Cargando…

Profiling and Functional Analysis of Long Noncoding RNAs and mRNAs during Porcine Skeletal Muscle Development

Gene transcripts or mRNAs and long noncoding RNAs (lncRNAs) are differentially expressed during porcine skeletal muscle development. However, only a few studies have been conducted on skeletal muscle transcriptome in pigs based on timepoints according to the growth curve for porcine. Here, we invest...

Descripción completa

Detalles Bibliográficos
Autores principales: Tan, Ya, Gan, Mailin, Shen, Linyuan, Li, Liang, Fan, Yuan, Chen, Ying, Chen, Lei, Niu, Lili, Zhao, Ye, Jiang, Anan, Jiang, Dongmei, Zhang, Shunhua, Zhu, Li
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7825455/
https://www.ncbi.nlm.nih.gov/pubmed/33419093
http://dx.doi.org/10.3390/ijms22020503
_version_ 1783640313268535296
author Tan, Ya
Gan, Mailin
Shen, Linyuan
Li, Liang
Fan, Yuan
Chen, Ying
Chen, Lei
Niu, Lili
Zhao, Ye
Jiang, Anan
Jiang, Dongmei
Zhang, Shunhua
Zhu, Li
author_facet Tan, Ya
Gan, Mailin
Shen, Linyuan
Li, Liang
Fan, Yuan
Chen, Ying
Chen, Lei
Niu, Lili
Zhao, Ye
Jiang, Anan
Jiang, Dongmei
Zhang, Shunhua
Zhu, Li
author_sort Tan, Ya
collection PubMed
description Gene transcripts or mRNAs and long noncoding RNAs (lncRNAs) are differentially expressed during porcine skeletal muscle development. However, only a few studies have been conducted on skeletal muscle transcriptome in pigs based on timepoints according to the growth curve for porcine. Here, we investigated gene expression in Qingyu pigs at three different growth stages: the inflection point with the maximum growth rate (MGI), the inflection point of the gradually increasing stage to the rapidly increasing stage (GRI), and the inflection point of the rapidly increasing stage to the slowly increasing stage (RSI). Subsequently, we explored gene expression profiles during muscle development at the MGI, GRI and RSI stages by Ribo-Zero RNA sequencing. Qingyu pigs reached the MGI, GRI and RSI stages at 156.40, 23.82 and 288.97 days of age with 51.73, 3.14 and 107.03 kg body weight, respectively. A total of 14,530 mRNAs and 11,970 lncRNAs were identified at the three stages, and 645, 323 differentially expressed genes (DEGs) and 696, 760 differentially expressed lncRNAs (DELs) were identified in the GRI vs. MGI, and RSI vs. MGI, comparisons. Functional enrichment analysis revealed that genes involved in immune system development and energy metabolism (mainly relate to amino acid, carbohydrate and lipid) were enriched at the GRI and MGI stages, respectively, whereas genes involved in lipid metabolism were enriched at the RSI stage. We further characterized G1430, an abundant lncRNA. The full-length sequence (316 nt) of lncRNA G1430 was determined by rapid amplification of cDNA ends (RACE). Subcellular distribution analysis by quantitative real-time PCR (qRT-PCR) revealed that G1430 is a cytoplasmic lncRNA. Binding site prediction and dual luciferase assay showed that lncRNA G1430 directly binds to microRNA 133a (miR-133a). Our findings provide the basis for further investigation of the regulatory mechanisms and molecular genetics of muscle development in pigs.
format Online
Article
Text
id pubmed-7825455
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-78254552021-01-24 Profiling and Functional Analysis of Long Noncoding RNAs and mRNAs during Porcine Skeletal Muscle Development Tan, Ya Gan, Mailin Shen, Linyuan Li, Liang Fan, Yuan Chen, Ying Chen, Lei Niu, Lili Zhao, Ye Jiang, Anan Jiang, Dongmei Zhang, Shunhua Zhu, Li Int J Mol Sci Article Gene transcripts or mRNAs and long noncoding RNAs (lncRNAs) are differentially expressed during porcine skeletal muscle development. However, only a few studies have been conducted on skeletal muscle transcriptome in pigs based on timepoints according to the growth curve for porcine. Here, we investigated gene expression in Qingyu pigs at three different growth stages: the inflection point with the maximum growth rate (MGI), the inflection point of the gradually increasing stage to the rapidly increasing stage (GRI), and the inflection point of the rapidly increasing