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Series GSE58535 Query DataSets for GSE58535
Status Public on Jun 30, 2020
Title H3K9 methylation fine-tunes coordination of transcription by regulating the conformational plasticity of chromosomal folding [RNA-Seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Despite that stochastic gene expression variations underlie lineage specification and adaptive responses, little is known about the plasticity of 3D chromatin folding and its effects on cell-to-cell transcriptional variability. Employing the Chromatin In Situ Proximity (ChrISP) technique we visualize here developmentally acquired chromosome 11-specific chromatin hubs rich in the repressive H3K9me2 mark that project towards the lamina in single cells. Inhibition of the H3Kme2 methyl-transferase G9a/Glp not only antagonizedperipheral chromatin compaction, but strikingly also induced the emergence of dense chromatin clusters in the nuclear interior. Changes in chromatin organization were accompanied by the spatial re-organization of transcriptional coordination without affecting the overall level of transcription. LOCKs thus topologically insulate active genes at the nuclear periphery, while allowing transcriptional coordination in the rest of the chromosome. We conclude that G9a/Glp controls not only the plasticity of chromatin conformations, but also spatial coordination of transcription to affect cellular gene expression variability.
Overall design 2 Biological replicates and 2 technical replicates where treated with both G9a Inhibitor and siRNA
Contributor(s) Chen X, Yammine S, Sumida N, Fernandez-Woodbridge A, Shi C, Shahin Varnoosfaderani F, Tark-Dame M, Imreh MP, Göndör A, Ohlsson R
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Submission date Jun 16, 2014
Last update date Jul 01, 2020
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 (16)
GSM1413016 RNASEQ001_G9a_control_1
GSM1413017 RNASEQ001_G9a_control_2
GSM1413018 RNASEQ001_G9a_inhibitor_1
BioProject PRJNA252842
SRA SRP043290

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Supplementary file Size Download File type/resource
GSE58535_RAW.tar 25.8 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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