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Analysis of allele-specific expression of seven candidate genes involved in lipid metabolism in pig skeletal muscle and fat tissues reveals allelic imbalance of ACACA, LEP, SCD, and TNF
Analysis of allele-specific expression may help to elucidate the genetic architecture of complex traits including fat deposition in pigs. Here, we used pyrosequencing to investigate the allele proportions of candidate genes (ACACA, ADIPOR1, FASN, LEP, ME1, SCD, and TNF) involved in regulation of lip...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer Berlin Heidelberg
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6373405/ https://www.ncbi.nlm.nih.gov/pubmed/30684136 http://dx.doi.org/10.1007/s13353-019-00485-z |
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author | Stachowiak, Monika Flisikowski, Krzysztof |
author_facet | Stachowiak, Monika Flisikowski, Krzysztof |
author_sort | Stachowiak, Monika |
collection | PubMed |
description | Analysis of allele-specific expression may help to elucidate the genetic architecture of complex traits including fat deposition in pigs. Here, we used pyrosequencing to investigate the allele proportions of candidate genes (ACACA, ADIPOR1, FASN, LEP, ME1, SCD, and TNF) involved in regulation of lipid metabolism in two fat deposits (subcutaneous and visceral fat) and longissimus dorsi muscle of pigs representing Polish Large White, Polish Landrace, Duroc, and Pietrain breeds. We detected differential allelic expression of ACACA, LEP, SCD, and TNF in all tissues analyzed. To search for putative cis-regulatory elements involved in allele-specific expression, we quantified the methylation level within CpG islands located in 5′-flanking regions of ACACA and SCD. Comparison between samples showing markedly disproportionate allelic expression and control groups with similar levels of both alleles did not reveal significant differences. We also assessed the association of rs321308225 (c.*195C>A) an SNP located in the 3′UTR of ACACA with its allelic expression in Polish Landrace pigs, but it was not significant. We conclude that allelic imbalance occurs frequently in regard to genes involved in regulation of lipid deposition in pigs, and further studies are necessary to identify cis-regulatory elements affecting ACACA, LEP, SCD, and TNF expression in porcine fat tissues and skeletal muscle. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13353-019-00485-z) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6373405 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Springer Berlin Heidelberg |
record_format | MEDLINE/PubMed |
spelling | pubmed-63734052019-03-01 Analysis of allele-specific expression of seven candidate genes involved in lipid metabolism in pig skeletal muscle and fat tissues reveals allelic imbalance of ACACA, LEP, SCD, and TNF Stachowiak, Monika Flisikowski, Krzysztof J Appl Genet Animal Genetics • Short Communication Analysis of allele-specific expression may help to elucidate the genetic architecture of complex traits including fat deposition in pigs. Here, we used pyrosequencing to investigate the allele proportions of candidate genes (ACACA, ADIPOR1, FASN, LEP, ME1, SCD, and TNF) involved in regulation of lipid metabolism in two fat deposits (subcutaneous and visceral fat) and longissimus dorsi muscle of pigs representing Polish Large White, Polish Landrace, Duroc, and Pietrain breeds. We detected differential allelic expression of ACACA, LEP, SCD, and TNF in all tissues analyzed. To search for putative cis-regulatory elements involved in allele-specific expression, we quantified the methylation level within CpG islands located in 5′-flanking regions of ACACA and SCD. Comparison between samples showing markedly disproportionate allelic expression and control groups with similar levels of both alleles did not reveal significant differences. We also assessed the association of rs321308225 (c.*195C>A) an SNP located in the 3′UTR of ACACA with its allelic expression in Polish Landrace pigs, but it was not significant. We conclude that allelic imbalance occurs frequently in regard to genes involved in regulation of lipid deposition in pigs, and further studies are necessary to identify cis-regulatory elements affecting ACACA, LEP, SCD, and TNF expression in porcine fat tissues and skeletal muscle. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13353-019-00485-z) contains supplementary material, which is available to authorized users. Springer Berlin Heidelberg 2019-01-26 2019 /pmc/articles/PMC6373405/ /pubmed/30684136 http://dx.doi.org/10.1007/s13353-019-00485-z Text en © The Author(s) 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. |
spellingShingle | Animal Genetics • Short Communication Stachowiak, Monika Flisikowski, Krzysztof Analysis of allele-specific expression of seven candidate genes involved in lipid metabolism in pig skeletal muscle and fat tissues reveals allelic imbalance of ACACA, LEP, SCD, and TNF |
title | Analysis of allele-specific expression of seven candidate genes involved in lipid metabolism in pig skeletal muscle and fat tissues reveals allelic imbalance of ACACA, LEP, SCD, and TNF |
title_full | Analysis of allele-specific expression of seven candidate genes involved in lipid metabolism in pig skeletal muscle and fat tissues reveals allelic imbalance of ACACA, LEP, SCD, and TNF |
title_fullStr | Analysis of allele-specific expression of seven candidate genes involved in lipid metabolism in pig skeletal muscle and fat tissues reveals allelic imbalance of ACACA, LEP, SCD, and TNF |
title_full_unstemmed | Analysis of allele-specific expression of seven candidate genes involved in lipid metabolism in pig skeletal muscle and fat tissues reveals allelic imbalance of ACACA, LEP, SCD, and TNF |
title_short | Analysis of allele-specific expression of seven candidate genes involved in lipid metabolism in pig skeletal muscle and fat tissues reveals allelic imbalance of ACACA, LEP, SCD, and TNF |
title_sort | analysis of allele-specific expression of seven candidate genes involved in lipid metabolism in pig skeletal muscle and fat tissues reveals allelic imbalance of acaca, lep, scd, and tnf |
topic | Animal Genetics • Short Communication |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6373405/ https://www.ncbi.nlm.nih.gov/pubmed/30684136 http://dx.doi.org/10.1007/s13353-019-00485-z |
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