Differential expression of miRNAs in the presence of B chromosome in the cichlid fish Astatotilapia latifasciata.

Autor: Nascimento-Oliveira JI; Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil., Fantinatti BEA; Medical School, University of Ninth of July (UNINOVE), Bauru, SP, Brazil., Wolf IR; Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil., Cardoso AL; Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil., Ramos E; Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil., Rieder N; Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany., de Oliveira R; Department of Biostatistics, Plant Biology, Parasitology and Zoology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil., Martins C; Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil. cesar.martins@unesp.br.
Jazyk: angličtina
Zdroj: BMC genomics [BMC Genomics] 2021 May 12; Vol. 22 (1), pp. 344. Date of Electronic Publication: 2021 May 12.
DOI: 10.1186/s12864-021-07651-w
Abstrakt: Background: B chromosomes (Bs) are extra elements observed in diverse eukaryotes, including animals, plants and fungi. Although Bs were first identified a century ago and have been studied in hundreds of species, their biology is still enigmatic. Recent advances in omics and big data technologies are revolutionizing the B biology field. These advances allow analyses of DNA, RNA, proteins and the construction of interactive networks for understanding the B composition and behavior in the cell. Several genes have been detected on the B chromosomes, although the interaction of B sequences and the normal genome remains poorly understood.
Results: We identified 727 miRNA precursors in the A. latifasciata genome, 66% which were novel predicted sequences that had not been identified before. We were able to report the A. latifasciata-specific miRNAs and common miRNAs identified in other fish species. For the samples carrying the B chromosome (B + ), we identified 104 differentially expressed (DE) miRNAs that are down or upregulated compared to samples without B chromosome (B - ) (p < 0.05). These miRNAs share common targets in the brain, muscle and gonads. These targets were used to construct a protein-protein-miRNA network showing the high interaction between the targets of differentially expressed miRNAs in the B + chromosome samples. Among the DE-miRNA targets there are protein-coding genes reported for the B chromosome that are present in the protein-protein-miRNA network. Additionally, Gene Ontology (GO) terms related to nuclear matrix organization and response to stimulus are exclusive to DE miRNA targets of B + samples.
Conclusions: This study is the first to report the connection of B chromosomes and miRNAs in a vertebrate species. We observed that the B chromosome impacts the miRNAs expression in several tissues and these miRNAs target several mRNAs involved with important biological processes.
Databáze: MEDLINE
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