Cargando…
Deep Sequencing Analysis of miRNA Expression in Breast Muscle of Fast-Growing and Slow-Growing Broilers
Growth performance is an important economic trait in chicken. MicroRNAs (miRNAs) have been shown to play important roles in various biological processes, but their functions in chicken growth are not yet clear. To investigate the function of miRNAs in chicken growth, breast muscle tissues of the two...
Autores principales: | , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2015
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4519947/ https://www.ncbi.nlm.nih.gov/pubmed/26193261 http://dx.doi.org/10.3390/ijms160716242 |
_version_ | 1782383585152466944 |
---|---|
author | Ouyang, Hongjia He, Xiaomei Li, Guihuan Xu, Haiping Jia, Xinzheng Nie, Qinghua Zhang, Xiquan |
author_facet | Ouyang, Hongjia He, Xiaomei Li, Guihuan Xu, Haiping Jia, Xinzheng Nie, Qinghua Zhang, Xiquan |
author_sort | Ouyang, Hongjia |
collection | PubMed |
description | Growth performance is an important economic trait in chicken. MicroRNAs (miRNAs) have been shown to play important roles in various biological processes, but their functions in chicken growth are not yet clear. To investigate the function of miRNAs in chicken growth, breast muscle tissues of the two-tail samples (highest and lowest body weight) from Recessive White Rock (WRR) and Xinghua Chickens (XH) were performed on high throughput small RNA deep sequencing. In this study, a total of 921 miRNAs were identified, including 733 known mature miRNAs and 188 novel miRNAs. There were 200, 279, 257 and 297 differentially expressed miRNAs in the comparisons of WRRh vs. WRRl, WRRh vs. XHh, WRRl vs. XHl, and XHh vs. XHl group, respectively. A total of 22 highly differentially expressed miRNAs (fold change > 2 or < 0.5; p-value < 0.05; q-value < 0.01), which also have abundant expression (read counts > 1000) were found in our comparisons. As far as two analyses (WRRh vs. WRRl, and XHh vs. XHl) are concerned, we found 80 common differentially expressed miRNAs, while 110 miRNAs were found in WRRh vs. XHh and WRRl vs. XHl. Furthermore, 26 common miRNAs were identified among all four comparisons. Four differentially expressed miRNAs (miR-223, miR-16, miR-205a and miR-222b-5p) were validated by quantitative real-time RT-PCR (qRT-PCR). Regulatory networks of interactions among miRNAs and their targets were constructed using integrative miRNA target-prediction and network-analysis. Growth hormone receptor (GHR) was confirmed as a target of miR-146b-3p by dual-luciferase assay and qPCR, indicating that miR-34c, miR-223, miR-146b-3p, miR-21 and miR-205a are key growth-related target genes in the network. These miRNAs are proposed as candidate miRNAs for future studies concerning miRNA-target function on regulation of chicken growth. |
format | Online Article Text |
id | pubmed-4519947 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-45199472015-08-03 Deep Sequencing Analysis of miRNA Expression in Breast Muscle of Fast-Growing and Slow-Growing Broilers Ouyang, Hongjia He, Xiaomei Li, Guihuan Xu, Haiping Jia, Xinzheng Nie, Qinghua Zhang, Xiquan Int J Mol Sci Article Growth performance is an important economic trait in chicken. MicroRNAs (miRNAs) have been shown to play important roles in various biological processes, but their functions in chicken growth are not yet clear. To investigate the function of miRNAs in chicken growth, breast muscle tissues of the two-tail samples (highest and lowest body weight) from Recessive White Rock (WRR) and Xinghua Chickens (XH) were performed on high throughput small RNA deep sequencing. In this study, a total of 921 miRNAs were identified, including 733 known mature miRNAs and 188 novel miRNAs. There were 200, 279, 257 and 297 differentially expressed miRNAs in the comparisons of WRRh vs. WRRl, WRRh vs. XHh, WRRl vs. XHl, and XHh vs. XHl group, respectively. A total of 22 highly differentially expressed miRNAs (fold change > 2 or < 0.5; p-value < 0.05; q-value < 0.01), which also have abundant expression (read counts > 1000) were found in our comparisons. As far as two analyses (WRRh vs. WRRl, and XHh vs. XHl) are concerned, we found 80 common differentially expressed miRNAs, while 110 miRNAs were found in WRRh vs. XHh and WRRl vs. XHl. Furthermore, 26 common miRNAs were identified among all four comparisons. Four differentially expressed miRNAs (miR-223, miR-16, miR-205a and miR-222b-5p) were validated by quantitative real-time RT-PCR (qRT-PCR). Regulatory networks of interactions among miRNAs and their targets were constructed using integrative miRNA target-prediction and network-analysis. Growth hormone receptor (GHR) was confirmed as a target of miR-146b-3p by dual-luciferase assay and qPCR, indicating that miR-34c, miR-223, miR-146b-3p, miR-21 and miR-205a are key growth-related target genes in the network. These miRNAs are proposed as candidate miRNAs for future studies concerning miRNA-target function on regulation of chicken growth. MDPI 2015-07-17 /pmc/articles/PMC4519947/ /pubmed/26193261 http://dx.doi.org/10.3390/ijms160716242 Text en © 2015 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 license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Ouyang, Hongjia He, Xiaomei Li, Guihuan Xu, Haiping Jia, Xinzheng Nie, Qinghua Zhang, Xiquan Deep Sequencing Analysis of miRNA Expression in Breast Muscle of Fast-Growing and Slow-Growing Broilers |
title | Deep Sequencing Analysis of miRNA Expression in Breast Muscle of Fast-Growing and Slow-Growing Broilers |
title_full | Deep Sequencing Analysis of miRNA Expression in Breast Muscle of Fast-Growing and Slow-Growing Broilers |
title_fullStr | Deep Sequencing Analysis of miRNA Expression in Breast Muscle of Fast-Growing and Slow-Growing Broilers |
title_full_unstemmed | Deep Sequencing Analysis of miRNA Expression in Breast Muscle of Fast-Growing and Slow-Growing Broilers |
title_short | Deep Sequencing Analysis of miRNA Expression in Breast Muscle of Fast-Growing and Slow-Growing Broilers |
title_sort | deep sequencing analysis of mirna expression in breast muscle of fast-growing and slow-growing broilers |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4519947/ https://www.ncbi.nlm.nih.gov/pubmed/26193261 http://dx.doi.org/10.3390/ijms160716242 |
work_keys_str_mv | AT ouyanghongjia deepsequencinganalysisofmirnaexpressioninbreastmuscleoffastgrowingandslowgrowingbroilers AT hexiaomei deepsequencinganalysisofmirnaexpressioninbreastmuscleoffastgrowingandslowgrowingbroilers AT liguihuan deepsequencinganalysisofmirnaexpressioninbreastmuscleoffastgrowingandslowgrowingbroilers AT xuhaiping deepsequencinganalysisofmirnaexpressioninbreastmuscleoffastgrowingandslowgrowingbroilers AT jiaxinzheng deepsequencinganalysisofmirnaexpressioninbreastmuscleoffastgrowingandslowgrowingbroilers AT nieqinghua deepsequencinganalysisofmirnaexpressioninbreastmuscleoffastgrowingandslowgrowingbroilers AT zhangxiquan deepsequencinganalysisofmirnaexpressioninbreastmuscleoffastgrowingandslowgrowingbroilers |