Systematic analysis of long intergenic non-coding RNAs in C. elegans germline uncovers roles in somatic growth

Male-specific roles of lincRNA in C. elegans fertility

The testis is the mammalian tissue with the highest expression levels of long intergenic non-coding RNAs (lincRNAs). However, most in vivo models have not found significant reductions in male fertility when highly expressed lincRNA genes were removed. This suggests that certain lincRNAs may act redundantly or lack functional roles. In the genome of the nematode Caenorhabditis elegans, there is an order of magnitude fewer lincRNA genes than in mammals. This characteristic lowers the potential for redundancy, making it an ideal model to test these possibilities. We identified five highly and dynamically expressed lincRNAs in male C. elegans gonads and quantified the fertility of worm strains in which these genes were removed. In contrast to the hermaphrodites of deletion strains, which exhibited no significant reductions in broods, smaller brood sizes were observed in the progeny of males of three of the lincRNA deleted strains. This demonstrates reduced male fertility in worms with those genes removed. Interestingly, reduced brood size was statistically significant only in the last days of egg laying in two of these strains. This suggests the effect is due to early deterioration and aging of the transferred sperm. We detected a mild increase in embryonic lethality in only one of the strains, supporting the possibility that these lincRNAs do not affect fertility through critical roles in essential meiotic processes. Together our results indicate a sexually dimorphic outcome on fertility when lincRNA are removed and show that, unlike mammals, individual lincRNAs in C. elegans do play significant roles in male fertility.

lncRNAs in fertility: redefining the gene expression paradigm?

Comparative transcriptome approaches assume that highly or dynamically expressed genes are important. This has led to the identification of many genes critical for cellular activity and organism development. However, while testes express the highest levels of long noncoding RNAs (lncRNAs), there is scarcely any evidence for lncRNAs with significant roles in fertility. This was explained by changes in chromatin structure during spermatogenesis that lead to 'promiscuous transcription' with no functional roles for the transcripts. Recent discoveries offer novel and surprising alternatives. Here, I review the current knowledge regarding the involvement of lncRNAs in fertility, why I find gametogenesis different from other developmental processes, offer models to explain why the experimental evidence did not meet theoretical predictions, and suggest possible approaches to test the models.

linc-20 and linc-9 do not have compensatory fertility roles in C. elegans

Long intergenic non-coding RNAs (lincRNAs) are transcripts longer than 200 nucleotides which are transcribed from regions that do not overlap with protein coding sequences. Reproductive organs express high levels of lincRNAs, yet removal of many lincRNA genes with high and dynamic germline expression did not lead to fertility defects. It was previously suggested this stems from redundant roles of different lincRNA genes. We previously reported engineering C. elegans strains in which we deleted lincRNA genes with high and dynamic expression in the gonad. The individual mutations did not lead to major effects on fertility. Two of those lincRNA genes, linc-9 and linc-20, are highly homologous, suggesting they could perform redundant roles. Here we report that in the double mutant linc-9; linc-20 the brood size and embryonic lethality do not significantly differ from wild-type worms. This could be explained by either lack of fertility roles, or redundancy with other lincRNA genes.

Bisection of the X chromosome disrupts the initiation of chromosome silencing during meiosis in Caenorhabditis elegans

During meiosis, gene expression is silenced in aberrantly unsynapsed chromatin and in heterogametic sex chromosomes. Initiation of sex chromosome silencing is disrupted in meiocytes with sex chromosome-autosome translocations. To determine whether this is due to aberrant synapsis or loss of continuity of sex chromosomes, we engineered Caenorhabditis elegans nematodes with non-translocated, bisected X chromosomes. In early meiocytes of mutant males and hermaphrodites, X segments are enriched with euchromatin assembly markers and active RNA polymerase II staining, indicating active transcription. Analysis of RNA-seq data showed that genes from the X chromosome are upregulated in gonads of mutant worms. Contrary to previous models, which predicted that any unsynapsed chromatin is silenced during meiosis, our data indicate that unsynapsed X segments are transcribed. Therefore, our results suggest that sex chromosome chromatin has a unique character that facilitates its meiotic expression when its continuity is lost, regardless of whether or not it is synapsed.