PMID- 33995471
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20210518
IS  - 1664-8021 (Print)
IS  - 1664-8021 (Electronic)
IS  - 1664-8021 (Linking)
VI  - 12
DP  - 2021
TI  - Network Analyses Predict Small RNAs That Might Modulate Gene Expression in the 
      Testis and Epididymis of Bos indicus Bulls.
PG  - 610116
LID - 10.3389/fgene.2021.610116 [doi]
LID - 610116
AB  - 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.
CI  - Copyright (c) 2021 de Lima, Afonso, Edson, Marcellin, Palfreyman, Porto-Neto, 
      Reverter and Fortes.
FAU - de Lima, Andressa O
AU  - de Lima AO
AD  - Department of Production and Animal Health, School of Veterinary Medicine, Sao 
      Paulo State University (UNESP), Aracatuba, Brazil.
FAU - Afonso, Juliana
AU  - Afonso J
AD  - Department of Animal Science, University of Sao Paulo/ESALQ, Piracicaba, Brazil.
FAU - Edson, Janette
AU  - Edson J
AD  - School of Chemistry and Molecular Biosciences, The University of Queensland, St 
      Lucia, QLD, Australia.
FAU - Marcellin, Esteban
AU  - Marcellin E
AD  - Australian Institute for Bioengineering and Nanotechnology (AIBN), The University 
      of Queensland, St Lucia, QLD, Australia.
FAU - Palfreyman, Robin
AU  - Palfreyman R
AD  - Australian Institute for Bioengineering and Nanotechnology (AIBN), The University 
      of Queensland, St Lucia, QLD, Australia.
FAU - Porto-Neto, Laercio R
AU  - Porto-Neto LR
AD  - CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD, 
      Australia.
FAU - Reverter, Antonio
AU  - Reverter A
AD  - CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD, 
      Australia.
FAU - Fortes, Marina R S
AU  - Fortes MRS
AD  - School of Chemistry and Molecular Biosciences, The University of Queensland, St 
      Lucia, QLD, Australia.
LA  - eng
PT  - Journal Article
DEP - 20210430
PL  - Switzerland
TA  - Front Genet
JT  - Frontiers in genetics
JID - 101560621
PMC - PMC8120238
OTO - NOTNLM
OT  - RNA-sequencing
OT  - bovine
OT  - bta-mir-2886
OT  - miRNA
OT  - small RNAs
OT  - spermatogenesis
OT  - spermatozoa
OT  - systems biology
COIS- The authors declare that the research was conducted in the absence of any 
      commercial or financial relationships that could be construed as a potential 
      conflict of interest.
EDAT- 2021/05/18 06:00
MHDA- 2021/05/18 06:01
PMCR- 2021/04/30
CRDT- 2021/05/17 06:04
PHST- 2020/09/25 00:00 [received]
PHST- 2021/03/19 00:00 [accepted]
PHST- 2021/05/17 06:04 [entrez]
PHST- 2021/05/18 06:00 [pubmed]
PHST- 2021/05/18 06:01 [medline]
PHST- 2021/04/30 00:00 [pmc-release]
AID - 10.3389/fgene.2021.610116 [doi]
PST - epublish
SO  - Front Genet. 2021 Apr 30;12:610116. doi: 10.3389/fgene.2021.610116. eCollection 
      2021.