Pol II docking and pausing at growth and stress genes in C. elegans.
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.
Department of Biology, Duke Center for Systems Biology, Duke University, Durham, NC 27708, USA.
Colin S
CS
Maxwell
Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
William S
WS
Kruesi
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
Leighton J
LJ
Core
Department of Biology, Duke Center for Systems Biology, Duke University, Durham, NC 27708, USA.
Nicole
N
Kurhanewicz
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
Colin T
CT
Waters
Department of Biology, Duke Center for Systems Biology, Duke University, Durham, NC 27708, USA.
Caitlin L
CL
Lewarch
Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.
Igor
I
Antoshechkin
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
John T
JT
Lis
Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
Barbara J
BJ
Meyer
Department of Biology, Duke Center for Systems Biology, Duke University, Durham, NC 27708, USA. Electronic address: ryan.baugh@duke.edu.
L Ryan
LR
Baugh
D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000254:growth & development*; D047369:Chromatin Immunoprecipitation; D018507:Gene Expression Regulation, Developmental; D017238:Genes, Helminth / Q000235:genetics*; D009154:Mutation / Q000235:genetics; D011401:Promoter Regions, Genetic; D012315:RNA Caps / Q000235:genetics; D012319:RNA Polymerase II / Q000378:metabolism*; D018510:RNA, Helminth / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D013312:Stress, Physiological / Q000235:genetics*; D024363:Transcription Initiation Site; D014158:Transcription, Genetic; D035602:Transcriptional Elongation Factors / Q000235:genetics / Q000378:metabolism
D012315:RNA Caps; D018510:RNA, Helminth; D035602:Transcriptional Elongation Factors; C018648:transcription factor S-II; D012319:RNA Polymerase II