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Series GSE269116 Query DataSets for GSE269116
Status Public on Jun 13, 2024
Title Notch induces transcription by stimulating release of paused RNA Pol II without increasing chromatin accessibility [TT-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Other
Summary Notch proteins undergo ligand-induced proteolysis to release a nuclear effector that influences a wide range of cell fate decisions by regulating gene activity. However, despite years of study, how Notch induces the transcription of its target genes remains unclear. Here, we comprehensively examined the response to human Notch1 across a time course of activation, using genomic assays of nascent RNA and chromatin accessibility. These data revealed that Notch induces target gene transcription primarily by releasing paused RNA polymerase II (RNAPII), in contrast to prevailing models suggesting that Notch acts by promoting chromatin accessibility. Indeed, we found that open chromatin is established at Notch-responsive regulatory elements prior to Notch signaling, through SWI/SNF-mediated remodeling. Notch activation, however, elicited no further chromatin opening at these loci. Together, these studies reveal that the nuclear response to Notch signaling is dictated by the pre-existing chromatin state and RNAPII distribution at the time of signal activation.
 
Overall design To determine which genes are induced by Notch signaling in SC2 cells, and how SWI/SNF inhibition affects gene expression in the Notch response, Notch signaling was induced in SC2 cells by GSI washout. Cells were harvested at 1 and 4 hours post Notch activation, and immediately after mock GSI washout, and harvested for TT-seq sample preparation. Mock washout control samples were also harvested at 1 and 4 hours. For each of these time points, cells were either treated with SWI/SNF inhibitor (1 ┬ÁM BRM014) or 0.01% DMSO at the time of washout or mock-washout. There are 10total conditions, and two replicates of the full experiment.
 
Contributor(s) Rogers JM, Mimoso CA, Martin BJ, Adelman K, Blacklow SC
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Submission date Jun 05, 2024
Last update date Jun 14, 2024
Contact name Julia M Rogers
E-mail(s) julia_rogers@hms.harvard.edu
Organization name Harvard Medical School
Department BCMP
Lab Blacklow Lab
Street address 45 Shattuck Street
City Boston
State/province Massachusetts
ZIP/Postal code 02115
Country USA
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (20)
GSM8306573 TT_0h_GSI_BRM014_rep1
GSM8306574 TT_0h_GSI_BRM014_rep2
GSM8306575 TT_0h_GSI_DMSO_rep1
This SubSeries is part of SuperSeries:
GSE269128 Notch induces transcription by stimulating release of paused RNA Pol II without increasing chromatin accessibility.
Relations
BioProject PRJNA1120341

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE269116_RAW.tar 24.5 Gb (http)(custom) TAR (of BW)
GSE269116_TTseq_normalized_genecounts.xlsx 3.8 Mb (ftp)(http) XLSX
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Raw data are available in SRA

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