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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...

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Autores principales: Kalita, Cynthia A., Brown, Christopher D., Freiman, Andrew, Isherwood, Jenna, Wen, Xiaoquan, Pique-Regi, Roger, Luca, Francesca
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2018
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.
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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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