A novel ncRNA gene from mouse chromosome 5 trans-splices with Dmrt1 on chromosome 19

Zhang, Lei; Lu, Hailiang; Xin, Dazhuan; Cheng, Hanhua; Zhou, Rongjia

doi:10.1016/j.bbrc.2010.08.130

Cited by 49 publications

(33 citation statements)

References 25 publications

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“…A newly defined conserved ncRNA gene Dmr (Dmrt1-related gene) in rodents was demonstrated to trans-splice with DMRT1 (Doublesex-related transcription factor) recently. Dmr was demonstrated to serve mainly as a 3′ UTR, which promotes trans-splicing to produce a novel chimeric transcript (Dmr-Dmrt1), down-regulating the Dmrt1 protein expression [58]. DMRT1, which was reported to function in coordinating spermatogonial development and mitotic amplification with meiosis, is considered as an important gene involved in spermatogenesis.…”

Section: Discussionmentioning

confidence: 99%

Identification and Characterization of a Novel Non-Coding RNA Involved in Sperm Maturation

Ni¹,

Hu²,

Liu³

et al. 2011

PLoS ONE

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A long and ever-expanding roster of small (∼20–30 nucleotides) RNAs has emerged during the last decade, and most can be subsumed under the three main headings of microRNAs(miRNAs), Piwi-interacting RNAs(piRNAs), and short interferingRNAs(siRNAs). Among the three categories, miRNAs is the most quickly expanded group. The most recent number of identified miRNAs is 16,772 (Sanger miRbase, April 2011). However, there are insufficient publications on their primary forms, and no tissue-specific small RNAs precursors have been reported in the epididymis. Here, we report the identification in rats of an epididymis-specific, chimeric, noncoding RNA that is spliced from two different chromosomes (chromosomes 5 and 19), which we named HongrES2. HongrES2 is a 1.6 kb mRNA-like precursor that gives rise to a new microRNA-like small RNA (mil-HongrES2) in rat epididymis. The generation of mil-HongrES2 is stimulated during epididymitis. An epididymis-specific carboxylesterase named CES7 had 100% cDNA sequence homology at the 3′end with HongrES2 and its protein product could be downregulated by HongrES2 via mil-HongrES2. This was confirmed in vivo by initiating mil-HongrES2 over-expression in rats and observing an effect on sperm capacitation.

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Section: Discussionmentioning

confidence: 99%

Identification and Characterization of a Novel Non-Coding RNA Involved in Sperm Maturation

Ni¹,

Hu²,

Liu³

et al. 2011

PLoS ONE

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“…The roles of lncRNAs can be reflected by their targets. We predicted protein-coding genes that were 10 K/100 K upstream and downstream of the lncRNAs as potential targets (Hu, Zhang, & Liang, 2016;Ni et al, 2011;Nishant, Ravishankar, & Rao, 2004;Wang & Chang, 2011;Zhang, Lu, Xin, Cheng, & Zhou, 2010). In order to analyse the functions of lncRNA in pathways, we performed the GO and KEGG analysis of lncRNAs target genes.…”

Section: Go and Kegg Analysismentioning

confidence: 99%

The interaction between DNA methylation and long non‐coding RNA during the onset of puberty in goats

Yang

Gao

et al. 2018

Reprod Domestic Animals

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Epigenetics plays an important role in controlling female puberty. Both DNA methylation and long non-coding RNAs (lncRNA) regulate the initiation of puberty by affecting the expression of genes related to puberty. While recent studies have indicated that DNA methylation of lncRNA represses the expression of lncRNA, its role in regulating puberty remains unclear. To explore the mechanism between DNA methylation and lncRNAs during puberty onset, we performed whole-genome bisulphite sequencing (WGBS) and RNA-sequencing (RNA-seq). We found that DNA methylation was inversely correlated to gene expression levels during puberty. Methylation levels gradually decreased near the transcription initiation site and were present at high levels in the exon, intron and 3' untranslated regions. In the promoter, lncRNA expression was negatively related to DNA methylation. We reported hypermethylation in the gene body and downstream of the lncRNA compared with upstream regions. In GO and KEGG analyses, we found enriched target genes of lncRNA, XLOC_960044 and XLOC_767346. During puberty, methylation of these genes increased while expression decreased. Our study indicates that DNA methylation of the promoter is negatively correlated with lncRNA during puberty onset, and methylation regulates the initiation of puberty via lncRNA, which provides new insight into the epigenetic mechanism of puberty onset.

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“…Some mitochondria and chloroplasts of low eukaryotes and plants also use trans -splicing to remove discontinuous group II introns [36,37]. Chimeric RNAs have been reported to occur in human cells and in cells of other animals in a physiological situation [5,38,39,40,41,42,43], with examples such as the KLK4 [44], Acy1-CoA and ACAT1 [45,46] RNAs in humans, the Dmr [47] and Msh4 mRNA variants [48] in mice, as well as some mdg4 mRNA variants in drosophila [49,50]. The IGH-BCL2 RNA chimera has been observed in normal spleen [51], whereas IGH-myc chimeric RNA has been found in mouse B lymphocytes [52] and in the Peyer’s patch follicles [53].…”

Section: Currently Chimeric Rnas Are Thought To Be Derived From Tmentioning

confidence: 99%

It Is Imperative to Establish a Pellucid Definition of Chimeric RNA and to Clear Up a Lot of Confusion in the Relevant Research

Yuan

Zellmer

Yang

et al. 2017

IJMS

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There have been tens of thousands of RNAs deposited in different databases that contain sequences of two genes and are coined chimeric RNAs, or chimeras. However, “chimeric RNA” has never been lucidly defined, partly because “gene” itself is still ill-defined and because the means of production for many RNAs is unclear. Since the number of putative chimeras is soaring, it is imperative to establish a pellucid definition for it, in order to differentiate chimeras from regular RNAs. Otherwise, not only will chimeric RNA studies be misled but also characterization of fusion genes and unannotated genes will be hindered. We propose that only those RNAs that are formed by joining two RNA transcripts together without a fusion gene as a genomic basis should be regarded as authentic chimeras, whereas those RNAs transcribed as, and cis-spliced from, single transcripts should not be deemed as chimeras. Many RNAs containing sequences of two neighboring genes may be transcribed via a readthrough mechanism, and thus are actually RNAs of unannotated genes or RNA variants of known genes, but not chimeras. In today’s chimeric RNA research, there are still several key flaws, technical constraints and understudied tasks, which are also described in this perspective essay.

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A novel ncRNA gene from mouse chromosome 5 trans-splices with Dmrt1 on chromosome 19

Cited by 49 publications

References 25 publications

Identification and Characterization of a Novel Non-Coding RNA Involved in Sperm Maturation

Identification and Characterization of a Novel Non-Coding RNA Involved in Sperm Maturation

The interaction between DNA methylation and long non‐coding RNA during the onset of puberty in goats

It Is Imperative to Establish a Pellucid Definition of Chimeric RNA and to Clear Up a Lot of Confusion in the Relevant Research

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