Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT

Abstract Differential abundance of allelic transcripts in a diploid organism, commonly referred to as allele specific expression (ASE), is a biologically significant phenomenon and can be examined using single nucleotide polymorphisms (SNPs) from RNA-seq. Quantifying ASE aids in our ability to ident...

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Autores principales:	M. Joseph Tomlinson, Shawn W. Polson, Jing Qiu, Juniper A. Lake, William Lee, Behnam Abasht
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/04d0322b49414b9b8419b0396d5bb228
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spelling	oai:doaj.org-article:04d0322b49414b9b8419b0396d5bb2282021-12-02T14:03:46ZInvestigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT10.1038/s41598-021-83459-82045-2322https://doaj.org/article/04d0322b49414b9b8419b0396d5bb2282021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-83459-8https://doaj.org/toc/2045-2322Abstract Differential abundance of allelic transcripts in a diploid organism, commonly referred to as allele specific expression (ASE), is a biologically significant phenomenon and can be examined using single nucleotide polymorphisms (SNPs) from RNA-seq. Quantifying ASE aids in our ability to identify and understand cis-regulatory mechanisms that influence gene expression, and thereby assist in identifying causal mutations. This study examines ASE in breast muscle, abdominal fat, and liver of commercial broiler chickens using variants called from a large sub-set of the samples (n = 68). ASE analysis was performed using a custom software called VCF ASE Detection Tool (VADT), which detects ASE of biallelic SNPs using a binomial test. On average ~ 174,000 SNPs in each tissue passed our filtering criteria and were considered informative, of which ~ 24,000 (~ 14%) showed ASE. Of all ASE SNPs, only 3.7% exhibited ASE in all three tissues, with ~ 83% showing ASE specific to a single tissue. When ASE genes (genes containing ASE SNPs) were compared between tissues, the overlap among all three tissues increased to 20.1%. Our results indicate that ASE genes show tissue-specific enrichment patterns, but all three tissues showed enrichment for pathways involved in translation.M. Joseph TomlinsonShawn W. PolsonJing QiuJuniper A. LakeWilliam LeeBehnam AbashtNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-13 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q M. Joseph Tomlinson Shawn W. Polson Jing Qiu Juniper A. Lake William Lee Behnam Abasht Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT
description	Abstract Differential abundance of allelic transcripts in a diploid organism, commonly referred to as allele specific expression (ASE), is a biologically significant phenomenon and can be examined using single nucleotide polymorphisms (SNPs) from RNA-seq. Quantifying ASE aids in our ability to identify and understand cis-regulatory mechanisms that influence gene expression, and thereby assist in identifying causal mutations. This study examines ASE in breast muscle, abdominal fat, and liver of commercial broiler chickens using variants called from a large sub-set of the samples (n = 68). ASE analysis was performed using a custom software called VCF ASE Detection Tool (VADT), which detects ASE of biallelic SNPs using a binomial test. On average ~ 174,000 SNPs in each tissue passed our filtering criteria and were considered informative, of which ~ 24,000 (~ 14%) showed ASE. Of all ASE SNPs, only 3.7% exhibited ASE in all three tissues, with ~ 83% showing ASE specific to a single tissue. When ASE genes (genes containing ASE SNPs) were compared between tissues, the overlap among all three tissues increased to 20.1%. Our results indicate that ASE genes show tissue-specific enrichment patterns, but all three tissues showed enrichment for pathways involved in translation.
format	article
author	M. Joseph Tomlinson Shawn W. Polson Jing Qiu Juniper A. Lake William Lee Behnam Abasht
author_facet	M. Joseph Tomlinson Shawn W. Polson Jing Qiu Juniper A. Lake William Lee Behnam Abasht
author_sort	M. Joseph Tomlinson
title	Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT
title_short	Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT
title_full	Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT
title_fullStr	Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT
title_full_unstemmed	Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT
title_sort	investigation of allele specific expression in various tissues of broiler chickens using the detection tool vadt
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/04d0322b49414b9b8419b0396d5bb228
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Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT

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