title: Transcription factors GAF and HSF act at distinct regulatory steps to modulate stress-induced gene activation.
abstract: The coordinated regulation of gene expression at the transcriptional level is fundamental to development and homeostasis. Inducible systems are invaluable when studying transcription because the regulatory process can be triggered instantaneously, allowing the tracking of ordered mechanistic events. Here, we use precision run-on sequencing (PRO-seq) to examine the genome-wide heat shock (HS) response in Drosophila and the function of two key transcription factors on the immediate transcription activation or repression of all genes regulated by HS. We identify the primary HS response genes and the rate-limiting steps in the transcription cycle that GAGA-associated factor (GAF) and HS factor (HSF) regulate. We demonstrate that GAF acts upstream of promoter-proximally paused RNA polymerase II (Pol II) formation (likely at the step of chromatin opening) and that GAF-facilitated Pol II pausing is critical for HS activation. In contrast, HSF is dispensable for establishing or maintaining Pol II pausing but is critical for the release of paused Pol II into the gene body at a subset of highly activated genes. Additionally, HSF has no detectable role in the rapid HS repression of thousands of genes.
authors: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14835, USA;
authors: Fabiana M
authors: 0000-0002-1261-4929
authors: FM
authors: Duarte
authors: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14835, USA;
authors: Nicholas J
authors: NJ
authors: Fuda
authors: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14835, USA;
authors: Dig B
authors: DB
authors: Mahat
authors: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14835, USA;
authors: Leighton J
authors: LJ
authors: Core
authors: Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, USA.
authors: Michael J
authors: MJ
authors: Guertin
authors: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14835, USA;
authors: John T
authors: 0000-0003-1201-9406
authors: JT
authors: Lis
mesh_terms: D000818:Animals; D002460:Cell Line; D004257:DNA Polymerase II / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D004330:Drosophila / Q000235:genetics* / Q000378:metabolism; D029721:Drosophila Proteins / Q000235:genetics / Q000378:metabolism*; D005786:Gene Expression Regulation / Q000235:genetics*; D000076249:Heat Shock Transcription Factors; D011401:Promoter Regions, Genetic / Q000235:genetics; D034622:RNA Interference; D013312:Stress, Physiological / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; D000076249:Heat Shock Transcription Factors; C053134:Hsf protein, Drosophila; C583285:M1BP protein, Drosophila; D014157:Transcription Factors; C063460:Trl protein, Drosophila; D004257:DNA Polymerase II
keywords: Pol II pausing; heat shock; transcription factors; transcription regulation