DNase I sensitivity QTLs are a major determinant of human expression variation (original) (raw)

• Letter
• Published: 05 February 2012
• Athma A. Pai1 na1,
• Roger Pique-Regi1 na1,
• Jean-Baptiste Veyrieras1,3,
• Daniel J. Gaffney1,4,
• Joseph K. Pickrell1,
• Sherryl De Leon4,
• Katelyn Michelini4,
• Noah Lewellen4,
• Gregory E. Crawford5,6,
• Matthew Stephens1,7,
• Yoav Gilad1 &
• …
• Jonathan K. Pritchard1,4

Nature volume 482, pages 390–394 (2012)Cite this article

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Abstract

The mapping of expression quantitative trait loci (eQTLs) has emerged as an important tool for linking genetic variation to changes in gene regulation1,2,3,4,5. However, it remains difficult to identify the causal variants underlying eQTLs, and little is known about the regulatory mechanisms by which they act. Here we show that genetic variants that modify chromatin accessibility and transcription factor binding are a major mechanism through which genetic variation leads to gene expression differences among humans. We used DNase I sequencing to measure chromatin accessibility in 70 Yoruba lymphoblastoid cell lines, for which genome-wide genotypes and estimates of gene expression levels are also available6,7,8. We obtained a total of 2.7 billion uniquely mapped DNase I-sequencing (DNase-seq) reads, which allowed us to produce genome-wide maps of chromatin accessibility for each individual. We identified 8,902 locations at which the DNase-seq read depth correlated significantly with genotype at a nearby single nucleotide polymorphism or insertion/deletion (false discovery rate = 10%). We call such variants ‘DNase I sensitivity quantitative trait loci’ (dsQTLs). We found that dsQTLs are strongly enriched within inferred transcription factor binding sites and are frequently associated with allele-specific changes in transcription factor binding. A substantial fraction (16%) of dsQTLs are also associated with variation in the expression levels of nearby genes (that is, these loci are also classified as eQTLs). Conversely, we estimate that as many as 55% of eQTL single nucleotide polymorphisms are also dsQTLs. Our observations indicate that dsQTLs are highly abundant in the human genome and are likely to be important contributors to phenotypic variation.

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Primary accessions

Gene Expression Omnibus

Data deposits

All raw data and tables of all dsQTLs are deposited in GEO under accession number GSE31388 and at http://eqtl.uchicago.edu.

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Acknowledgements

We thank members of the Pritchard, Przeworski, Stephens and Gilad laboratories for many helpful comments or discussions, and the ENCODE Project for publicly available ChIP-seq data. This work was supported by grants from the National Institutes of Health to Y.G. (HG006123) and J.K.P. (MH084703 and MH090951), by the Howard Hughes Medical Institute, by the Chicago Fellows Program (to R.P.R.), by the American Heart Association (to A.A.P.), and by the NIH Genetics and Regulation Training grant (A.A.P. and J.F.D.).

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Author notes

1. Jacob F. Degner, Athma A. Pai and Roger Pique-Regi: These authors contributed equally to this work.

Authors and Affiliations

1. Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA,
   Jacob F. Degner, Athma A. Pai, Roger Pique-Regi, Jean-Baptiste Veyrieras, Daniel J. Gaffney, Joseph K. Pickrell, Matthew Stephens, Yoav Gilad & Jonathan K. Pritchard
2. Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, Illinois 60637, USA,
   Jacob F. Degner
3. BioMiningLabs, 69001 Lyon, France,
   Jean-Baptiste Veyrieras
4. Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois 60637, USA,
   Daniel J. Gaffney, Sherryl De Leon, Katelyn Michelini, Noah Lewellen & Jonathan K. Pritchard
5. Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27708, USA,
   Gregory E. Crawford
6. Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina 27708, USA,
   Gregory E. Crawford
7. Department of Statistics, University of Chicago, Chicago, Illinois 60637, USA,
   Matthew Stephens

Authors

1. Jacob F. Degner
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2. Athma A. Pai
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3. Roger Pique-Regi
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4. Jean-Baptiste Veyrieras
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5. Daniel J. Gaffney
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6. Joseph K. Pickrell
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7. Sherryl De Leon
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8. Katelyn Michelini
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9. Noah Lewellen
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10. Gregory E. Crawford
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11. Matthew Stephens
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12. Yoav Gilad
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13. Jonathan K. Pritchard
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Contributions

A.A.P. led the data collection with assistance from S.D.L., K.M. and N.L. The data analysis was performed jointly by J.F.D. and R.P.R., with contributions from A.A.P., J.B.V., D.J.G. and J.K.Pi. G.E.C. and M.S. provided technical assistance and discussion of methods and results. The manuscript was written by J.F.D., A.A.P., R.P.R., Y.G. and J.K.Pr. The project was jointly supervised by Y.G. and J.K.Pr.

Corresponding authors

Correspondence toYoav Gilad or Jonathan K. Pritchard.

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The authors declare no competing financial interests.

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This file contains Supplementary Text and Data, Supplementary Figures 1-28 with legends, Supplementary Tables 1-9 and additional references. (PDF 3101 kb)

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Degner, J., Pai, A., Pique-Regi, R. et al. DNase I sensitivity QTLs are a major determinant of human expression variation.Nature 482, 390–394 (2012). https://doi.org/10.1038/nature10808

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• Received: 23 June 2011
• Accepted: 15 December 2011
• Published: 05 February 2012
• Issue Date: 16 February 2012
• DOI: https://doi.org/10.1038/nature10808

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Editorial Summary

Mapping genetic variation

Expression quantitative trait loci (eQTLs) are stretches of DNA that regulate gene transcription and expression and contribute to a particular phenotypic trait. eQTL mapping is an important tool for linking genetic variation to changes in gene regulation, but identifying the causal variants underlying eQTLs and the regulatory mechanisms involved remains a challenge. Degner et al. used DNaseI sequencing to measure genome-wide chromatin accessibility in 70 Yoruba lymphoblastoid cell lines to produce genome-wide maps of chromatin accessibility for each individual. They identify variants that they call DNaseI sensitivity quantitative trait loci (dsQTLs). The implication is that changes in chromatin accessibility or transcription-factor binding occur at many gene loci and are likely to be important contributors to phenotypic variation.