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Genome-Wide Detection of Key Genes and Epigenetic Markers for Chicken Fatty Liver
Chickens are one of the most important sources of meat worldwide, and the occurrence of fatty liver syndrome (FLS) is closely related to production efficiency. However, the potential mechanism of FLS remains poorly understood. An integrated analysis of data from whole-genome bisulfite sequencing and...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7084419/ https://www.ncbi.nlm.nih.gov/pubmed/32151087 http://dx.doi.org/10.3390/ijms21051800 |
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author | Tan, Xiaodong Liu, Ranran Xing, Siyuan Zhang, Yonghong Li, Qinghe Zheng, Maiqing Zhao, Guiping Wen, Jie |
author_facet | Tan, Xiaodong Liu, Ranran Xing, Siyuan Zhang, Yonghong Li, Qinghe Zheng, Maiqing Zhao, Guiping Wen, Jie |
author_sort | Tan, Xiaodong |
collection | PubMed |
description | Chickens are one of the most important sources of meat worldwide, and the occurrence of fatty liver syndrome (FLS) is closely related to production efficiency. However, the potential mechanism of FLS remains poorly understood. An integrated analysis of data from whole-genome bisulfite sequencing and long noncoding RNA (lncRNA) sequencing was conducted. A total of 1177 differentially expressed genes (DEGs) and 1442 differentially methylated genes (DMGs) were found. There were 72% of 83 lipid- and glucose-related genes upregulated; 81% of 150 immune-related genes were downregulated in fatty livers. Part of those genes was within differentially methylated regions (DMRs). Besides, sixty-seven lncRNAs were identified differentially expressed and divided into 13 clusters based on their expression pattern. Some lipid- and glucose-related lncRNAs (e.g., LNC_006756, LNC_012355, and LNC_005024) and immune-related lncRNAs (e.g., LNC_010111, LNC_010862, and LNC_001272) were found through a co-expression network and functional annotation. From the expression and epigenetic profiles, 23 target genes (e.g., HAO1, ABCD3, and BLMH) were found to be hub genes that were regulated by both methylation and lncRNAs. We have provided comprehensive epigenetic and transcriptomic profiles on FLS in chicken, and the identification of key genes and epigenetic markers will expand our understanding of the molecular mechanism of chicken FLS. |
format | Online Article Text |
id | pubmed-7084419 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-70844192020-03-24 Genome-Wide Detection of Key Genes and Epigenetic Markers for Chicken Fatty Liver Tan, Xiaodong Liu, Ranran Xing, Siyuan Zhang, Yonghong Li, Qinghe Zheng, Maiqing Zhao, Guiping Wen, Jie Int J Mol Sci Article Chickens are one of the most important sources of meat worldwide, and the occurrence of fatty liver syndrome (FLS) is closely related to production efficiency. However, the potential mechanism of FLS remains poorly understood. An integrated analysis of data from whole-genome bisulfite sequencing and long noncoding RNA (lncRNA) sequencing was conducted. A total of 1177 differentially expressed genes (DEGs) and 1442 differentially methylated genes (DMGs) were found. There were 72% of 83 lipid- and glucose-related genes upregulated; 81% of 150 immune-related genes were downregulated in fatty livers. Part of those genes was within differentially methylated regions (DMRs). Besides, sixty-seven lncRNAs were identified differentially expressed and divided into 13 clusters based on their expression pattern. Some lipid- and glucose-related lncRNAs (e.g., LNC_006756, LNC_012355, and LNC_005024) and immune-related lncRNAs (e.g., LNC_010111, LNC_010862, and LNC_001272) were found through a co-expression network and functional annotation. From the expression and epigenetic profiles, 23 target genes (e.g., HAO1, ABCD3, and BLMH) were found to be hub genes that were regulated by both methylation and lncRNAs. We have provided comprehensive epigenetic and transcriptomic profiles on FLS in chicken, and the identification of key genes and epigenetic markers will expand our understanding of the molecular mechanism of chicken FLS. MDPI 2020-03-05 /pmc/articles/PMC7084419/ /pubmed/32151087 http://dx.doi.org/10.3390/ijms21051800 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Tan, Xiaodong Liu, Ranran Xing, Siyuan Zhang, Yonghong Li, Qinghe Zheng, Maiqing Zhao, Guiping Wen, Jie Genome-Wide Detection of Key Genes and Epigenetic Markers for Chicken Fatty Liver |
title | Genome-Wide Detection of Key Genes and Epigenetic Markers for Chicken Fatty Liver |
title_full | Genome-Wide Detection of Key Genes and Epigenetic Markers for Chicken Fatty Liver |
title_fullStr | Genome-Wide Detection of Key Genes and Epigenetic Markers for Chicken Fatty Liver |
title_full_unstemmed | Genome-Wide Detection of Key Genes and Epigenetic Markers for Chicken Fatty Liver |
title_short | Genome-Wide Detection of Key Genes and Epigenetic Markers for Chicken Fatty Liver |
title_sort | genome-wide detection of key genes and epigenetic markers for chicken fatty liver |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7084419/ https://www.ncbi.nlm.nih.gov/pubmed/32151087 http://dx.doi.org/10.3390/ijms21051800 |
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