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Series GSE142377 Query DataSets for GSE142377
Status Public on Sep 06, 2020
Title Diversification of posterior Hox patterning by graded ability to engage inaccessible chromatin [ChIP-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary While Hox genes encode for similar transcription factors (TFs), they induce different fates across body axes. We sought to understand how Hox TF genomic binding preferences relate to their patterning activities during neuronal differentiation. To generate the required neuronal diversity for locomotor activity, Hox TFs specify spinal motor neuron and interneuron subtypes along the rostro-caudal axis. Our data revelated that Hoxc6 and Hoxc8 of the central group induce limb-innervating fates by binding to the same sites. On the other hand, the posterior group Hox genes assign different positional identities: Hoxc9 (thoracic), Hoxc10 (limb-innervating) and Hox13 (axial elongation termination) by binding to distinct sites with the same primary motif. We find that their genomic binding distributions are explained by differential abilities to bind to previously inaccessible chromatin. Thus, the vertebrate posterior Hox expansion and its associated patterning diversification is the product of their differential abilities to associate with less accessible chromatin.
 
Overall design ChIP-Seq was used to characterize Hox TF binding during ESC-to-MN differentiation
 
Contributor(s) Bulajić M, Srivastava D, Dasen JS, Wichterle H, Mahony S, Mazzoni EO
Citation(s) 33028607
Submission date Dec 19, 2019
Last update date Dec 06, 2020
Contact name Shaun Mahony
E-mail(s) mahony@psu.edu
Phone 814-865-3008
Organization name Penn State University
Department Biochemistry & Molecular Biology
Lab Shaun Mahony
Street address 404 South Frear Bldg
City University Park
State/province PA
ZIP/Postal code 16802
Country USA
 
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (42)
GSM4226434 ChIPseq Hoxc6 in EB-Day3[D0+RA+SAG][D2+24hDox(iFlag.Hoxc6)] replicate 1
GSM4226435 ChIPseq Hoxc6 in EB-Day3[D0+RA+SAG][D2+24hDox(iFlag.Hoxc6)] replicate 2
GSM4226436 ChIPseq Hoxc8 in EB-Day3[D0+RA+SAG][D2+24hDox(iFlag.Hoxc8)] replicate 1
This SubSeries is part of SuperSeries:
GSE142379 Diversification of posterior Hox patterning by graded ability to engage inaccessible chromatin
Relations
BioProject PRJNA596780
SRA SRP238219

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
GSE142377_RAW.tar 42.1 Mb (http)(custom) TAR (of BED, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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