Cargando…

Analysis of Differential miRNA Expression in the Duodenum of Escherichia coli F18-Sensitive and -Resistant Weaned Piglets

Small RNA duodenal libraries were constructed for Escherichia coli F18-sensitive and -resistant weaned piglets in full-sib pair groups and sequenced using Illumina Solexa high-throughput sequencing technology. The identification of differentially expressed miRNAs provides the basis for improved data...

Descripción completa

Detalles Bibliográficos
Autores principales: Ye, Lan, Su, Xianmin, Wu, Zhengchang, Zheng, Xianrui, Wang, Jin, Zi, Chen, Zhu, Guoqiang, Wu, Shenglong, Bao, Wenbin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427155/
https://www.ncbi.nlm.nih.gov/pubmed/22937089
http://dx.doi.org/10.1371/journal.pone.0043741
_version_ 1782241573945212928
author Ye, Lan
Su, Xianmin
Wu, Zhengchang
Zheng, Xianrui
Wang, Jin
Zi, Chen
Zhu, Guoqiang
Wu, Shenglong
Bao, Wenbin
author_facet Ye, Lan
Su, Xianmin
Wu, Zhengchang
Zheng, Xianrui
Wang, Jin
Zi, Chen
Zhu, Guoqiang
Wu, Shenglong
Bao, Wenbin
author_sort Ye, Lan
collection PubMed
description Small RNA duodenal libraries were constructed for Escherichia coli F18-sensitive and -resistant weaned piglets in full-sib pair groups and sequenced using Illumina Solexa high-throughput sequencing technology. The identification of differentially expressed miRNAs provides the basis for improved database information on pig miRNAs, understanding the genetic basics of differences in resistance to E. coli F18 between local Chinese and exotic pig breeds, and finding new resistance markers for E. coli F18 infection. The duodenum of all individuals contained more than 90% of known swine miRNAs. A total of 58 differentially expressing miRNAs were identified, of which 46 were increased and 12 were decreased in E. coli F18-sensitive pigs. Of miRNAs with increased expression, ssc-miR-143 was most highly expressed, followed by ssc-let-7f, ssc-miR-192, and ssc-miR-21. We identified a total of 2036 intersection target genes by comparing TargetScan data and previous gene expression profile results. Gene ontology and pathway analysis of intersection genes showed that differentially expressed miRNAs were mainly involved in the immune response and transcriptional regulation. Combining information on differential miRNA expression and their regulatory relationships with transcription factors, identified 12 candidate miRNA disease markers, including 11 miRNAs with increased expression, ssc-miR-143, ssc-let-7f, ssc-miR-30e, ssc-miR-148a, ssc-miR-148b, ssc-miR-181a, ssc-miR-192, ssc-miR-27b, ssc-miR-15b, ssc-miR-21, and ssc-miR-215, and one with decreased expression, ssc-miR-152. Quantitative real-time PCR analysis of candidate miRNA expression in a larger cohort of E coli F18-sensitive and -resistant animals confirmed the high-throughput sequencing results.
format Online
Article
Text
id pubmed-3427155
institution National Center for Biotechnology Information
language English
publishDate 2012
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-34271552012-08-30 Analysis of Differential miRNA Expression in the Duodenum of Escherichia coli F18-Sensitive and -Resistant Weaned Piglets Ye, Lan Su, Xianmin Wu, Zhengchang Zheng, Xianrui Wang, Jin Zi, Chen Zhu, Guoqiang Wu, Shenglong Bao, Wenbin PLoS One Research Article Small RNA duodenal libraries were constructed for Escherichia coli F18-sensitive and -resistant weaned piglets in full-sib pair groups and sequenced using Illumina Solexa high-throughput sequencing technology. The identification of differentially expressed miRNAs provides the basis for improved database information on pig miRNAs, understanding the genetic basics of differences in resistance to E. coli F18 between local Chinese and exotic pig breeds, and