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

Ishtayeh, Hasan; Achache, Hanna; Kroizer, Eitan; Rappaport, Yisrael; Itskovits, Eyal; Gingold, Hila; Best, Corinne; Rechavi, Oded; Tzur, Yonatan B

doi:10.1080/15476286.2020.1814549

Cited by 5 publications

(28 citation statements)

References 98 publications

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“…Similarly, a strain we engineered with full deletion of linc-20 had normal brood size and levels of embryonic lethality (Fig. S7c, d ) as previously reported 50 . These results suggest that the meiotic defects in YBT7 are not the result of the loss-of-function of either deg-1 or linc-20 .…”

Section: Resultssupporting

confidence: 72%

“…We identified a 2.2-kb region (X:16508962-16511217) on the right side of the X chromosome encompassing the noncoding gene linc-20 , which is homologous (>92% identity) to a region near the center of the X chromosome (X:7769295-7771552) within the 14th intron (i14) of deg-1 . Neither of these genes have previously been associated with germline roles 48 – 50 . As previously described 51 , 52 , we directed Cas9 to these loci with four guide RNAs (gRNAs) to create multiple breaks.…”

Section: Resultsmentioning

confidence: 99%

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

et al. 2021

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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.

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Section: Resultssupporting

confidence: 72%

Section: Resultsmentioning

confidence: 99%

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

et al. 2021

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“…We used the RNAseq datasets of male gonad sections published in (Tzur et al, 2018) to find the expression patterns of these lincRNAs in males. We found that five lincRNAs (linc-4, linc-7, linc-9, linc-20, and linc168) which were found to be redundant for hermaphrodite fertility (Ishtayeh et al, 2021)…”

Section: Analysis Of Lincrna Gene Expressionmentioning

confidence: 88%

“…Previous reports identified genes that play a role in male, but not hermaphrodite, spermatogenesis [e.g., (Stanfield and Villeneuve, 2006)]. To find lincRNA genes with fertility roles only in males we focused on lincRNAs found to be redundant for hermaphrodite fertility (Ishtayeh et al, 2021) and have significant and dynamic expression in the male gonad (see Methods).…”

Section: Analysis Of Lincrna Gene Expressionmentioning

confidence: 99%

“…RNASeq analysis allowed us to quantitatively compare gene expression between the two gametogenesis processes and between different stages within oogenesis or spermatogenesis. To assess the roles of lincRNAs in oogenesis, we previously used these databases and found lincRNAs that are highly and dynamically expressed in the hermaphrodite gonad ( Ishtayeh et al, 2021 ). We engineered full genomic homozygous deletion strains for these lincRNA genes, thus preventing expression of any part of the gene (( Ishtayeh et al, 2021 ) and Methods).…”

Section: Introductionmentioning

confidence: 99%

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Male-specific roles of lincRNA in C. elegans fertility

Shabtai

Tzur

2023

Front. Cell Dev. Biol.

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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.

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lncRNAs in fertility: redefining the gene expression paradigm?

Tzur¹

2022

Trends in Genetics

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

Cited by 5 publications

References 98 publications

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

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

Male-specific roles of lincRNA in C. elegans fertility

lncRNAs in fertility: redefining the gene expression paradigm?

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