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Systematic identification of human SNPs affecting regulatory element activity

Joris van Arensbergen, Ludo Pagie, Vincent FitzPatrick, Marcel de Haas, Marijke Baltissen, Federico Comoglio, Robin van der Weide, Hans Teunissen, Urmo Võsa, Lude Franke, Elzo de Wit, Michiel Vermeulen, Harmen Bussemaker, Bas van Steensel
doi: https://doi.org/10.1101/460402
Joris van Arensbergen
1Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
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  • For correspondence: joris.van.arensbergen@gmail.com b.v.steensel@nki.nl
Ludo Pagie
1Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
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Vincent FitzPatrick
2Department of Biological Sciences, Columbia University, New York, New York, USA
3Department of Systems Biology, Columbia University Medical Center, New York, New York, USA
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Marcel de Haas
1Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
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Marijke Baltissen
4Department of Molecular Biology and Oncode Institute, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 Nijmegen, The Netherlands
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Federico Comoglio
1Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
5Department of Haematology, University of Cambridge, Cambridge, UK
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Robin van der Weide
1Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
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Hans Teunissen
1Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
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Urmo Võsa
6Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
7Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
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Lude Franke
6Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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Elzo de Wit
1Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
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Michiel Vermeulen
4Department of Molecular Biology and Oncode Institute, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 Nijmegen, The Netherlands
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Harmen Bussemaker
2Department of Biological Sciences, Columbia University, New York, New York, USA
3Department of Systems Biology, Columbia University Medical Center, New York, New York, USA
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Bas van Steensel
1Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
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  • For correspondence: joris.van.arensbergen@gmail.com b.v.steensel@nki.nl
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Abstract

Most of the millions of single-nucleotide polymorphisms (SNPs) in the human genome are non-coding, and many overlap with putative regulatory elements. Genome-wide association studies have linked many of these SNPs to human traits or to gene expression levels, but rarely with sufficient resolution to identify the causal SNPs. Functional screens based on reporter assays have previously been of insufficient throughput to test the vast space of SNPs for possible effects on enhancer and promoter activity. Here, we have leveraged the throughput of the SuRE reporter technology to survey a total of 5.9 million SNPs, including 57% of the known common SNPs. We identified more than 30 thousand SNPs that alter the activity of putative regulatory elements, often in a cell-type specific manner. These data indicate that a large proportion of human non-coding SNPs may affect gene regulation. Integration of these SuRE data with genome-wide association studies may help pinpoint SNPs that underlie human traits.

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Posted November 04, 2018.
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Systematic identification of human SNPs affecting regulatory element activity
Joris van Arensbergen, Ludo Pagie, Vincent FitzPatrick, Marcel de Haas, Marijke Baltissen, Federico Comoglio, Robin van der Weide, Hans Teunissen, Urmo Võsa, Lude Franke, Elzo de Wit, Michiel Vermeulen, Harmen Bussemaker, Bas van Steensel
bioRxiv 460402; doi: https://doi.org/10.1101/460402
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Systematic identification of human SNPs affecting regulatory element activity
Joris van Arensbergen, Ludo Pagie, Vincent FitzPatrick, Marcel de Haas, Marijke Baltissen, Federico Comoglio, Robin van der Weide, Hans Teunissen, Urmo Võsa, Lude Franke, Elzo de Wit, Michiel Vermeulen, Harmen Bussemaker, Bas van Steensel
bioRxiv 460402; doi: https://doi.org/10.1101/460402

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