finding new resistance markers for E. coli F18 infection. The duodenum of all individuals contained more than 90% of known swine miRNAs. A total of 58 differentially expressing miRNAs were identified, of which 46 were increased and 12 were decreased in E. coli F18-sensitive pigs. Of miRNAs with increased expression, ssc-miR-143 was most highly expressed, followed by ssc-let-7f, ssc-miR-192, and ssc-miR-21. We identified a total of 2036 intersection target genes by comparing TargetScan data and previous gene expression profile results. Gene ontology and pathway analysis of intersection genes showed that differentially expressed miRNAs were mainly involved in the immune response and transcriptional regulation. Combining information on differential miRNA expression and their regulatory relationships with transcription factors, identified 12 candidate miRNA disease markers, including 11 miRNAs with increased expression, ssc-miR-143, ssc-let-7f, ssc-miR-30e, ssc-miR-148a, ssc-miR-148b, ssc-miR-181a, ssc-miR-192, ssc-miR-27b, ssc-miR-15b, ssc-miR-21, and ssc-miR-215, and one with decreased expression, ssc-miR-152. Quantitative real-time PCR analysis of candidate miRNA expression in a larger cohort of E coli F18-sensitive and -resistant animals confirmed the high-throughput sequencing results. Public Library of Science 2012-08-24 /pmc/articles/PMC3427155/ /pubmed/22937089 http://dx.doi.org/10.1371/journal.pone.0043741 Text en © 2012 Ye et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Ye, Lan
Su, Xianmin
Wu, Zhengchang
Zheng, Xianrui
Wang, Jin
Zi, Chen
Zhu, Guoqiang
Wu, Shenglong
Bao, Wenbin
Analysis of Differential miRNA Expression in the Duodenum of Escherichia coli F18-Sensitive and -Resistant Weaned Piglets
title Analysis of Differential miRNA Expression in the Duodenum of Escherichia coli F18-Sensitive and -Resistant Weaned Piglets
title_full Analysis of Differential miRNA Expression in the Duodenum of Escherichia coli F18-Sensitive and -Resistant Weaned Piglets
title_fullStr Analysis of Differential miRNA Expression in the Duodenum of Escherichia coli F18-Sensitive and -Resistant Weaned Piglets
title_full_unstemmed Analysis of Differential miRNA Expression in the Duodenum of Escherichia coli F18-Sensitive and -Resistant Weaned Piglets
title_short Analysis of Differential miRNA Expression in the Duodenum of Escherichia coli F18-Sensitive and -Resistant Weaned Piglets
title_sort analysis of differential mirna expression in the duodenum of escherichia coli f18-sensitive and -resistant weaned piglets
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427155/
https://www.ncbi.nlm.nih.gov/pubmed/22937089
http://dx.doi.org/10.1371/journal.pone.0043741
work_keys_str_mv AT yelan analysisofdifferentialmirnaexpressionintheduodenumofescherichiacolif18sensitiveandresistantweanedpiglets
AT suxianmin analysisofdifferentialmirnaexpressionintheduodenumofescherichiacolif18sensitiveandresistantweanedpiglets
AT wuzhengchang analysisofdifferentialmirnaexpressionintheduodenumofescherichiacolif18sensitiveandresistantweanedpiglets
AT zhengxianrui analysisofdifferentialmirnaexpressionintheduodenumofescherichiacolif18sensitiveandresistantweanedpiglets
AT wangjin analysisofdifferentialmirnaexpressionintheduodenumofescherichiacolif18sensitiveandresistantweanedpiglets
AT zichen analysisofdifferentialmirnaexpressionintheduodenumofescherichiacolif18sensitiveandresistantweanedpiglets
AT zhuguoqiang analysisofdifferentialmirnaexpressionintheduodenumofescherichiacolif18sensitiveandresistantweanedpiglets
AT wushenglong analysisofdifferentialmirnaexpressionintheduodenumofescherichiacolif18sensitiveandresistantweanedpiglets
AT baowenbin analysisofdifferentialmirnaexpressionintheduodenumofescherichiacolif18sensitiveandresistantweanedpiglets