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

Abstract

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.

First characterization of PIWI-interacting RNA clusters in a cichlid fish with a B chromosome

“…The sRNA-seq libraries of gonads from FB− (female without the B chromosome), FB+ (female with the B chromosome), MB− (male without the B chromosome), and MB+ (male with the B chromosome) A. latifasciata were filtered by size to characterize piRNAs and compare them with miRNAs from A. latifasciata [ 20 ], highlighting the two different length distributions in each type of small RNA dataset (Fig. 1 a).…”

“…While piRNAs are located in repetitive regions, miRNAs are close to euchromatin in gene-rich regions, and we expected to find piRNA clusters that were not superposed on miRNAs. The contigs that carried the expressed piRNAs predicted in each sample (FB−, FB+, MB−, MB+) and the annotated miRNA genes [ 20 ] were included in a Venn diagram, showing the number of contigs that carried either piRNAs or miRNAs. The A. latifasciata genome carried 941 contigs according to sRNA annotation (piRNA or miRNA); of these, 569 contigs carried miRNA genes, while 372 carried piRNA clusters (Fig.…”

“…For piRNA and miRNA predictions, we used the same sRNA-seq libraries, which is why the analysis considered several specific characteristics of each molecule. In the case of miRNA, the steps adopted were as described in [ 20 ], and in addition to the putative miRNAs from the sRNA-seq alignment to the reference genome, the secondary structures of the miRNA genes (hairpins) were considered. Here, as detailed in the results, the putative piRNAs from sRNA-seq were filtered based on several piRNA characteristics done in cluster prediction.…”

“…Additionally, in rye, RNA slicer activity for an Argonaute-like B chromosome copy has been observed in vitro [ 10 ], and some B chromosome peptides have been identified by mass spectrometry [ 19 ]. Furthermore, several studies have shown that B chromosomes can affect the expression of A complement sequences [ 14 , 20 ] or affect various biological processes in the cell [ 21 ].…”

“…How the B chromosome and its excess TEs affect piRNAs or vice versa has not yet been investigated. Few studies have examined the relationship between the B chromosome and small RNAs, and most of them have been related to microRNAs [ 14 , 15 , 20 ]. Thus, this study was designed to investigate the relationship of piRNAs and B chromosomes by examining the African cichlid fish species Astatotilapia latifasciata as a model organism.…”