Extensive Variation in Chromatin States Across Humans

M. Kasowski; S. Kyriazopoulou-Panagiotopoulou; F. Grubert; J. B. Zaugg; A. Kundaje; Y. Liu; A. P. Boyle; Q. C. Zhang; F. Zakharia; D. V. Spacek; J. Li; D. Xie; A. Olarerin-George; L. M. Steinmetz; J. B. Hogenesch; M. Kellis; S. Batzoglou; M. Snyder

doi:10.1126/science.1242510

Extensive Variation in Chromatin States Across Humans

M. Kasowski, S. Kyriazopoulou-Panagiotopoulou, F. Grubert, J. B. Zaugg, A. Kundaje, Y. Liu, A. P. Boyle, Q. C. Zhang, F. Zakharia, D. V. Spacek, J. Li, D. Xie, A. Olarerin-George, L. M. Steinmetz, J. B. Hogenesch, M. Kellis, S. Batzoglou, M. Snyder

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

275 Scopus citations

Abstract

The majority of disease-associated variants lie outside protein-coding regions, suggesting a link between variation in regulatory regions and disease predisposition. We studied differences in chromatin states using five histone modifications, cohesin, and CTCF in lymphoblastoid lines from 19 individuals of diverse ancestry. We found extensive signal variation in regulatory regions, which often switch between active and repressed states across individuals. Enhancer activity is particularly diverse among individuals, whereas gene expression remains relatively stable. Chromatin variability shows genetic inheritance in trios, correlates with genetic variation and population divergence, and is associated with disruptions of transcription factor binding motifs. Overall, our results provide insights into chromatin variation among humans.

Original language	English (US)
Pages (from-to)	750-752
Number of pages	3
Journal	Science
Volume	342
Issue number	6159
DOIs	https://doi.org/10.1126/science.1242510
State	Published - Oct 17 2013
Externally published	Yes

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: Funded by grants from the NIH and Genetics Department, Stanford University, Vera Moulton Wall Center for Pulmonary Vascular Disease and NIH MSTP TG T32GM07205 (M. K.), the Siebel Scholars Foundation (S.-K.P.), the KAUST-Stanford Academic Excellence Alliance program (S.-K.P. and S. B.), the Swiss National Foundation, and the Janggen-Poehn Foundation (J.B.Z.). Data sets are available at the Gene Expression Omnibus (GEO) database with accession no. GSE50893. We thank S. Montgomery, W. Huber, C. Bustamante, H. Tang, S. Anders, G. Euskirchen, B. Altshuler, M. Eaton, and L. Ward. M. S. is a founder and member of the science advisory board for Personalis and a science advisory board member for Genapsys and AxioMx. S. B. is a founder and advisor for DNAnexus and serves on the advisory boards of 23andMe and Eve Biomedical. Genotype calls and BAM files with mapped sequencing reads for the San individuals are available through a data access agreement for transfer of genetic data by contacting M.S.
This publication acknowledges KAUST support, but has no KAUST affiliated authors.

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Kasowski, M., Kyriazopoulou-Panagiotopoulou, S., Grubert, F., Zaugg, J. B., Kundaje, A., Liu, Y., Boyle, A. P., Zhang, Q. C., Zakharia, F., Spacek, D. V., Li, J., Xie, D., Olarerin-George, A., Steinmetz, L. M., Hogenesch, J. B., Kellis, M., Batzoglou, S., & Snyder, M. (2013). Extensive Variation in Chromatin States Across Humans. Science, 342(6159), 750-752. https://doi.org/10.1126/science.1242510

@article{a325a999111f492cb3ac34d14dc5fba4,

title = "Extensive Variation in Chromatin States Across Humans",

abstract = "The majority of disease-associated variants lie outside protein-coding regions, suggesting a link between variation in regulatory regions and disease predisposition. We studied differences in chromatin states using five histone modifications, cohesin, and CTCF in lymphoblastoid lines from 19 individuals of diverse ancestry. We found extensive signal variation in regulatory regions, which often switch between active and repressed states across individuals. Enhancer activity is particularly diverse among individuals, whereas gene expression remains relatively stable. Chromatin variability shows genetic inheritance in trios, correlates with genetic variation and population divergence, and is associated with disruptions of transcription factor binding motifs. Overall, our results provide insights into chromatin variation among humans.",

author = "M. Kasowski and S. Kyriazopoulou-Panagiotopoulou and F. Grubert and Zaugg, {J. B.} and A. Kundaje and Y. Liu and Boyle, {A. P.} and Zhang, {Q. C.} and F. Zakharia and Spacek, {D. V.} and J. Li and D. Xie and A. Olarerin-George and Steinmetz, {L. M.} and Hogenesch, {J. B.} and M. Kellis and S. Batzoglou and M. Snyder",

