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Series GSE66865 Query DataSets for GSE66865
Status Public on Mar 13, 2015
Title A nucleosome turnover map reveals that the stability of histone H4 Lys20 methylation depend on histone recycling in transcribed chromatin [ChIP-exo]
Organism Schizosaccharomyces pombe
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Nucleosome composition actively contribute to the chromatin structure and accessibility. To preserve chromatin state during replication, transcription and DNA repair, cells have evolved mechanisms to evict or recycle histones, generating a landscape of differentially aged nucleosomes. To map the stability of nucleosomes, we have adapted the recombination induced tag exchange (RITE) method to Schizosaccharomyces pombe histone H3. The RITE method allows us to study replication-independent protein turnover both through the occurrence of, in our case, new histone H3 and the disappearance or preservation of old histone H3. We contrast the RITE system to nucleosome turnover measured by chromatin incorporation of an epitope-tagged H3 under an inducible promoter. We confirm previous findings that stable nucleosomes are found at heterochromatin, but also at coding regions of actively transcribed genes. Genome-wide comparisons with several chromatin marks showed that high turnover nucleosomes correlate with H2A.Z, acetylated H4 and H3K4me2. The histones with high turnover are primarily found at the nucleosomes on the 5´and/or 3´ edges of the transcribed unit. In addition, in this study we have determined genome-wide maps of all three methylation marks at H4K20. All methylation of H4K20 appeared in low turnover nucleosomes and particularly in euchromatic regions. H4K20me1 marks stable nucleosomes at loci proximal to nucleosome depleted regions (NDR) and H4K20me2/3 were found further inside of transcribed units, especially at coding regions of long genes expressed at low levels. Further, this transcription-dependent accumulation of histone methylations was dependent on the histone chaperone complex FACT (Facilitates Chromatin Transcription), as predicited from its role in recycling nucleosomes during transcription.
 
Overall design In total 4 samples: ChIP-exo of old H3 (antibody HA) and new H3 (antibody T7) at 0h and 2h after estradiol treatment
 
Contributor(s) Svensson JP, Audergon P, Menendez-Benito V, Shukla M, Sinha I, Norman-Axelsson U, Jemt E, Allshire RC, Ekwall K
Citation(s) 25778913
BioProject PRJNA275627
Submission date Mar 13, 2015
Last update date May 15, 2019
Contact name Karl Ekwall
E-mail(s) karl.ekwall@ki.se
Phone +46 8 6089133
Organization name Karolinska Inst
Street address Alfred Nobels Alle 7
City Stockholm
ZIP/Postal code S-141 89
Country Sweden
 
Platforms (2)
GPL13988 Illumina HiSeq 2000 (Schizosaccharomyces pombe)
GPL19887 Illumina Miseq (Schizosaccharomyces pombe)
Samples (8)
GSM1633567 HA_0h 1
GSM1633568 HA_0h 2
GSM1633569 HA_2h 1
This SubSeries is part of SuperSeries:
GSE66866 A nucleosome turnover map reveals that the stability of histone H4 Lys20 methylation depend on histone recycling in transcribed chromatin
Relations
SRA SRP055086

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Supplementary file Size Download File type/resource
GSE66865_HA_0h.wig.gz 4.8 Mb (ftp)(http) WIG
GSE66865_HA_2h.wig.gz 4.8 Mb (ftp)(http) WIG
GSE66865_T7_0h.wig.gz 2.7 Mb (ftp)(http) WIG
GSE66865_T7_2h.wig.gz 4.9 Mb (ftp)(http) WIG
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Processed data are available on Series record
Raw data are available in SRA

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