Cargando…
Whole-transcriptome RNA sequencing reveals the global molecular responses and circRNA/lncRNA-miRNA-mRNA ceRNA regulatory network in chicken fat deposition
Fat deposition is a vital factor affecting the economics of poultry production. Numerous studies on fat deposition have been done. However, the molecular regulatory mechanism is still unclear. In the present study, the whole-transcriptome RNA sequencing in abdominal fat, back skin, and liver both hi...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9485216/ https://www.ncbi.nlm.nih.gov/pubmed/36116349 http://dx.doi.org/10.1016/j.psj.2022.102121 |
_version_ | 1784792042112548864 |
---|---|
author | Xiao, Cong Sun, Tiantian Yang, Zhuliang Zou, Leqin Deng, Jixian Yang, Xiurong |
author_facet | Xiao, Cong Sun, Tiantian Yang, Zhuliang Zou, Leqin Deng, Jixian Yang, Xiurong |
author_sort | Xiao, Cong |
collection | PubMed |
description | Fat deposition is a vital factor affecting the economics of poultry production. Numerous studies on fat deposition have been done. However, the molecular regulatory mechanism is still unclear. In the present study, the whole-transcriptome RNA sequencing in abdominal fat, back skin, and liver both high- and low-abdominal fat groups was used to uncover the competitive endogenous RNA (ceRNA) regulation network related to chicken fat deposition. The results showed that differentially expressed (DE) genes in abdominal fat, back skin, liver were 1207(784 mRNAs, 330 lncRNAs, 41 circRNAs, 52 miRNAs), 860 (607 mRNAs, 166 lncRNAs, 26 circRNAs, 61 miRNAs), and 923 (501 mRNAs, 262 lncRNAs, 15 circRNAs, 145 miRNAs), respectively. The ceRNA regulatory network analysis indicated that the fatty acid metabolic process, monocarboxylic acid metabolic process, carboxylic acid metabolic process, glycerolipid metabolism, fatty acid metabolism, and peroxisome proliferator-activated receptor (PPAR) signaling pathway took part in chicken fat deposition. Meanwhile, we scan the important genes, FADS2, HSD17B12, ELOVL5, AKR1E2, DGKQ, GPAM, PLIN2, which were regulated by gga-miR-460b-5p, gga-miR-199-5p, gga-miR-7470-3p, gga-miR-6595-5p, gga-miR-101-2-5p. While these miRNAs were competitive combined by lncRNAs including MSTRG.18043, MSTRG.7738, MSTRG.21310, MSTRG.19577, and circRNAs including novel_circ_PTPN2, novel_circ_CTNNA1, novel_circ_PTPRD. This finding provides new insights into the regulatory mechanism of mRNA, miRNA, lncRNA, and circRNA in chicken fat deposition. |
format | Online Article Text |
id | pubmed-9485216 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-94852162022-09-21 Whole-transcriptome RNA sequencing reveals the global molecular responses and circRNA/lncRNA-miRNA-mRNA ceRNA regulatory network in chicken fat deposition Xiao, Cong Sun, Tiantian Yang, Zhuliang Zou, Leqin Deng, Jixian Yang, Xiurong Poult Sci GENETICS AND MOLECULAR BIOLOGY Fat deposition is a vital factor affecting the economics of poultry production. Numerous studies on fat deposition have been done. However, the molecular regulatory mechanism is still unclear. In the present study, the whole-transcriptome RNA sequencing in abdominal fat, back skin, and liver both high- and low-abdominal fat groups was used to uncover the competitive endogenous RNA (ceRNA) regulation network related to chicken fat deposition. The results showed that differentially expressed (DE) genes in abdominal fat, back skin, liver were 1207(784 mRNAs, 330 lncRNAs, 41 circRNAs, 52 miRNAs), 860 (607 mRNAs, 166 lncRNAs, 26 