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: Funded by grants from the NIH and Genetics Department, Stanford University, Vera Moulton Wall Center for Pulmonary Vascular Disease and NIH MSTP TG T32GM07205 (M. K.), the Siebel Scholars Foundation (S.-K.P.), the KAUST-Stanford Academic Excellence Alliance program (S.-K.P. and S. B.), the Swiss National Foundation, and the Janggen-Poehn Foundation (J.B.Z.). Data sets are available at the Gene Expression Omnibus (GEO) database with accession no. GSE50893. We thank S. Montgomery, W. Huber, C. Bustamante, H. Tang, S. Anders, G. Euskirchen, B. Altshuler, M. Eaton, and L. Ward. M. S. is a founder and member of the science advisory board for Personalis and a science advisory board member for Genapsys and AxioMx. S. B. is a founder and advisor for DNAnexus and serves on the advisory boards of 23andMe and Eve Biomedical. Genotype calls and BAM files with mapped sequencing reads for the San individuals are available through a data access agreement for transfer of genetic data by contacting M.S. This publication acknowledges KAUST support, but has no KAUST affiliated authors.",

year = "2013",

month = oct,

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doi = "10.1126/science.1242510",

language = "English (US)",

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Kasowski, M, Kyriazopoulou-Panagiotopoulou, S, Grubert, F, Zaugg, JB, Kundaje, A, Liu, Y, Boyle, AP, Zhang, QC, Zakharia, F, Spacek, DV, Li, J, Xie, D, Olarerin-George, A, Steinmetz, LM, Hogenesch, JB, Kellis, M, Batzoglou, S & Snyder, M 2013, 'Extensive Variation in Chromatin States Across Humans', Science, vol. 342, no. 6159, pp. 750-752. https://doi.org/10.1126/science.1242510

TY - JOUR

T1 - Extensive Variation in Chromatin States Across Humans

AU - Kasowski, M.

AU - Kyriazopoulou-Panagiotopoulou, S.

AU - Grubert, F.

AU - Zaugg, J. B.

AU - Kundaje, A.

AU - Liu, Y.

AU - Boyle, A. P.

AU - Zhang, Q. C.

AU - Zakharia, F.

AU - Spacek, D. V.

AU - Li, J.

AU - Xie, D.

AU - Olarerin-George, A.

AU - Steinmetz, L. M.

AU - Hogenesch, J. B.

AU - Kellis, M.

AU - Batzoglou, S.

AU - Snyder, M.

N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: Funded by grants from the NIH and Genetics Department, Stanford University, Vera Moulton Wall Center for Pulmonary Vascular Disease and NIH MSTP TG T32GM07205 (M. K.), the Siebel Scholars Foundation (S.-K.P.), the KAUST-Stanford Academic Excellence Alliance program (S.-K.P. and S. B.), the Swiss National Foundation, and the Janggen-Poehn Foundation (J.B.Z.). Data sets are available at the Gene Expression Omnibus (GEO) database with accession no. GSE50893. We thank S. Montgomery, W. Huber, C. Bustamante, H. Tang, S. Anders, G. Euskirchen, B. Altshuler, M. Eaton, and L. Ward. M. S. is a founder and member of the science advisory board for Personalis and a science advisory board member for Genapsys and AxioMx. S. B. is a founder and advisor for DNAnexus and serves on the advisory boards of 23andMe and Eve Biomedical. Genotype calls and BAM files with mapped sequencing reads for the San individuals are available through a data access agreement for transfer of genetic data by contacting M.S. This publication acknowledges KAUST support, but has no KAUST affiliated authors.

PY - 2013/10/17

Y1 - 2013/10/17

N2 - The majority of disease-associated variants lie outside protein-coding regions, suggesting a link between variation in regulatory regions and disease predisposition. We studied differences in chromatin states using five histone modifications, cohesin, and CTCF in lymphoblastoid lines from 19 individuals of diverse ancestry. We found extensive signal variation in regulatory regions, which often switch between active and repressed states across individuals. Enhancer activity is particularly diverse among individuals, whereas gene expression remains relatively stable. Chromatin variability shows genetic inheritance in trios, correlates with genetic variation and population divergence, and is associated with disruptions of transcription factor binding motifs. Overall, our results provide insights into chromatin variation among humans.

AB - The majority of disease-associated variants lie outside protein-coding regions, suggesting a link between variation in regulatory regions and disease predisposition. We studied differences in chromatin states using five histone modifications, cohesin, and CTCF in lymphoblastoid lines from 19 individuals of diverse ancestry. We found extensive signal variation in regulatory regions, which often switch between active and repressed states across individuals. Enhancer activity is particularly diverse among individuals, whereas gene expression remains relatively stable. Chromatin variability shows genetic inheritance in trios, correlates with genetic variation and population divergence, and is associated with disruptions of transcription factor binding motifs. Overall, our results provide insights into chromatin variation among humans.

UR - http://hdl.handle.net/10754/598296

UR - https://www.sciencemag.org/lookup/doi/10.1126/science.1242510

UR - http://www.scopus.com/inward/record.url?scp=84887320760&partnerID=8YFLogxK

U2 - 10.1126/science.1242510

DO - 10.1126/science.1242510

M3 - Article

C2 - 24136358

SN - 0036-8075

VL - 342

SP - 750

EP - 752

JO - Science

JF - Science

IS - 6159

ER -

Extensive Variation in Chromatin States Across Humans

Abstract

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