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Cell Rep. 2014 Feb 13;6(3):455-66. doi: 10.1016/j.celrep.2014.01.008. Epub 2014 Jan 30.

Pol II docking and pausing at growth and stress genes in C. elegans.

Author information

1
Department of Biology, Duke Center for Systems Biology, Duke University, Durham, NC 27708, USA.
2
Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
3
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
4
Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.
5
Department of Biology, Duke Center for Systems Biology, Duke University, Durham, NC 27708, USA. Electronic address: ryan.baugh@duke.edu.

Abstract

Fluctuations in nutrient availability profoundly impact gene expression. Previous work revealed postrecruitment regulation of RNA polymerase II (Pol II) during starvation and recovery in Caenorhabditis elegans, suggesting that promoter-proximal pausing promotes rapid response to feeding. To test this hypothesis, we measured Pol II elongation genome wide by two complementary approaches and analyzed elongation in conjunction with Pol II binding and expression. We confirmed bona fide pausing during starvation and also discovered Pol II docking. Pausing occurs at active stress-response genes that become downregulated in response to feeding. In contrast, "docked" Pol II accumulates without initiating upstream of inactive growth genes that become rapidly upregulated upon feeding. Beyond differences in function and expression, these two sets of genes have different core promoter motifs, suggesting alternative transcriptional machinery. Our work suggests that growth and stress genes are both regulated postrecruitment during starvation but at initiation and elongation, respectively, coordinating gene expression with nutrient availability.

PMID:
24485661
PMCID:
PMC4026043
DOI:
10.1016/j.celrep.2014.01.008
[Indexed for MEDLINE]
Free PMC Article

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