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Series GSE214438 Query DataSets for GSE214438
Status Public on Mar 01, 2024
Title Age-associated chromatin re-organization in progenitor B cells
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
Genome variation profiling by high throughput sequencing
Summary Three-dimensional (3D) organization of the genome is essential for precise patterns of gene expression required for biological processes, however its role in physiological aging is not known.Here we show that large scale chromatin re-organization distinguishes bone marrow progenitor (pro-) B cells of old mice from that of young mice.These changes result in increased interactions at the compartment level and reduced interactions within topologically associated domains (TADs).One genomic region that transitions from compartment A to B with age contains the gene encoding Ebf1, a key regulator of normal B cell development.Genetically reducing Ebf1 recapitulates some features of old pro-B cells.TADs that are most reduced with age also harbor genes important for function and development of pro-B cells, including the immunoglobulin heavy chain (IgH) gene locus.Weaker intra-TAD interactions at IgH correlate with reduced utilization of distally located variable gene segments in VDJ recombination.Our observations implicate 3D chromatin re-organization as a major driver of pro-B cell phenotypes that impair B lymphopoiesis with age.
 
Overall design Hi-C, capture Hi-C, ChIP-seq, HiChIP and RNA-seq were used to study the changes of chromatin structures in progenitor B cells during aging.
 
Contributor(s) Ma F, Cao Y, Du H, Braikia FZ, Ollikainen N, Zong L, Bayer M, Qiu X, Park B, Roy R, Nandi S, Sanrantopoulou D, Bianchi AH, Beerman I, Zhao K, Grosschedl R, Sen R
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Submission date Sep 29, 2022
Last update date Mar 18, 2024
Contact name Yaqiang Cao
E-mail(s) caoyaqiang0410@gmail.com
Organization name NHLBI
Department System Biology Center
Lab Laboratory of Epigenome Biology
Street address 9000 Rockville Pike
City Bethesda
State/province Maryland
ZIP/Postal code 20892
Country USA
 
Platforms (3)
GPL16417 Illumina MiSeq (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (76)
GSM6605797 CaptureHiC_Old
GSM6605798 CaptureHiC_Young
GSM6605799 HiC_young_rep1
Relations
BioProject PRJNA885415

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
GSE214438_RAW.tar 105.4 Gb (http)(custom) TAR (of BED, BEDPE, TXT)
GSE214438_RNA_EBF1_OE.txt.gz 1.9 Mb (ftp)(http) TXT
GSE214438_RNA_Ebf1.txt.gz 1.6 Mb (ftp)(http) TXT
GSE214438_RNA_YoungVsOld.txt.gz 1.3 Mb (ftp)(http) TXT
GSE214438_RNA_wapl+.txt.gz 1.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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