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Series GSE58534 Query DataSets for GSE58534
Status Public on Aug 27, 2015
Title PARP1- and CTCF-mediated interactions between active and repressed chromatin at the lamina promote oscillating transcription
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Transcriptionally active and inactive chromatin domains tend to segregate into separate sub-nuclear compartments to maintain stable expression patterns. However, we have uncovered here an inter-chromosomal network connecting active loci enriched in circadian genes to repressed lamina-associated domains (LADs). The interactome is regulated by PARP1 and its co-factor, CTCF, which not only mediate chromatin fiber interactions, but also promote the recruitment of circadian genes to the lamina. Synchronization of circadian rhythm by serum shock induces oscillations in PARP1-CTCF interactions, which is accompanied by oscillating recruitment of circadian loci to the lamina, followed by the acquisition of repressive H3K9me2 marks and transcriptional attenuation. Furthermore, depletion of H3K9me2/3, inhibition of PARP activity by Olaparib or down-regulation of PARP1 or CTCF expression counteracts both recruitment to the envelope and circadian transcription. PARP1- and CTCF-regulated contacts between circadian loci and the repressive chromatin environment at the lamina thus mediate circadian transcriptional plasticity.
Overall design ChIP-Seq for H3k9me2 in HCT116 colon cancer cells (2 replicates)
Contributor(s) Zhao H, Sifakis EG, Sumida N, Millán-Ariño L, Scholz BA, Svensson PJ, Chen X, Ronnegren AL, Diettrich Mallet de Lima C, Shahin Varnoosfaderani F, Shi C, Loseva O, Yammine S, Israelsson M, Rathje L, Németi B, Fredlund E, Helleday T, Imreh MP, Göndör A
Citation(s) 26321255
Submission date Jun 16, 2014
Last update date May 15, 2019
Contact name Anita Göndör
Organization name Karolinska Institutet
Department MTC
Lab Anita Göndör group
Street address Nobels väg 16, KI Solna Campus, Karolinska Institutet, Box 280
City Stockholm
ZIP/Postal code 171 77
Country Sweden
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (2)
GSM1413014 ChIP-Seq for H3k9me2 Replicate 1
GSM1413015 ChIP-Seq for H3k9me2 Replicate 2
BioProject PRJNA252844
SRA SRP043283

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Supplementary file Size Download File type/resource
GSE58534_RAW.tar 35.8 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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