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Series GSE239883 Query DataSets for GSE239883
Status Public on Nov 19, 2023
Title Intrinsically disordered regions of transcription factor encode multiple functions using interwoven sequence grammars (RNA-Seq)
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by high throughput sequencing
Summary Intrinsically disordered regions (IDRs) are abundant within eukaryotic proteins, but their sequence-function relationship remains poorly understood. IDRs of transcription factors (TFs) can direct promoter selection and recruit coactivators, as exemplified by the budding-yeast TF- Msn2. To examine how low-complexity IDRs encode multiple functions, we compared genomic binding preferences, gene induction, and coactivator recruitment amongst a large set of designed Mns2-IDR mutants. We show that multiple regions across the >500AA IDR contribute to both functions. Yet, transcription activity was readily disrupted by variants having no consequences on Msn2 binding. Our data attribute this differential sensitivity to the integration of relaxed, composition-based code directing binding preferences with a more stringent, motif-based code controlling the recruitment of coactivators and transcription activity. Interwoven sequence grammar may present a general paradigm through which low-complexity IDRs encode multiple functions.
 
Overall design The experimetns here are RNA-seq samples, collection of samples was performed at OD600 of 0.4 after treatment with 0.3 mM of H2O2 to induce stress, for controls we used the expresion profiling of non-genetically modified yeast strain (BY4741) or ΔMsn2
 
Contributor(s) Mindel V, Brodsky S, Cohen A, Manadre W, Jonas F, Carmi M, Barkai N
Citation(s) 38109289
Submission date Aug 02, 2023
Last update date Dec 20, 2023
Contact name Naama Barkai
E-mail(s) naama.barkai@weizmann.ac.il
Phone +972-8-934-4429
Organization name Weizmann Institute of Science
Department Molecular Genetics
Lab Barkai Lab
Street address Herzl 234
City Rehovot
State/province HaMerkaz
ZIP/Postal code 7630031
Country Israel
 
Platforms (1)
GPL27812 Illumina NovaSeq 6000 (Saccharomyces cerevisiae)
Samples (336)
GSM7676275 90p_10n_chargeratio_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4
GSM7676276 A_nextto_N_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4
GSM7676277 A_nextto_N_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4
This SubSeries is part of SuperSeries:
GSE239884 Intrinsically disordered regions of the Msn2 transcription factor encode multiple functions using interwoven sequence grammars
Relations
BioProject PRJNA1001337

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
GSE239883_RAW.tar 31.6 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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