stage to the slowly increasing stage (RSI). Subsequently, we explored gene expression profiles during muscle development at the MGI, GRI and RSI stages by Ribo-Zero RNA sequencing. Qingyu pigs reached the MGI, GRI and RSI stages at 156.40, 23.82 and 288.97 days of age with 51.73, 3.14 and 107.03 kg body weight, respectively. A total of 14,530 mRNAs and 11,970 lncRNAs were identified at the three stages, and 645, 323 differentially expressed genes (DEGs) and 696, 760 differentially expressed lncRNAs (DELs) were identified in the GRI vs. MGI, and RSI vs. MGI, comparisons. Functional enrichment analysis revealed that genes involved in immune system development and energy metabolism (mainly relate to amino acid, carbohydrate and lipid) were enriched at the GRI and MGI stages, respectively, whereas genes involved in lipid metabolism were enriched at the RSI stage. We further characterized G1430, an abundant lncRNA. The full-length sequence (316 nt) of lncRNA G1430 was determined by rapid amplification of cDNA ends (RACE). Subcellular distribution analysis by quantitative real-time PCR (qRT-PCR) revealed that G1430 is a cytoplasmic lncRNA. Binding site prediction and dual luciferase assay showed that lncRNA G1430 directly binds to microRNA 133a (miR-133a). Our findings provide the basis for further investigation of the regulatory mechanisms and molecular genetics of muscle development in pigs. MDPI 2021-01-06 /pmc/articles/PMC7825455/ /pubmed/33419093 http://dx.doi.org/10.3390/ijms22020503 Text en © 2021 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, Ya
Gan, Mailin
Shen, Linyuan
Li, Liang
Fan, Yuan
Chen, Ying
Chen, Lei
Niu, Lili
Zhao, Ye
Jiang, Anan
Jiang, Dongmei
Zhang, Shunhua
Zhu, Li
Profiling and Functional Analysis of Long Noncoding RNAs and mRNAs during Porcine Skeletal Muscle Development
title Profiling and Functional Analysis of Long Noncoding RNAs and mRNAs during Porcine Skeletal Muscle Development
title_full Profiling and Functional Analysis of Long Noncoding RNAs and mRNAs during Porcine Skeletal Muscle Development
title_fullStr Profiling and Functional Analysis of Long Noncoding RNAs and mRNAs during Porcine Skeletal Muscle Development
title_full_unstemmed Profiling and Functional Analysis of Long Noncoding RNAs and mRNAs during Porcine Skeletal Muscle Development
title_short Profiling and Functional Analysis of Long Noncoding RNAs and mRNAs during Porcine Skeletal Muscle Development
title_sort profiling and functional analysis of long noncoding rnas and mrnas during porcine skeletal muscle development
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7825455/
https://www.ncbi.nlm.nih.gov/pubmed/33419093
http://dx.doi.org/10.3390/ijms22020503
work_keys_str_mv AT tanya profilingandfunctionalanalysisoflongnoncodingrnasandmrnasduringporcineskeletalmuscledevelopment
AT ganmailin profilingandfunctionalanalysisoflongnoncodingrnasandmrnasduringporcineskeletalmuscledevelopment
AT shenlinyuan profilingandfunctionalanalysisoflongnoncodingrnasandmrnasduringporcineskeletalmuscledevelopment
AT liliang profilingandfunctionalanalysisoflongnoncodingrnasandmrnasduringporcineskeletalmuscledevelopment
AT fanyuan profilingandfunctionalanalysisoflongnoncodingrnasandmrnasduringporcineskeletalmuscledevelopment
AT chenying profilingandfunctionalanalysisoflongnoncodingrnasandmrnasduringporcineskeletalmuscledevelopment
AT chenlei profilingandfunctionalanalysisoflongnoncodingrnasandmrnasduringporcineskeletalmuscledevelopment
AT niulili profilingandfunctionalanalysisoflongnoncodingrnasandmrnasduringporcineskeletalmuscledevelopment
AT zhaoye profilingandfunctionalanalysisoflongnoncodingrnasandmrnasduringporcineskeletalmuscledevelopment
AT jianganan profilingandfunctionalanalysisoflongnoncodingrnasandmrnasduringporcineskeletalmuscledevelopment
AT jiangdongmei profilingandfunctionalanalysisoflongnoncodingrnasandmrnasduringporcineskeletalmuscledevelopment
AT zhangshunhua profilingandfunctionalanalysisoflongnoncodingrnasandmrnasduringporcineskeletalmuscledevelopment
AT zhuli profilingandfunctionalanalysisoflongnoncodingrnasandmrnasduringporcineskeletalmuscledevelopment