Profiling of testis-specific long noncoding RNAs in mice

Hong, Seong Hyeon; Kwon, Jun Tae; Kim, Jihye; Jeong, Ji Won; Kim, Jaehwan; Lee, Seonhee; Cho, Chunghee

doi:10.1186/s12864-018-4931-3

Cited by 62 publications

(56 citation statements)

References 47 publications

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“…3D). This is not unexpected, as these have been reported to be the two most highly represented categories among lncRNAs in general [17], and particularly in testis as well [29,35,38]. However, the proportion of AS lncRNAs overlapping protein-coding genes in our lists was surprisingly high in relation to the small proportion of the genome occupied by protein-coding genes (see Fig.…”

Section: Characterization Of Lncrnas In the Different Testicular Cellsupporting

confidence: 61%

“…An increasing number of studies have shown that lincRNAs can affect the expression of their neighbouring protein-coding genes or other target genes by acting through different mechanisms, either in cis or in trans [27,46,47]. Thus, in order to identify possible functional relations, different studies have correlated lincRNAs with neighbour mRNA loci located at varying distances such as <300 Kb [47], <100 Kb [48,49], <30 Kb [35], or <10 Kb [29], depending on the study.…”

Section: Co-expression Of Lncrnas With Overlapping and Neighbouring Cmentioning

confidence: 99%

“…Different reports coincide with the fact that the testes express the largest numbers of lncRNAs among different tissues [10,17,20,21,29]. A number of studies have addressed the characterization of testicular lncRNAs in different mammalian species, disclosing that they tend to share the general traits described for lncRNAs [30][31][32], and revealing that at least some testicular lncRNAs are functional during spermatogenesis [33,34].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Revealing stage-specific expression patterns of long noncoding RNAs along mouse spermatogenesis

et al. 2019

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The discovery of a large number of long noncoding RNAs (lncRNAs), and the finding that they may play key roles in different biological processes, have started to provide a new perspective in the understanding of gene regulation. It has been shown that the testes express the highest amount of lncRNAs among different vertebrate tissues. However, although some studies have addressed the characterization of lncRNAs along spermatogenesis, an exhaustive analysis of the differential expression of lncRNAs at its different stages is still lacking. Here, we present the results for lncRNA transcriptome profiling along mouse spermatogenesis, employing highly pure flow sorted spermatogenic stage-specific cell populations, strand-specific RNAseq, and a combination of up-to-date bioinformatic pipelines for analysis. We found that the vast majority of testicular lncRNA genes are expressed at post-meiotic stages (i.e. spermiogenesis), which are characterized by extensive post-transcriptional regulation. LncRNAs at different spermatogenic stages shared common traits in terms of transcript length, exon number, and biotypes. Most lncRNAs were lincRNAs, followed by a high representation of antisense (AS) lncRNAs. Co-expression analyses showed a high correlation along the different spermatogenic stage transitions between the expression patterns of AS lncRNAs and their overlapping protein-coding genes, raising possible clues about lncRNA-related regulatory mechanisms. Interestingly, we observed the colocalization of an AS lncRNA and its host sense mRNA in the chromatoid body, a round spermatidsspecific organelle that has been proposed as a reservoir of RNA-related regulatory machinery. An additional, intriguing observation is the almost complete lack of detectable expression for Y-linked testicular lncRNAs, despite that a high number of lncRNA genes are annotated for this chromosome.

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Section: Characterization Of Lncrnas In the Different Testicular Cellsupporting

confidence: 61%

Section: Co-expression Of Lncrnas With Overlapping and Neighbouring Cmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Revealing stage-specific expression patterns of long noncoding RNAs along mouse spermatogenesis

et al. 2019

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“…Previous studies have shown that lincRNAs can regulate gene expression in certain ways, including cis and trans [34,35]. Hong and Kwon used genomic analysis to identify protein-coding genes near (≤ 10 kb) testis-specific lincRNAs to predict the functions of lincRNAs [36]. Zhang and Chen predicted 1061 cis-regulated and 782 trans-regulated targets of DE lincRNAs in their study to explore the DE lincRNAs functions [37].…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Analysis Reveals Long Intergenic Non-Coding RNAs Contributed to Intramuscular Fat Content Differences between Yorkshire and Wei Pigs

