Chromatin accessibility dynamics across C. elegans development and ageing.
eLife Sciences Publications
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Jänes, J., Dong, Y., Schoof, M., Serizay, J., Appert, A., Cerrato, C., Woodbury, C., et al. (2018). Chromatin accessibility dynamics across C. elegans development and ageing.. Elife, 7 (e37344)https://doi.org/10.7554/eLife.37344
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 Caenorhabditis 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.
ATAC-seq, C. elegans, chromatin accessibility, chromosomes, enhancer, gene expression, genetics, genomics, promoter, regulatory element
The work was supported by Wellcome Trust Senior Research Fellowships to JA (054523 and 101863), a Wellcome Trust PhD fellowship to JJ (097679), a Sir Robert Edwards Scholarship from Churchill College, an English Speaking Union Graduate Scholarship, and funding from the Cambridge Trust to MS, a Medical Research Council DTP studentship to JS, and a Thouron award to CW. This study was also supported by the European Sequencing and Genotyping Infrastructure (funded by the EC, FP7/2007-2013) under Grant Agreement 26205 (ESGI) as part of the transnational access program. We thank Drs. Hans Lehrach and Marie-Laure Yaspo for generous support of the ESGI project, Dr. Marc Sultan for setting up sequencing technology platforms, and Mathias Linser and the rest of the sequencing team of the Department of Vertebrate Genomics at the Max Planck Institute for Molecular Genetics for technical assistance. We also acknowledge core support from the Wellcome Trust (092096) and Cancer Research UK (C6946/A14492).
Wellcome Trust (084598/Z/07/Z)
Wellcome Trust (101863/Z/13/Z)
Wellcome Trust (097679/Z/11/Z)
Wellcome Trust (092096/Z/10/Z)
Wellcome Trust (054523/Z/98/C)
Cancer Research UK (A14492)
External DOI: https://doi.org/10.7554/eLife.37344
This record's URL: https://www.repository.cam.ac.uk/handle/1810/288765
Attribution 4.0 International
Licence URL: http://creativecommons.org/licenses/by/4.0/
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