The hnRNP Q-like gene is retroinserted into the B chromosomes of the cichlid fish Astatotilapia latifasciata

Abstract

B chromosomes are dispensable elements observed in many eukaryotic species, including the African cichlid Astatotilapia latifasciata, which might have one or two B chromosomes. Although there have been many studies focused on the biology of these chromosomes, questions about the evolution, maintenance, and potential effects of these chromosomes remain. Here, we identified a variant form of the hnRNP Q-like gene inserted into the B chromosome of A. latifasciata that is characterized by a high copy number and intron-less structure. The absence of introns and presence of transposable elements with a reverse transcriptase domain flanking hnRNP Q-like sequences suggest that this gene was retroinserted into the B chromosome. RNA-Seq analysis did not show that the B variant retroinserted copies are transcriptionally active. However, RT-qPCR results showed variations in the canonical hnRNP Q-like copy expression levels among exons, tissues, sex, and B presence/absence. Although the patterns of transcription are not well understood, the exons of the B retrocopies were overexpressed, and a bias for female B+ expression was also observed. These results suggest that retroinsertion is an additional and important mechanism contributing to B chromosome formation. Furthermore, these findings indicate a bias towards female differential expression of B chromosome sequences, suggesting that B chromosomes and sex determination are somehow associated in cichlids.

Epigenetic DNA Modifications Are Correlated With B Chromosomes and Sex in the Cichlid Astatotilapia latifasciata

“…The B chromosome presence was correlated with global reduction of 5mC in ovaries of FB+ and reduction of 5hmC in muscle of MB+. Association of sex and B chromosomes has already been reported for A. latifasciata , as in the transcriptional variation of the non-coding BncRNA (Ramos et al, 2017) and the hnRNP Q-like gene (Carmello et al, 2017). Furthermore, the sex–B chromosome association has long been described in many species as diverse as fish and invertebrates (Camacho et al, 2011).…”

“…The results of the global quantification of 5mC and 5hmC, mRNA and miRNA transcription were analyzed as in Carmello et al (2017) and Ramos et al (2017) using a generalized linear model (GLM) statistical approach with averages adjusted by the asymmetric gamma distribution of all the variables, implemented in SAS version 9.3, procedure GENMOD, followed by Bonferroni’s post hoc test. Associations of 5mC level and BncRNA expression were determined by Pearson’s correlation.…”

“…Expansion of several transposable elements in the B chromosome was found (Coan and Martins, 2018). The B chromosome carries potentially duplicated protein-coding genes (Valente et al, 2014) and retro-inserted hnRNP Q-like genes (Carmello et al, 2017). To the best of our knowledge, the B chromosome presence seems to impact the transcription levels of several classes of RNA, thereby influencing cellular function (Carmello et al, 2017; Ramos et al, 2017; Valente et al, 2017; Coan and Martins, 2018).…”

“…Considering that B chromosomes of A. latifasciata are the source of several classes of RNAs (Valente et al, 2014, 2017; Carmello et al, 2017; Ramos et al, 2017; Coan and Martins, 2018), it is possible these chromosomal elements regulate DNA modification genes in several ways and promote epigenetic effects on a DNA level. Therefore, to understand if the B chromosome promotes epigenetic DNA modifications in the host cells, we analyzed the DNA modification status of this chromosome and its effects on the routes of DNA methylation and demethylation.…”

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

“…A proto-B chromosome can emerge from chromosomal rearrangements, partial duplication of A chromosomes (normal chromosomes of the karyotype) or nonmeiotic disjunction [ 5 ]. This new element increases its genomic content by insertion of A chromosome sequences copies, including various repetitive DNA classes [ 7 – 9 ], protein-coding genes [ 2 , 10 – 13 ], pseudogenes [ 14 ], retrogenes [ 15 ], organellar DNA sequences [ 16 ] and noncoding sequences [ 17 – 20 ]. Duplicated sequences in B chromosomes have been proposed to facilitate its permanence in the host genome.…”