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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...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2012
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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 |
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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 |
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