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Department of Health and Human ServicesNational Institutes of HealthNational Heart Lung and Blood Institute
High-Resolution Profiling of Histone Methylations in the Human Genome
NHLBI Division of Intramural ResearchLaboratory of Molecular Immunology

Artem Barski1,3, Suresh Cuddapah1,3, Kairong Cui1,3, Tae-Young Roh1,3, Dustin E. Schones1,3, Zhibin Wang1,3, Gang Wei1,3, Iouri Chepelev2, and Keji Zhao1,4

1 Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892
2 Department of Human Genetics, Gonda Neuroscience and Genetics Research Center, University of California at Los Angeles, CA 90095
3 These authors made equal contributions and are are listed alphabetically
4 Corresponding author

Summary

We have generated high-resolution maps for the genome-wide distribution of 20 histone lysine and arginine methylations as well as the distribution of histone variant H2A.Z, RNA polymerase II, and the insulator binding protein CTCF across the human genome using the Solexa 1G sequencing technology. We have identified the typical patterns of histone methylations exhibited at promoters, insulators, enhancers, and transcribed regions. The monomethylation of H3K27, H3K9, H4K20, H3K79, and H2BK5 are all linked to gene activation, whereas trimethylation of H3K27, H3K9, H4K20, and H3K79 are linked to repression. H2A.Z associates with functional regulatory elements, and CTCF marks boundaries of histone methylation domains. Large chromosome domains are correlated with unique patterns of histone modifications. Chromosome breakpoints detected in T cell cancers frequently reside in chromatin regions associated with H3K4 methylations. Our data provide new insights into the function of histone methylation and chromatin organization in genome function.

Data

Data Set Tag coordinate bed file Summary bed file UCSC track
H3K4me1 H3K4me1 H3K4me1 H3K4me1
H3K4me2 H3K4me2 H3K4me2 H3K4me2
H3K4me3 H3K4me3 H3K4me3 H3K4me3
H3K9me1 H3K9me1 H3K9me1 H3K9me1
H3K9me2 H3K9me2 H3K9me2 H3K9me2
H3K9me3 H3K9me3 H3K9me3 H3K9me3
H3K27me1 H3K27me1 H3K27me1 H3K27me1
H3K27me2 H3K27me2 H3K27me2 H3K27me2
H3K27me3 H3K27me3 H3K27me3 H3K27me3
H3K36me1 H3K36me1 H3K36me1 H3K36me1
H3K36me3 H3K36me3 H3K36me3 H3K36me3
H3K79me1 H3K79me1 H3K79me1 H3K79me1
H3K79me2 H3K79me2 H3K79me2 H3K79me2
H3K79me3 H3K79me3 H3K79me3 H3K79me3
H3R2me1 H3R2me1 H3R2me1 H3R2me1
H3R2me2 (as) H3R2me2 H3R2me2 H3R2me2
H4K20me1 H4K20me1 H4K20me1 H4K20me1
H4K20me3 H4K20me3 H4K20me3 H4K20me3
H2A+H4R3me2 H2A+H4R3me2 H2A+H4R3me2 H2A+H4R3me2
H2BK5me1 H2BK5me1 H2BK5me1 H2BK5me1
H2A.Z H2A.Z H2A.Z H2A.Z
Pol II Pol II Pol II Pol II
CTCF CTCF CTCF CTCF

(Note: all coordinates are from the Human Mar. 2006 (hg18) assembly)

Data corresponding to this project have been deposited in the NCBI Short Read Archive with accession number SRA000206