Format

Send to

Choose Destination
Nat Genet. 2018 Aug;50(8):1180-1188. doi: 10.1038/s41588-018-0159-z. Epub 2018 Jul 16.

High-throughput identification of noncoding functional SNPs via type IIS enzyme restriction.

Author information

1
Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. lig@pitt.edu.
2
Division of Cardiology and The Aging Institute, University of Pittsburgh, Pittsburgh, PA, USA. lig@pitt.edu.
3
Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
4
Department of Periodontology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
5
Division of Cardiology and The Aging Institute, University of Pittsburgh, Pittsburgh, PA, USA.
6
Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
7
Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan.
8
Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan.
9
Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
10
Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
11
School of Biological Sciences, University of Manchester, Manchester, UK.
12
Biochemistry, Molecular Biology and Biophysics Department, University of Minnesota Medical School, Minneapolis, MN, USA.
13
Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. pnigrovic@bwh.harvard.edu.
14
Division of Immunology, Boston Children's Hospital, Boston, MA, USA. pnigrovic@bwh.harvard.edu.

Abstract

Genome-wide association studies (GWAS) have identified many disease-associated noncoding variants, but cannot distinguish functional single-nucleotide polymorphisms (fSNPs) from others that reside incidentally within risk loci. To address this challenge, we developed an unbiased high-throughput screen that employs type IIS enzymatic restriction to identify fSNPs that allelically modulate the binding of regulatory proteins. We coupled this approach, termed SNP-seq, with flanking restriction enhanced pulldown (FREP) to identify regulation of CD40 by three disease-associated fSNPs via four regulatory proteins, RBPJ, RSRC2 and FUBP-1/TRAP150. Applying this approach across 27 loci associated with juvenile idiopathic arthritis, we identified 148 candidate fSNPs, including two that regulate STAT4 via the regulatory proteins SATB2 and H1.2. Together, these findings establish the utility of tandem SNP-seq/FREP to bridge the gap between GWAS and disease mechanism.

PMID:
30013183
PMCID:
PMC6072570
DOI:
10.1038/s41588-018-0159-z
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Nature Publishing Group Icon for PubMed Central
Loading ...
Support Center