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Series GSE76174 Query DataSets for GSE76174
Status Public on Dec 19, 2015
Title Cause and consequence of tethering a sub-TAD to different nuclear compartments
Organism Mus musculus
Experiment type Other
Summary Detailed genomic contact maps have revealed that chromosomes are composed of developmentally stable topologically associated domains (TADs) and more flexible sub-TADs. These domains reside in active and inactive nuclear compartments, but cause and consequence of compartmentalization are largely unknown. Here, we combined lacO/lacR binding platforms with allele-specific 4C technologies to track their precise position in the three-dimensional genome upon recruitment of NANOG, SUV39H1 or EZH2. We observed locked genomic loci resistant to spatial repositioning and unlocked loci that could be repositioned to different nuclear sub-compartments with distinct chromatin signatures. Focal protein recruitment caused the entire sub- TAD, but not surrounding regions, to engage in new genomic contacts. Compartment switching was uncoupled from gene expression changes and enzymatically modifying histones per se was insufficient for repositioning. Collectively this suggests that transassociated factors determine three-dimensional compartmentalization independent of their cis-effect on local chromatin composition and activity.
Overall design 4C-seq was performed on a range of viewpoints in 129/Sv;C57BL/6 embryonic stem cells carying a lacO array in chromosome 8 and 11.
Contributor(s) Wijchers PJ, Krijger PL, Geeven G, de Laat W
Citation(s) 26833089
Submission date Dec 18, 2015
Last update date May 15, 2019
Contact name Geert Geeven
Organization name Hubrecht Institute
Department Biomedical Genomics
Lab Wouter de Laat
Street address Uppsalalaan 8
City Utrecht
State/province Utrecht
ZIP/Postal code 3584 CT
Country Netherlands
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (45)
GSM1975782 chr11_LacO_Untransduced_4C-Seq_R1
GSM1975783 chr11_LacO_Untransduced_4C-Seq_R2
GSM1975784 chr11_LacR_4C-Seq_R1
BioProject PRJNA306520
SRA SRP067587

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Supplementary file Size Download File type/resource
GSE76174_RAW.tar 10.6 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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