delays replication timing, and it demonstrates, for the first time, that activation of a specific replication origin in vivo relies on the nucleosome context shaped by a single chromatin remodeler.
