Genetic architecture of protein expression and its regulation in the mouse brain

Abstract Background Natural variation in protein expression is common in all organisms and contributes to phenotypic differences among individuals. While variation in gene expression at the transcript level has been extensively investigated, the genetic mechanisms underlying variation in protein exp...

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Autores principales:	Alyssa Erickson, Suiping Zhou, Jie Luo, Ling Li, Xin Huang, Zachary Even, He Huang, Hai-Ming Xu, Junmin Peng, Lu Lu, Xusheng Wang
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Proteome Mouse Brain Protein expression Allele-specific expression Protein regulation Biotechnology TP248.13-248.65 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/60239a5d9557496f9d1f68c754dfb8a5
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spelling	oai:doaj.org-article:60239a5d9557496f9d1f68c754dfb8a52021-12-05T12:17:17ZGenetic architecture of protein expression and its regulation in the mouse brain10.1186/s12864-021-08168-y1471-2164https://doaj.org/article/60239a5d9557496f9d1f68c754dfb8a52021-12-01T00:00:00Zhttps://doi.org/10.1186/s12864-021-08168-yhttps://doaj.org/toc/1471-2164Abstract Background Natural variation in protein expression is common in all organisms and contributes to phenotypic differences among individuals. While variation in gene expression at the transcript level has been extensively investigated, the genetic mechanisms underlying variation in protein expression have lagged considerably behind. Here we investigate genetic architecture of protein expression by profiling a deep mouse brain proteome of two inbred strains, C57BL/6 J (B6) and DBA/2 J (D2), and their reciprocal F1 hybrids using two-dimensional liquid chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) technology. Results By comparing protein expression levels in the four mouse strains, we observed 329 statistically significant differentially expressed proteins between the two parental strains and characterized the genetic basis of protein expression. We further applied a proteogenomic approach to detect variant peptides and define protein allele-specific expression (pASE), identifying 33 variant peptides with cis-effects and 17 variant peptides showing trans-effects. Comparison of regulation at transcript and protein levels show a significant divergence. Conclusions The results provide a comprehensive analysis of genetic architecture of protein expression and the contribution of cis- and trans-acting regulatory differences to protein expression.Alyssa EricksonSuiping ZhouJie LuoLing LiXin HuangZachary EvenHe HuangHai-Ming XuJunmin PengLu LuXusheng WangBMCarticleProteomeMouseBrainProtein expressionAllele-specific expressionProtein regulationBiotechnologyTP248.13-248.65GeneticsQH426-470ENBMC Genomics, Vol 22, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Proteome Mouse Brain Protein expression Allele-specific expression Protein regulation Biotechnology TP248.13-248.65 Genetics QH426-470
spellingShingle	Proteome Mouse Brain Protein expression Allele-specific expression Protein regulation Biotechnology TP248.13-248.65 Genetics QH426-470 Alyssa Erickson Suiping Zhou Jie Luo Ling Li Xin Huang Zachary Even He Huang Hai-Ming Xu Junmin Peng Lu Lu Xusheng Wang Genetic architecture of protein expression and its regulation in the mouse brain
description	Abstract Background Natural variation in protein expression is common in all organisms and contributes to phenotypic differences among individuals. While variation in gene expression at the transcript level has been extensively investigated, the genetic mechanisms underlying variation in protein expression have lagged considerably behind. Here we investigate genetic architecture of protein expression by profiling a deep mouse brain proteome of two inbred strains, C57BL/6 J (B6) and DBA/2 J (D2), and their reciprocal F1 hybrids using two-dimensional liquid chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) technology. Results By comparing protein expression levels in the four mouse strains, we observed 329 statistically significant differentially expressed proteins between the two parental strains and characterized the genetic basis of protein expression. We further applied a proteogenomic approach to detect variant peptides and define protein allele-specific expression (pASE), identifying 33 variant peptides with cis-effects and 17 variant peptides showing trans-effects. Comparison of regulation at transcript and protein levels show a significant divergence. Conclusions The results provide a comprehensive analysis of genetic architecture of protein expression and the contribution of cis- and trans-acting regulatory differences to protein expression.
format	article
author	Alyssa Erickson Suiping Zhou Jie Luo Ling Li Xin Huang Zachary Even He Huang Hai-Ming Xu Junmin Peng Lu Lu Xusheng Wang
author_facet	Alyssa Erickson Suiping Zhou Jie Luo Ling Li Xin Huang Zachary Even He Huang Hai-Ming Xu Junmin Peng Lu Lu Xusheng Wang
author_sort	Alyssa Erickson
title	Genetic architecture of protein expression and its regulation in the mouse brain
title_short	Genetic architecture of protein expression and its regulation in the mouse brain
title_full	Genetic architecture of protein expression and its regulation in the mouse brain
title_fullStr	Genetic architecture of protein expression and its regulation in the mouse brain
title_full_unstemmed	Genetic architecture of protein expression and its regulation in the mouse brain
title_sort	genetic architecture of protein expression and its regulation in the mouse brain
publisher	BMC
publishDate	2021
url	https://doaj.org/article/60239a5d9557496f9d1f68c754dfb8a5
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Genetic architecture of protein expression and its regulation in the mouse brain

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