E-MTAB-454 - Transcription profiling by array of HaCaT keratinocytes synchronised during the cell cycle and sampled at 3 hour intervals

Status
Released on 31 December 2011, last updated on 20 October 2014
Organism
Homo sapiens
Samples (36)
Arrays (2)
Protocols (6)
Description
HaCat cell cycle experiment: During the somatic cell cycle, DNA and epigenetic modifications in DNA and histones are copied to daughter cells. DNA replication timing is tightly regulated and linked to GC content, chromatin structure, andgene transcription, but how maintenance of histone modifications relates to replication timing and transcription is less understood.The gene expression patters on HaCaT keratinocytes during the cell cycle is studied by a time series analysis of synchroniced cells sampled at 3 hour intervals. We show that genes enriched with the repressive chromatin mark histone H3 lysine 27 tri-methylation are transcribed during DNA replication . The gene expression is related to replication timing, as genes expressed during G1/S transition andearly S phase generally have higher GC content and are replicated earlier than genes expressed during late S phase. These results indicate widespread replication-dependent expression in mammals and support a role for replication in transiently activating transcription of epigenetically silenced genes.
Experiment types
transcription profiling by array, cell cycle, co-expression, in vitro, time series
Contact
Citations
Transcription profiling during the cell cycle shows that a subset of Polycomb-targeted genes is upregulated during DNA replication. Javier Peña-Diaz; Siv A. Hegre; Endre Anderssen; Per A. Aas; Robin Mjelle; Gregor D. Gilfillan; Robert Lyle; Finn Drabløs; Hans E. Krokan; Pål Sætrom. Nucleic Acids Res 41(5):2846 (2013), PMID:23325852
Transcription profiling during the cell cycle shows that a subset of Polycomb-targeted genes is upregulated during DNA replication. Peña-Diaz J, Hegre SA, Anderssen E, Aas PA, Mjelle R, Gilfillan GD, Lyle R, Drabløs F, Krokan HE, Sætrom P. :2846-2856 (2013), PMID:23325852
Transcription profiling during the cell cycle shows that a subset of Polycomb-targeted genes is upregulated during DNA replication. Peña-Diaz J, Hegre SA, Anderssen E, Aas PA, Mjelle R, Gilfillan GD, Lyle R, Drabløs F, Krokan HE, Sætrom P. Nucleic Acids Res 41(5):2846-2856 (2013), PMID:23325852
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-MTAB-454.idf.txt
Sample and data relationshipE-MTAB-454.sdrf.txt
Raw data (2)E-MTAB-454.raw.1.zip, E-MTAB-454.raw.2.zip
Processed data (1)E-MTAB-454.processed.1.zip
Array designsA-AFFY-33.adf.txt, A-AFFY-34.adf.txt
Links