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Series GSE242066 Query DataSets for GSE242066
Status Public on Aug 13, 2024
Title Genome access is transcription factor specific and defined by nucleosome position [NOMe-seq]
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary Mammalian gene expression is controlled by transcription factors (TFs) that engage sequence motifs in a chromatinized genome, where nucleosomes can restrict DNA access. Yet, how nucleosomes affect individual TFs remains unclear. Here, we measure the ability of over one hundred TF motifs to recruit TFs in a defined chromosomal locus in mouse embryonic stem cells. This identifies a set sufficient to enable binding of TFs with diverse tissue specificities, functions, and DNA binding domains. These chromatin-competent factors are further classified when challenged to engage motifs within a highly-phased nucleosome. The pluripotency factors OCT4- SOX2 preferentially engage non-nucleosomal and entry-exit motifs, but not nucleosome internal sites, a preference that also guides binding genome-wide. By contrast, factors such as BANP, REST, or CTCF, engage throughout causing nucleosomal displacement.This reveals that TFs vary widely in their sensitivity to nucleosomes and that genome access is TF-specific and influenced by nucleosome position in the cell.
 
Overall design Amplicon NOMe-seq in mouse ESCs. Replicates of pools of TF motifs inserted in defined sequence contexts and integrated in the RMCE-locus.
 
Contributor(s) Grand R, Pregnolato M, Baumgartner L, Hoerner L, Burger L, Schubeler D
Citation(s) 39208807
Submission date Aug 31, 2023
Last update date Oct 10, 2024
Contact name Dirk Schuebeler
Organization name Friedrich Miescher Institute for Biomedical Research
Street address Maulbeerstrasse 66
City Basel
ZIP/Postal code 4058
Country Switzerland
 
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (115)
GSM7748350 unphased_pool1_R1
GSM7748351 unphased_pool1_R2
GSM7748352 unphased_pool2_R1
This SubSeries is part of SuperSeries:
GSE242067 Genome access is transcription factor specific and defined by nucleosome position
Relations
BioProject PRJNA1011290

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
GSE242066_RAW.tar 194.1 Mb (http)(custom) TAR (of TAR, TXT)
GSE242066_non_nuc_pool1.fasta.gz 375 b (ftp)(http) FASTA
GSE242066_non_nuc_pool2.fasta.gz 384 b (ftp)(http) FASTA
GSE242066_non_nuc_pool3.fasta.gz 373 b (ftp)(http) FASTA
GSE242066_nuc_pool1.fasta.gz 312 b (ftp)(http) FASTA
GSE242066_nuc_pool2.fasta.gz 377 b (ftp)(http) FASTA
GSE242066_nuc_pool3.fasta.gz 245 b (ftp)(http) FASTA
GSE242066_nuc_pool4.fasta.gz 371 b (ftp)(http) FASTA
GSE242066_nuc_pool5.fasta.gz 218 b (ftp)(http) FASTA
GSE242066_tiles_pool1.fasta.gz 312 b (ftp)(http) FASTA
GSE242066_tiles_pool10.fasta.gz 345 b (ftp)(http) FASTA
GSE242066_tiles_pool11.fasta.gz 344 b (ftp)(http) FASTA
GSE242066_tiles_pool12.fasta.gz 275 b (ftp)(http) FASTA
GSE242066_tiles_pool13.fasta.gz 210 b (ftp)(http) FASTA
GSE242066_tiles_pool14.fasta.gz 331 b (ftp)(http) FASTA
GSE242066_tiles_pool2.fasta.gz 301 b (ftp)(http) FASTA
GSE242066_tiles_pool3.fasta.gz 312 b (ftp)(http) FASTA
GSE242066_tiles_pool4.fasta.gz 313 b (ftp)(http) FASTA
GSE242066_tiles_pool5.fasta.gz 319 b (ftp)(http) FASTA
GSE242066_tiles_pool6.fasta.gz 345 b (ftp)(http) FASTA
GSE242066_tiles_pool7.fasta.gz 299 b (ftp)(http) FASTA
GSE242066_tiles_pool8.fasta.gz 334 b (ftp)(http) FASTA
GSE242066_tiles_pool9.fasta.gz 336 b (ftp)(http) FASTA
GSE242066_unphased_pool1.fasta.gz 189 b (ftp)(http) FASTA
GSE242066_unphased_pool10.fasta.gz 299 b (ftp)(http) FASTA
GSE242066_unphased_pool11.fasta.gz 350 b (ftp)(http) FASTA
GSE242066_unphased_pool12.fasta.gz 359 b (ftp)(http) FASTA
GSE242066_unphased_pool13.fasta.gz 325 b (ftp)(http) FASTA
GSE242066_unphased_pool14.fasta.gz 353 b (ftp)(http) FASTA
GSE242066_unphased_pool15.fasta.gz 336 b (ftp)(http) FASTA
GSE242066_unphased_pool16.fasta.gz 342 b (ftp)(http) FASTA
GSE242066_unphased_pool17.fasta.gz 356 b (ftp)(http) FASTA
GSE242066_unphased_pool18.fasta.gz 188 b (ftp)(http) FASTA
GSE242066_unphased_pool2.fasta.gz 287 b (ftp)(http) FASTA
GSE242066_unphased_pool3.fasta.gz 209 b (ftp)(http) FASTA
GSE242066_unphased_pool4.fasta.gz 334 b (ftp)(http) FASTA
GSE242066_unphased_pool5.fasta.gz 347 b (ftp)(http) FASTA
GSE242066_unphased_pool6.fasta.gz 327 b (ftp)(http) FASTA
GSE242066_unphased_pool7.fasta.gz 336 b (ftp)(http) FASTA
GSE242066_unphased_pool8.fasta.gz 339 b (ftp)(http) FASTA
GSE242066_unphased_pool9.fasta.gz 346 b (ftp)(http) FASTA
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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