circRNAs, 61 miRNAs), and 923 (501 mRNAs, 262 lncRNAs, 15 circRNAs, 145 miRNAs), respectively. The ceRNA regulatory network analysis indicated that the fatty acid metabolic process, monocarboxylic acid metabolic process, carboxylic acid metabolic process, glycerolipid metabolism, fatty acid metabolism, and peroxisome proliferator-activated receptor (PPAR) signaling pathway took part in chicken fat deposition. Meanwhile, we scan the important genes, FADS2, HSD17B12, ELOVL5, AKR1E2, DGKQ, GPAM, PLIN2, which were regulated by gga-miR-460b-5p, gga-miR-199-5p, gga-miR-7470-3p, gga-miR-6595-5p, gga-miR-101-2-5p. While these miRNAs were competitive combined by lncRNAs including MSTRG.18043, MSTRG.7738, MSTRG.21310, MSTRG.19577, and circRNAs including novel_circ_PTPN2, novel_circ_CTNNA1, novel_circ_PTPRD. This finding provides new insights into the regulatory mechanism of mRNA, miRNA, lncRNA, and circRNA in chicken fat deposition. Elsevier 2022-08-09 /pmc/articles/PMC9485216/ /pubmed/36116349 http://dx.doi.org/10.1016/j.psj.2022.102121 Text en © 2022 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | GENETICS AND MOLECULAR BIOLOGY Xiao, Cong Sun, Tiantian Yang, Zhuliang Zou, Leqin Deng, Jixian Yang, Xiurong Whole-transcriptome RNA sequencing reveals the global molecular responses and circRNA/lncRNA-miRNA-mRNA ceRNA regulatory network in chicken fat deposition |
title | Whole-transcriptome RNA sequencing reveals the global molecular responses and circRNA/lncRNA-miRNA-mRNA ceRNA regulatory network in chicken fat deposition |
title_full | Whole-transcriptome RNA sequencing reveals the global molecular responses and circRNA/lncRNA-miRNA-mRNA ceRNA regulatory network in chicken fat deposition |
title_fullStr | Whole-transcriptome RNA sequencing reveals the global molecular responses and circRNA/lncRNA-miRNA-mRNA ceRNA regulatory network in chicken fat deposition |
title_full_unstemmed | Whole-transcriptome RNA sequencing reveals the global molecular responses and circRNA/lncRNA-miRNA-mRNA ceRNA regulatory network in chicken fat deposition |
title_short | Whole-transcriptome RNA sequencing reveals the global molecular responses and circRNA/lncRNA-miRNA-mRNA ceRNA regulatory network in chicken fat deposition |
title_sort | whole-transcriptome rna sequencing reveals the global molecular responses and circrna/lncrna-mirna-mrna cerna regulatory network in chicken fat deposition |
topic | GENETICS AND MOLECULAR BIOLOGY |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9485216/ https://www.ncbi.nlm.nih.gov/pubmed/36116349 http://dx.doi.org/10.1016/j.psj.2022.102121 |
work_keys_str_mv | AT xiaocong wholetranscriptomernasequencingrevealstheglobalmolecularresponsesandcircrnalncrnamirnamrnacernaregulatorynetworkinchickenfatdeposition AT suntiantian wholetranscriptomernasequencingrevealstheglobalmolecularresponsesandcircrnalncrnamirnamrnacernaregulatorynetworkinchickenfatdeposition AT yangzhuliang wholetranscriptomernasequencingrevealstheglobalmolecularresponsesandcircrnalncrnamirnamrnacernaregulatorynetworkinchickenfatdeposition AT zouleqin wholetranscriptomernasequencingrevealstheglobalmolecularresponsesandcircrnalncrnamirnamrnacernaregulatorynetworkinchickenfatdeposition AT dengjixian wholetranscriptomernasequencingrevealstheglobalmolecularresponsesandcircrnalncrnamirnamrnacernaregulatorynetworkinchickenfatdeposition AT yangxiurong wholetranscriptomernasequencingrevealstheglobalmolecularresponsesandcircrnalncrnamirnamrnacernaregulatorynetworkinchickenfatdeposition |