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Series GSE98245 Query DataSets for GSE98245
Status Public on Apr 25, 2018
Title Topological demarcation by HMGB2 is disrupted early upon senescence entry and induces CTCF clustering across cell types [ChIP-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We hypothesized that entry into senescence of different primary human cells can be triggered by one early molecular event affecting the spatial organization of chromosomes. To test this, we combined whole-genome chromosome conformation capture, population and single-cell transcriptomics, super-resolution imaging, and functional analyses applied on proliferating and replicatively-senescent populations from three distinct human cell types. We found a number of genes involved in DNA conformation maintenance being suppressed upon senescence across cell types. Of these, the abundant high mobility group (HMG) B1 and B2 nuclear factors are quantitatively removed from cell nuclei before typical senescence markers appear, and mark a subset of topologically-associating domain (TAD) boundaries. Their loss coincides with obvious reorganization of chromatin interactions via the dramatic spatial clustering of CTCF foci. HMGB2 knock-down recapitulates this senescence-induced CTCF clustering, while also affecting insulation at TAD boundaries.
 
Overall design Genome-wide binding profiles for the non-histone DNA-binding proteins HMGB1 and HMGB2 were investigated in HUVEC and IMR90
 
Contributor(s) Papantonis A, Nikolic M, Zirkel A
Citation(s) 29706538
http://dx.doi.org/10.1101/540146
Submission date Apr 26, 2017
Last update date Jul 25, 2021
Contact name Milos Nikolic
E-mail(s) milosn@gmail.com
Organization name Center for Molecular Medicine Cologne
Street address Robert Koch Str. 21
City Koeln
State/province Nordrhein-Westfalen
ZIP/Postal code 50674
Country Germany
 
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (7)
GSM2589814 HUVEC_input (proliferating)
GSM2589815 HUVEC_HMGB1_ChIP (proliferating)
GSM2589816 HUVEC_HMGB2_ChIP (proliferating)
This SubSeries is part of SuperSeries:
GSE98448 Topological demarcation by HMGB2 is disrupted early upon senescence entry and induces CTCF clustering across cell types
Relations
BioProject PRJNA384392
SRA SRP105278

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
GSE98245_RAW.tar 170.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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