Huang

Zhao

et al. 2020

IJMS

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Intramuscular fat (IMF) content is closely related to various meat traits, such as tenderness, juiciness, and flavor. The IMF content varies considerably among pig breeds with different genetic backgrounds. Long intergenic non-coding RNAs (lincRNAs) have been widely identified in many species and found to be an important class of regulators that can participate in multiple biological processes. However, the mechanism behind lincRNAs regulation of pig IMF content remains unknown and requires further study. In our study, we identified a total of 156 lincRNAs in the longissimus dorsi muscle of Wei (fat-type) and Yorkshire (lean-type) pigs using previously published data. These identified lincRNAs have shorter transcript length, longer exon length, lower exon number, and lower expression level as compared with protein-coding transcripts. We predicted potential target genes (PTGs) that are potentially regulated by lincRNAs in cis or trans regulation. Gene ontology and pathway analyses indicated that many potential lincRNAs target genes are involved in IMF-related processes or pathways, such as fatty acid catabolic process and adipocytokine signaling pathway. In addition, we analyzed quantitative trait locus (QTL) sites that differentially expressed lincRNAs (DE lincRNAs) between Wei and Yorkshire pigs co-localized. The QTL sites where DE lincRNAs co-localize are mostly related to IMF content. Furthermore, we constructed a co-expressed network between DE lincRNAs and their differentially expressed PTGs (DEPTGs). On the basis of their expression levels, we suggest that many DE lincRNAs can affect IMF development by positively or negatively regulating their PTGs. This study identified and analyzed some lincRNAs- and PTGs-related IMF development of the two pig breeds and provided new insight into research on the roles of lincRNAs in the two types of breeds.

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“…For ncRNAs to have an effect across generations, they must be physically transferred from the parents to the offspring via the germline. A large body of evidence demonstrates that male germ cells at mitotic, meiotic and post-meiotic stages and female gametes stably express thousands of ncRNAs [109][110][111]. An earlier RNA profiling study of human sperm led the authors to conclude that the male gamete is not only a vector of DNA but also appears to contribute to the initial transcriptome of the fertilized egg [112,113].…”

Section: Epigenetic Control Mediated By Short and Long Non-coding Rnasmentioning

confidence: 99%

Transgenerational Inheritance of Environmentally Induced Epigenetic Alterations during Mammalian Development

Legoff

D’Cruz

Tevosian

et al. 2019

Cells

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Genetic studies traditionally focus on DNA as the molecule that passes information on from parents to their offspring. Changes in the DNA code alter heritable information and can more or less severely affect the progeny’s phenotype. While the idea that information can be inherited between generations independently of the DNA’s nucleotide sequence is not new, the outcome of recent studies provides a mechanistic foundation for the concept. In this review, we attempt to summarize our current knowledge about the transgenerational inheritance of environmentally induced epigenetic changes. We focus primarily on studies using mice but refer to other species to illustrate salient points. Some studies support the notion that there is a somatic component within the phenomenon of epigenetic inheritance. However, here, we will mostly focus on gamete-based processes and the primary molecular mechanisms that are thought to contribute to epigenetic inheritance: DNA methylation, histone modifications, and non-coding RNAs. Most of the rodent studies published in the literature suggest that transgenerational epigenetic inheritance through gametes can be modulated by environmental factors. Modification and redistribution of chromatin proteins in gametes is one of the major routes for transmitting epigenetic information from parents to the offspring. Our recent studies provide additional specific cues for this concept and help better understand environmental exposure influences fitness and fidelity in the germline. In summary, environmental cues can induce parental alterations and affect the phenotypes of offspring through gametic epigenetic inheritance. Consequently, epigenetic factors and their heritability should be considered during disease risk assessment.

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Profiling of testis-specific long noncoding RNAs in mice

Cited by 62 publications

References 47 publications

Revealing stage-specific expression patterns of long noncoding RNAs along mouse spermatogenesis

Revealing stage-specific expression patterns of long noncoding RNAs along mouse spermatogenesis

Transcriptome Analysis Reveals Long Intergenic Non-Coding RNAs Contributed to Intramuscular Fat Content Differences between Yorkshire and Wei Pigs

Transgenerational Inheritance of Environmentally Induced Epigenetic Alterations during Mammalian Development

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