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Series GSE110389 Query DataSets for GSE110389
Status Public on Apr 26, 2018
Title Histone H3.3 G34 mutations alter histone H3K36 and H3K27 methylation in cis
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary High-throughput sequencing of numerous patient samples has identified a myriad of frequent mutations of epigenetic regulators in human cancers, including recently discovered mutations in histone-encoding genes. Lysine-to-methionine mutations such as H3K27M and H3K36M share a common mechanism of inhibiting methylation pathways at the genome-wide level to promote tumorigenesis. However, the mechanism underlying the molecular and cellular changes due to H3G34 alterations is yet to be determined. H3G34 itself is not post-translationally modified; however, G34 lies in close proximity to K36, which undergoes methylation during transcriptional elongation. In Hela cells, H3.3G34L/W mutations have no effect on global levels of methylation on H3K36, H3K27, or other major methylation sites on endogenous histone H3, which include both H3.3 and the canonical H3.1/H3.2 proteins. However, long exposures of the blots revealed that methylation on the ectopic Flag-H3.3 proteins are affected by G34 mutations: with di- and trimethylation on H3K36 and H3K27ac reduced whereas H3K27me3 increased in the G34L and G34W mutated H3.3 compared to the WT H3.3. ChIP-seq results showed that mutations of H3.3G34 affect methylation on H3K36 and H3K27 in cis. G34L/W mutants abolish SETD2 methylation of H3K36. In contrast, the enzymatic activities of both EZH2 and p300 on H3K27 are not affected by G34 mutations. Consistent with changes in H3K27me3 and H3K36m3 levels, we found increased binding of PRC2 (EZH2, SUZ12 and EED) and PRC1 complex components (CBX8 and RING2) and reduced binding of H3.3K36me3 reader such as ZMYND11 to the G34 mutants. In summary, our study revealed that histone H3.3 G34 mutations alter histone K36 and K27 methylation in cis, and affect the binding of readers specific to K36 or K27 methylation.
Overall design ChIP-seq of H3.3, Flag-H3.3, H3K27ac, H3K27me3, H3K36me2, and H3K36me3 were applied in HeLa cells stably expressing WT or mutant (G34L/G34W) H3.3 and control vector (Ctrl). ChIP-seq of Flag-H3.3, H3K36me2, and H3K36me3 were also applied in HeLa cells stably expressing mutant K36M H3.3.
Contributor(s) Shi J, Shi L, Shi X
Citation(s) 29689253
Submission date Feb 08, 2018
Last update date Dec 23, 2018
Contact name Jiejun Shi
Organization name University of California Irvine
Department School of Medicine
Lab Li lab
Street address 5270 California Ave
City Irvine
State/province CA
ZIP/Postal code 92617
Country USA
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (22)
GSM2990403 H3K27ac ChIP-seq in G34L
GSM2990404 H3K27me3 ChIP-seq in G34L
GSM2990405 H3.3 ChIP-seq in G34L
BioProject PRJNA433584
SRA SRP132532

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Supplementary file Size Download File type/resource
GSE110389_RAW.tar 11.6 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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