Whole-Genome Mapping of Histone H3 Lys4 and 27 Trimethylations Reveals Distinct Genomic Compartments in Human Embryonic Stem Cells

Xiao Dong Zhao; Xu Han; Joon Lin Chew; Jun Liu; Kuo Ping Chiu; Andre Choo; Yuriy L. Orlov; Wing Kin Sung; Atif Shahab; Vladimir A. Kuznetsov; Guillaume Bourque; Steve Oh; Yijun Ruan; Huck Hui Ng; Chia Lin Wei

doi:10.1016/j.stem.2007.08.004

Whole-Genome Mapping of Histone H3 Lys4 and 27 Trimethylations Reveals Distinct Genomic Compartments in Human Embryonic Stem Cells

Xiao Dong Zhao, Xu Han, Joon Lin Chew, Jun Liu, Kuo Ping Chiu, Andre Choo, Yuriy L. Orlov, Wing Kin Sung, Atif Shahab, Vladimir A. Kuznetsov, Guillaume Bourque, Steve Oh, Yijun Ruan, Huck Hui Ng, Chia Lin Wei

Research output: Contribution to journal › Article › peer-review

493 Scopus citations

Abstract

Epigenetic modifications are crucial for proper lineage specification and embryo development. To explore the chromatin modification landscapes in human ES cells, we profiled two histone modifications, H3K4me3 and H3K27me3, by ChIP coupled with the paired-end ditags sequencing strategy. H3K4me3 was found to be a prevalent mark and occurred in close proximity to the promoters of two-thirds of total human genes. Among the H3K27me3 loci identified, 56% are associated with promoters and the vast majority of them are comodified by H3K4me3. By deep-transcript digital counting, 80% of H3K4me3 and 36% of comodified promoters were found to be transcribed. Remarkably, we observed that different combinations of histone methylations are associated with genes from distinct functional categories. These global histone methylation maps provide an epigenetic framework that enables the discovery of novel transcriptional networks and delineation of different genetic compartments of the pluripotent cell genome.

Original language	English (US)
Pages (from-to)	286-298
Number of pages	13
Journal	Cell Stem Cell
Volume	1
Issue number	3
DOIs	https://doi.org/10.1016/j.stem.2007.08.004
State	Published - Sep 13 2007
Externally published	Yes

Keywords

STEMCELL

ASJC Scopus subject areas

Molecular Medicine
Genetics
Cell Biology

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10.1016/j.stem.2007.08.004

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Zhao, X. D., Han, X., Chew, J. L., Liu, J., Chiu, K. P., Choo, A., Orlov, Y. L., Sung, W. K., Shahab, A., Kuznetsov, V. A., Bourque, G., Oh, S., Ruan, Y., Ng, H. H., & Wei, C. L. (2007). Whole-Genome Mapping of Histone H3 Lys4 and 27 Trimethylations Reveals Distinct Genomic Compartments in Human Embryonic Stem Cells. Cell Stem Cell, 1(3), 286-298. https://doi.org/10.1016/j.stem.2007.08.004

Zhao, XD, Han, X, Chew, JL, Liu, J, Chiu, KP, Choo, A, Orlov, YL, Sung, WK, Shahab, A, Kuznetsov, VA, Bourque, G, Oh, S, Ruan, Y, Ng, HH & Wei, CL 2007, 'Whole-Genome Mapping of Histone H3 Lys4 and 27 Trimethylations Reveals Distinct Genomic Compartments in Human Embryonic Stem Cells', Cell Stem Cell, vol. 1, no. 3, pp. 286-298. https://doi.org/10.1016/j.stem.2007.08.004

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abstract = "Epigenetic modifications are crucial for proper lineage specification and embryo development. To explore the chromatin modification landscapes in human ES cells, we profiled two histone modifications, H3K4me3 and H3K27me3, by ChIP coupled with the paired-end ditags sequencing strategy. H3K4me3 was found to be a prevalent mark and occurred in close proximity to the promoters of two-thirds of total human genes. Among the H3K27me3 loci identified, 56% are associated with promoters and the vast majority of them are comodified by H3K4me3. By deep-transcript digital counting, 80% of H3K4me3 and 36% of comodified promoters were found to be transcribed. Remarkably, we observed that different combinations of histone methylations are associated with genes from distinct functional categories. These global histone methylation maps provide an epigenetic framework that enables the discovery of novel transcriptional networks and delineation of different genetic compartments of the pluripotent cell genome.",

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author = "Zhao, {Xiao Dong} and Xu Han and Chew, {Joon Lin} and Jun Liu and Chiu, {Kuo Ping} and Andre Choo and Orlov, {Yuriy L.} and Sung, {Wing Kin} and Atif Shahab and Kuznetsov, {Vladimir A.} and Guillaume Bourque and Steve Oh and Yijun Ruan and Ng, {Huck Hui} and Wei, {Chia Lin}",

note = "Funding Information: The authors would like to acknowledge Mr. H. Thoreau and the Genome Technology & Biology Group at the Genome Institute of Singapore for HTP sequencing support. We also would like to thank Ms. Melissa Jane Fullwood for her suggestions and critical reading to improve the quality and clarity of the text. This work is supported by the Agency for Science, Technology and Research (A ∗ STAR) of Singapore, Singapore Stem Cell Consortium grant (to H.-H.N), and the NIH ENCODE grant 1R01HG003521-01 (to Y.R. and C.-L.W.). ",

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AU - Liu, Jun

AU - Chiu, Kuo Ping

AU - Choo, Andre

AU - Orlov, Yuriy L.

AU - Sung, Wing Kin

AU - Shahab, Atif

AU - Kuznetsov, Vladimir A.

AU - Bourque, Guillaume

AU - Oh, Steve

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AU - Ng, Huck Hui

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N2 - Epigenetic modifications are crucial for proper lineage specification and embryo development. To explore the chromatin modification landscapes in human ES cells, we profiled two histone modifications, H3K4me3 and H3K27me3, by ChIP coupled with the paired-end ditags sequencing strategy. H3K4me3 was found to be a prevalent mark and occurred in close proximity to the promoters of two-thirds of total human genes. Among the H3K27me3 loci identified, 56% are associated with promoters and the vast majority of them are comodified by H3K4me3. By deep-transcript digital counting, 80% of H3K4me3 and 36% of comodified promoters were found to be transcribed. Remarkably, we observed that different combinations of histone methylations are associated with genes from distinct functional categories. These global histone methylation maps provide an epigenetic framework that enables the discovery of novel transcriptional networks and delineation of different genetic compartments of the pluripotent cell genome.

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Whole-Genome Mapping of Histone H3 Lys4 and 27 Trimethylations Reveals Distinct Genomic Compartments in Human Embryonic Stem Cells

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Keywords

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