Cargando…
Dynamic expression and functional analysis of circRNA in granulosa cells during follicular development in chicken
BACKGROUND: Circular RNA (circRNA) is a type of noncoding RNA involved in a variety of biological processes, especially in post-transcriptional regulation. The granulosa cells of follicles play a determining role in ovarian development. However, the function of circRNA in chicken follicles is unclea...
Autores principales: | , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6354403/ https://www.ncbi.nlm.nih.gov/pubmed/30700247 http://dx.doi.org/10.1186/s12864-019-5462-2 |
_version_ | 1783391182871592960 |
---|---|
author | Shen, Manman Li, Tingting Zhang, Genxi Wu, Pengfei Chen, Fuxiang Lou, Qiuhong Chen, Lan Yin, Xuemei Zhang, Tao Wang, Jinyu |
author_facet | Shen, Manman Li, Tingting Zhang, Genxi Wu, Pengfei Chen, Fuxiang Lou, Qiuhong Chen, Lan Yin, Xuemei Zhang, Tao Wang, Jinyu |
author_sort | Shen, Manman |
collection | PubMed |
description | BACKGROUND: Circular RNA (circRNA) is a type of noncoding RNA involved in a variety of biological processes, especially in post-transcriptional regulation. The granulosa cells of follicles play a determining role in ovarian development. However, the function of circRNA in chicken follicles is unclear. To better understand the molecular mechanism underlying follicular development and granulosa cell function, we performed a strategy of second-generation sequencing and linear RNA depletion for granulosa cells from small yellow follicles (SYF, 5–8 mm), the smallest hierarchal follicles (F6, 9–12 mm), and the largest hierarchal follicles (F1, ~ 40 mm). RESULTS: We predicted a total of 11,642 circRNAs that distributed on almost all chromosomes. The majority of the splice lengths of circRNAs were 200–500 nt and mainly produced from intron and CDS regions. During follicle growth, differentially expressed (DE) circRNAs showed dynamic changes which were tissue- and stage-specific. The host genes of DE circRNAs were functionally enriched in GTPase activity and several pathways involved in reproduction. Moreover, bioinformatic prediction analysis for circRalGPS2 demonstrated that circRNAs from the same genes may share common miRNA to act as a sponge. The predicted target genes were enriched in various biological processes including cognition, cell communication, and regulation of signaling, and several pathways related to reproduction such as tight junction, oocyte meiosis, progesterone-mediated oocyte maturation, and GnRH signaling. CONCLUSIONS: This study provides a starting point for further experimental investigations into chicken circRNAs and casts a light on the understanding of follicle development. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5462-2) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6354403 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-63544032019-02-07 Dynamic expression and functional analysis of circRNA in granulosa cells during follicular development in chicken Shen, Manman Li, Tingting Zhang, Genxi Wu, Pengfei Chen, Fuxiang Lou, Qiuhong Chen, Lan Yin, Xuemei Zhang, Tao Wang, Jinyu BMC Genomics Research Article BACKGROUND: Circular RNA (circRNA) is a type of noncoding RNA involved in a variety of biological processes, especially in post-transcriptional regulation. The granulosa cells of follicles play a determining role in ovarian development. However, the function of circRNA in chicken follicles is unclear. To better understand the molecular mechanism underlying follicular development and granulosa cell function, we performed a strategy of second-generation sequencing and linear RNA depletion for granulosa cells from small yellow follicles (SYF, 5–8 mm), the smallest hierarchal follicles (F6, 9–12 mm), and the largest hierarchal follicles (F1, ~ 40 mm). RESULTS: We predicted a total of 11,642 circRNAs that distributed on almost all chromosomes. The majority of the splice lengths of circRNAs were 200–500 nt and mainly produced from intron and CDS regions. During follicle growth, differentially expressed (DE) circRNAs showed dynamic changes which were tissue- and stage-specific. The host genes of DE circRNAs were functionally enriched in GTPase activity and several pathways involved in reproduction. Moreover, bioinformatic prediction analysis for circRalGPS2 demonstrated that circRNAs from the same genes may share common miRNA to act as a sponge. The predicted target genes were enriched in various biological processes including cognition, cell communication, and regulation of signaling, and several pathways related to reproduction such as tight junction, oocyte meiosis, progesterone-mediated oocyte maturation, and GnRH signaling. CONCLUSIONS: This study provides a starting point for further experimental investigations into chicken circRNAs and casts a light on the understanding of follicle development. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5462-2) contains supplementary material, which is available to authorized users. BioMed Central 2019-01-30 /pmc/articles/PMC6354403/ /pubmed/30700247 http://dx.doi.org/10.1186/s12864-019-5462-2 Text en © The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Shen, Manman Li, Tingting Zhang, Genxi Wu, Pengfei Chen, Fuxiang Lou, Qiuhong Chen, Lan Yin, Xuemei Zhang, Tao Wang, Jinyu Dynamic expression and functional analysis of circRNA in granulosa cells during follicular development in chicken |
title | Dynamic expression and functional analysis of circRNA in granulosa cells during follicular development in chicken |
title_full | Dynamic expression and functional analysis of circRNA in granulosa cells during follicular development in chicken |
title_fullStr | Dynamic expression and functional analysis of circRNA in granulosa cells during follicular development in chicken |
title_full_unstemmed | Dynamic expression and functional analysis of circRNA in granulosa cells during follicular development in chicken |
title_short | Dynamic expression and functional analysis of circRNA in granulosa cells during follicular development in chicken |
title_sort | dynamic expression and functional analysis of circrna in granulosa cells during follicular development in chicken |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6354403/ https://www.ncbi.nlm.nih.gov/pubmed/30700247 http://dx.doi.org/10.1186/s12864-019-5462-2 |
work_keys_str_mv | AT shenmanman dynamicexpressionandfunctionalanalysisofcircrnaingranulosacellsduringfolliculardevelopmentinchicken AT litingting dynamicexpressionandfunctionalanalysisofcircrnaingranulosacellsduringfolliculardevelopmentinchicken AT zhanggenxi dynamicexpressionandfunctionalanalysisofcircrnaingranulosacellsduringfolliculardevelopmentinchicken AT wupengfei dynamicexpressionandfunctionalanalysisofcircrnaingranulosacellsduringfolliculardevelopmentinchicken AT chenfuxiang dynamicexpressionandfunctionalanalysisofcircrnaingranulosacellsduringfolliculardevelopmentinchicken AT louqiuhong dynamicexpressionandfunctionalanalysisofcircrnaingranulosacellsduringfolliculardevelopmentinchicken AT chenlan dynamicexpressionandfunctionalanalysisofcircrnaingranulosacellsduringfolliculardevelopmentinchicken AT yinxuemei dynamicexpressionandfunctionalanalysisofcircrnaingranulosacellsduringfolliculardevelopmentinchicken AT zhangtao dynamicexpressionandfunctionalanalysisofcircrnaingranulosacellsduringfolliculardevelopmentinchicken AT wangjinyu dynamicexpressionandfunctionalanalysisofcircrnaingranulosacellsduringfolliculardevelopmentinchicken |