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High-throughput characterization of genetic effects on DNA–protein binding and gene transcription
Many variants associated with complex traits are in noncoding regions and contribute to phenotypes by disrupting regulatory sequences. To characterize these variants, we developed a streamlined protocol for a high-throughput reporter assay, Biallelic Targeted STARR-seq (BiT-STARR-seq), that identifi...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory Press
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211638/ https://www.ncbi.nlm.nih.gov/pubmed/30254052 http://dx.doi.org/10.1101/gr.237354.118 |
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author | Kalita, Cynthia A. Brown, Christopher D. Freiman, Andrew Isherwood, Jenna Wen, Xiaoquan Pique-Regi, Roger Luca, Francesca |
author_facet | Kalita, Cynthia A. Brown, Christopher D. Freiman, Andrew Isherwood, Jenna Wen, Xiaoquan Pique-Regi, Roger Luca, Francesca |
author_sort | Kalita, Cynthia A. |
collection | PubMed |
description | Many variants associated with complex traits are in noncoding regions and contribute to phenotypes by disrupting regulatory sequences. To characterize these variants, we developed a streamlined protocol for a high-throughput reporter assay, Biallelic Targeted STARR-seq (BiT-STARR-seq), that identifies allele-specific expression (ASE) while accounting for PCR duplicates through unique molecular identifiers. We tested 75,501 oligos (43,500 SNPs) and identified 2720 SNPs with significant ASE (FDR < 10%). To validate disruption of binding as one of the mechanisms underlying ASE, we developed a new high-throughput allele-specific binding assay for NFKB1. We identified 2684 SNPs with allele-specific binding (ASB) (FDR < 10%); 256 of these SNPs also had ASE (OR = 1.97, P-value = 0.0006). Of variants associated with complex traits, 1531 resulted in ASE, and 1662 showed ASB. For example, we characterized that the Crohn's disease risk variant for rs3810936 increases NFKB1 binding and results in altered gene expression. |
format | Online Article Text |
id | pubmed-6211638 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-62116382018-11-13 High-throughput characterization of genetic effects on DNA–protein binding and gene transcription Kalita, Cynthia A. Brown, Christopher D. Freiman, Andrew Isherwood, Jenna Wen, Xiaoquan Pique-Regi, Roger Luca, Francesca Genome Res Method Many variants associated with complex traits are in noncoding regions and contribute to phenotypes by disrupting regulatory sequences. To characterize these variants, we developed a streamlined protocol for a high-throughput reporter assay, Biallelic Targeted STARR-seq (BiT-STARR-seq), that identifies allele-specific expression (ASE) while accounting for PCR duplicates through unique molecular identifiers. We tested 75,501 oligos (43,500 SNPs) and identified 2720 SNPs with significant ASE (FDR < 10%). To validate disruption of binding as one of the mechanisms underlying ASE, we developed a new high-throughput allele-specific binding assay for NFKB1. We identified 2684 SNPs with allele-specific binding (ASB) (FDR < 10%); 256 of these SNPs also had ASE (OR = 1.97, P-value = 0.0006). Of variants associated with complex traits, 1531 resulted in ASE, and 1662 showed ASB. For example, we characterized that the Crohn's disease risk variant for rs3810936 increases NFKB1 binding and results in altered gene expression. Cold Spring Harbor Laboratory Press 2018-11 /pmc/articles/PMC6211638/ /pubmed/30254052 http://dx.doi.org/10.1101/gr.237354.118 Text en © 2018 Kalita et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by/4.0/ This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Method Kalita, Cynthia A. Brown, Christopher D. Freiman, Andrew Isherwood, Jenna Wen, Xiaoquan Pique-Regi, Roger Luca, Francesca High-throughput characterization of genetic effects on DNA–protein binding and gene transcription |
title | High-throughput characterization of genetic effects on DNA–protein binding and gene transcription |
title_full | High-throughput characterization of genetic effects on DNA–protein binding and gene transcription |
title_fullStr | High-throughput characterization of genetic effects on DNA–protein binding and gene transcription |
title_full_unstemmed | High-throughput characterization of genetic effects on DNA–protein binding and gene transcription |
title_short | High-throughput characterization of genetic effects on DNA–protein binding and gene transcription |
title_sort | high-throughput characterization of genetic effects on dna–protein binding and gene transcription |
topic | Method |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211638/ https://www.ncbi.nlm.nih.gov/pubmed/30254052 http://dx.doi.org/10.1101/gr.237354.118 |
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