GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE26880 Query DataSets for GSE26880
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 Other
Expression 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 Examination of intra- and interchromosomal interactions in human embryonic stem cells (HESCs) and derived embryoid bodies (HEBs) generated by 4C-seq, as described in (Zhao et al., 2006), using Illumina Genome Analyzer II and Illumina MiSeq.
Examination of mRNA profiles in HESCs and derived HEBs generated by deep sequencing, in duplicate, using Illumina HiSeq 2500.
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 Jan 26, 2011
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 (3)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (23)
GSM1436337 HESC Protected replicate 1
GSM1436338 HESC Protected replicate 2
GSM1436339 HESC RNAse replicate 1
SRA SRP005858
BioProject PRJNA136121

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
GSE26880_RAW.tar 1.6 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap