Network Analyses Predict Small RNAs That Might Modulate Gene Expression in the Testis and Epididymis of Bos indicus Bulls
Autor(a) principal: | |
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Data de Publicação: | 2021 |
Outros Autores: | , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.3389/fgene.2021.610116 http://hdl.handle.net/11449/206350 |
Resumo: | Spermatogenesis relies on complex molecular mechanisms, essential for the genesis and differentiation of the male gamete. Germ cell differentiation starts at the testicular parenchyma and finishes in the epididymis, which has three main regions: head, body, and tail. RNA-sequencing data of the testicular parenchyma (TP), head epididymis (HE), and tail epididymis (TE) from four bulls (three biopsies per bull: 12 samples) were subjected to differential expression analyses, functional enrichment analyses, and co-expression analyses. The aim was to investigate the co-expression and infer possible regulatory roles for transcripts involved in the spermatogenesis of Bos indicus bulls. Across the three pairwise comparisons, 3,826 differentially expressed (DE) transcripts were identified, of which 384 are small RNAs. Functional enrichment analysis pointed to gene ontology (GO) terms related to ion channel activity, detoxification of copper, neuroactive receptors, and spermatogenesis. Using the regulatory impact factor (RIF) algorithm, we detected 70 DE small RNAs likely to regulate the DE transcripts considering all pairwise comparisons among tissues. The pattern of small RNA co-expression suggested that these elements are involved in spermatogenesis regulation. The 3,826 DE transcripts (mRNAs and small RNAs) were further subjected to co-expression analyses using the partial correlation and information theory (PCIT) algorithm for network prediction. Significant correlations underpinned the co-expression network, which had 2,216 transcripts connected by 158,807 predicted interactions. The larger network cluster was enriched for male gamete generation and had 15 miRNAs with significant RIF. The miRNA bta-mir-2886 showed the highest number of connections (601) and was predicted to down-regulate ELOVL3, FEZF2, and HOXA13 (negative co-expression correlations and confirmed with TargetScan). In short, we suggest that bta-mir-2886 and other small RNAs might modulate gene expression in the testis and epididymis, in Bos indicus cattle. |
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Network Analyses Predict Small RNAs That Might Modulate Gene Expression in the Testis and Epididymis of Bos indicus Bullsbovinebta-mir-2886miRNARNA-sequencingsmall RNAsspermatogenesisspermatozoasystems biologySpermatogenesis relies on complex molecular mechanisms, essential for the genesis and differentiation of the male gamete. Germ cell differentiation starts at the testicular parenchyma and finishes in the epididymis, which has three main regions: head, body, and tail. RNA-sequencing data of the testicular parenchyma (TP), head epididymis (HE), and tail epididymis (TE) from four bulls (three biopsies per bull: 12 samples) were subjected to differential expression analyses, functional enrichment analyses, and co-expression analyses. The aim was to investigate the co-expression and infer possible regulatory roles for transcripts involved in the spermatogenesis of Bos indicus bulls. Across the three pairwise comparisons, 3,826 differentially expressed (DE) transcripts were identified, of which 384 are small RNAs. Functional enrichment analysis pointed to gene ontology (GO) terms related to ion channel activity, detoxification of copper, neuroactive receptors, and spermatogenesis. Using the regulatory impact factor (RIF) algorithm, we detected 70 DE small RNAs likely to regulate the DE transcripts considering all pairwise comparisons among tissues. The pattern of small RNA co-expression suggested that these elements are involved in spermatogenesis regulation. The 3,826 DE transcripts (mRNAs and small RNAs) were further subjected to co-expression analyses using the partial correlation and information theory (PCIT) algorithm for network prediction. Significant correlations underpinned the co-expression network, which had 2,216 transcripts connected by 158,807 predicted interactions. The larger network cluster was enriched for male gamete generation and had 15 miRNAs with significant RIF. The miRNA bta-mir-2886 showed the highest number of connections (601) and was predicted to down-regulate ELOVL3, FEZF2, and HOXA13 (negative co-expression correlations and confirmed with TargetScan). In short, we suggest that bta-mir-2886 and other small RNAs might modulate gene expression in the testis and epididymis, in Bos indicus cattle.Global Change Institute, University of QueenslandInstitute for Molecular Bioscience, University Of QueenslandQueensland Alliance for Agriculture and Food Innovation, University of QueenslandResearch Computing Centre, University of QueenslandUniversity of QueenslandCentre for Natural Gas, University of QueenslandSchool of Agriculture and Food Sciences, University of QueenslandSchool of Pharmacy, University of QueenslandDepartment of Production and Animal Health School of Veterinary Medicine São Paulo State University (UNESP)Department of Animal Science University of São Paulo/ESALQSchool of Chemistry and Molecular Biosciences The University of QueenslandAustralian Institute for Bioengineering and Nanotechnology (AIBN) The University of QueenslandCSIRO Agriculture and Food Queensland Bioscience PrecinctDepartment of Production and Animal Health School of Veterinary Medicine São Paulo State University (UNESP)Universidade Estadual Paulista (Unesp)Universidade de São Paulo (USP)The University of QueenslandQueensland Bioscience Precinctde Lima, Andressa O. [UNESP]Afonso, JulianaEdson, JanetteMarcellin, EstebanPalfreyman, RobinPorto-Neto, Laercio R.Reverter, AntonioFortes, Marina R. S.2021-06-25T10:30:37Z2021-06-25T10:30:37Z2021-04-30info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.3389/fgene.2021.610116Frontiers in Genetics, v. 12.1664-8021http://hdl.handle.net/11449/20635010.3389/fgene.2021.6101162-s2.0-85105934252Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengFrontiers in Geneticsinfo:eu-repo/semantics/openAccess2021-10-23T03:22:26Zoai:repositorio.unesp.br:11449/206350Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T17:01:40.591135Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Network Analyses Predict Small RNAs That Might Modulate Gene Expression in the Testis and Epididymis of Bos indicus Bulls |
title |
Network Analyses Predict Small RNAs That Might Modulate Gene Expression in the Testis and Epididymis of Bos indicus Bulls |
spellingShingle |
Network Analyses Predict Small RNAs That Might Modulate Gene Expression in the Testis and Epididymis of Bos indicus Bulls de Lima, Andressa O. [UNESP] bovine bta-mir-2886 miRNA RNA-sequencing small RNAs spermatogenesis spermatozoa systems biology |
title_short |
Network Analyses Predict Small RNAs That Might Modulate Gene Expression in the Testis and Epididymis of Bos indicus Bulls |
title_full |
Network Analyses Predict Small RNAs That Might Modulate Gene Expression in the Testis and Epididymis of Bos indicus Bulls |
title_fullStr |
Network Analyses Predict Small RNAs That Might Modulate Gene Expression in the Testis and Epididymis of Bos indicus Bulls |
title_full_unstemmed |
Network Analyses Predict Small RNAs That Might Modulate Gene Expression in the Testis and Epididymis of Bos indicus Bulls |
title_sort |
Network Analyses Predict Small RNAs That Might Modulate Gene Expression in the Testis and Epididymis of Bos indicus Bulls |
author |
de Lima, Andressa O. [UNESP] |
author_facet |
de Lima, Andressa O. [UNESP] Afonso, Juliana Edson, Janette Marcellin, Esteban Palfreyman, Robin Porto-Neto, Laercio R. Reverter, Antonio Fortes, Marina R. S. |
author_role |
author |
author2 |
Afonso, Juliana Edson, Janette Marcellin, Esteban Palfreyman, Robin Porto-Neto, Laercio R. Reverter, Antonio Fortes, Marina R. S. |
author2_role |
author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) Universidade de São Paulo (USP) The University of Queensland Queensland Bioscience Precinct |
dc.contributor.author.fl_str_mv |
de Lima, Andressa O. [UNESP] Afonso, Juliana Edson, Janette Marcellin, Esteban Palfreyman, Robin Porto-Neto, Laercio R. Reverter, Antonio Fortes, Marina R. S. |
dc.subject.por.fl_str_mv |
bovine bta-mir-2886 miRNA RNA-sequencing small RNAs spermatogenesis spermatozoa systems biology |
topic |
bovine bta-mir-2886 miRNA RNA-sequencing small RNAs spermatogenesis spermatozoa systems biology |
description |
Spermatogenesis relies on complex molecular mechanisms, essential for the genesis and differentiation of the male gamete. Germ cell differentiation starts at the testicular parenchyma and finishes in the epididymis, which has three main regions: head, body, and tail. RNA-sequencing data of the testicular parenchyma (TP), head epididymis (HE), and tail epididymis (TE) from four bulls (three biopsies per bull: 12 samples) were subjected to differential expression analyses, functional enrichment analyses, and co-expression analyses. The aim was to investigate the co-expression and infer possible regulatory roles for transcripts involved in the spermatogenesis of Bos indicus bulls. Across the three pairwise comparisons, 3,826 differentially expressed (DE) transcripts were identified, of which 384 are small RNAs. Functional enrichment analysis pointed to gene ontology (GO) terms related to ion channel activity, detoxification of copper, neuroactive receptors, and spermatogenesis. Using the regulatory impact factor (RIF) algorithm, we detected 70 DE small RNAs likely to regulate the DE transcripts considering all pairwise comparisons among tissues. The pattern of small RNA co-expression suggested that these elements are involved in spermatogenesis regulation. The 3,826 DE transcripts (mRNAs and small RNAs) were further subjected to co-expression analyses using the partial correlation and information theory (PCIT) algorithm for network prediction. Significant correlations underpinned the co-expression network, which had 2,216 transcripts connected by 158,807 predicted interactions. The larger network cluster was enriched for male gamete generation and had 15 miRNAs with significant RIF. The miRNA bta-mir-2886 showed the highest number of connections (601) and was predicted to down-regulate ELOVL3, FEZF2, and HOXA13 (negative co-expression correlations and confirmed with TargetScan). In short, we suggest that bta-mir-2886 and other small RNAs might modulate gene expression in the testis and epididymis, in Bos indicus cattle. |
publishDate |
2021 |
dc.date.none.fl_str_mv |
2021-06-25T10:30:37Z 2021-06-25T10:30:37Z 2021-04-30 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.3389/fgene.2021.610116 Frontiers in Genetics, v. 12. 1664-8021 http://hdl.handle.net/11449/206350 10.3389/fgene.2021.610116 2-s2.0-85105934252 |
url |
http://dx.doi.org/10.3389/fgene.2021.610116 http://hdl.handle.net/11449/206350 |
identifier_str_mv |
Frontiers in Genetics, v. 12. 1664-8021 10.3389/fgene.2021.610116 2-s2.0-85105934252 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Frontiers in Genetics |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
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1808128741731205120 |