Systematic Analysis of Long Non-Coding RNAs and mRNAs in the Ovaries of Duroc Pigs During Different Follicular Stages Using RNA Sequencing

Liu, Yi; Li, Mengxun; Bo, Xiaochen; Li, Tao; Ma, Ligeng; Zhai, Tenjiao; Huang, Tao

doi:10.3390/ijms19061722

Cited by 35 publications

(40 citation statements)

References 42 publications

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“…In the present study, we used the pig genome assembly (Sscrofa 10.2) to analyze the expression pro les of each sample, which is consistent with other published studies [30-32, 38, and 39]. Based on comparative analysis, we found that the number of lncRNAs (n = 24,447) detected in this study was much higher than that reported in the study by Liu et al (n = 2076) [30]; however, the number was much lower compared to that of human lnRNAs reported in LNCipedia 4.1 [37]. We also observed that the lncRNAs identi ed in ovarian tissues have fewer exons, lower expression levels, and shorter ORFs than those of the protein-coding genes (Fig.…”

Section: Discussionsupporting

confidence: 88%

“…lncRNAs expression pro les in ovarian tissues at different stages of follicle development in pigs were rst investigated using RNA sequencing analysis by Liu et al (2018) [30]. In the present study, we used the pig genome assembly (Sscrofa 10.2) to analyze the expression pro les of each sample, which is consistent with other published studies [30-32, 38, and 39].…”

Section: Discussionsupporting

confidence: 75%

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Integrated Analysis of lncRNA, miRNA and mRNA Reveals Novel Insights into the Fertility Regulation of Large White Sows

Jia²,

et al. 2020

Preprint

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Background: Improving sow fertility is extremely important as it can lead to increased reproductive efficiency and thus profitability for swine producers. There are considerable differences in fertility rates among individual animals, but the underlying molecular mechanisms remain unclear. In this study, by using different types of RNA libraries, we investigated the complete transcriptome of ovarian tissue during the luteal (L) and follicular (F) phases of the estrous cycle in Large White pigs with high (H) and low (L) fecundity, and performed a comprehensive analysis of long noncoding RNAs (lncRNAs), mRNAs and micro RNAs (miRNAs) from 16 samples by combining RNA sequencing (RNA-seq) with bioinformatics.Results: In total, 24,447 lncRNAs, 27,370 mRNAs, and 216 known miRNAs were identified in ovarian tissues. The genomic features of lncRNAs, such as length distribution and number of exons, were further analyzed. We selected a threshold of P <0.05 and |log2 (fold change)| ≥ 1 to obtain the differentially expressed lncRNAs, miRNAs and mRNAs by pairwise comparison (LH vs. LL, FH vs. FL). Bioinformatics analysis of these differentially expressed RNAs revealed multiple significantly enriched pathways (P <0.05) that were closely involved in the reproductive process, such as ovarian steroidogenesis, lysosome, steroid biosynthesis, and the estrogen and GnRH signaling pathways. Moreover, bioinformatics screening of differentially expressed miRNAs that share common miRNA response elements (MREs) with lncRNAs and their downstream mRNA targets were performed. Finally, we constructed lncRNA–miRNA–mRNA regulation networks. The key genes in these networks were verified by Reverse Transcription Real-time Quantitative PCR (RT-qRCR), which were consistent with the results from RNA-Seq data.Conclusions: These results provide further insights into the fertility of pigs andcan contribute to further experimental investigation of the functions of these genes.

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Section: Discussionsupporting

confidence: 88%

Section: Discussionsupporting

confidence: 75%

Integrated Analysis of lncRNA, miRNA and mRNA Reveals Novel Insights into the Fertility Regulation of Large White Sows

Jia²,

et al. 2020

Preprint

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“…Whereas the annotated lncRNAs were in the range of 204-4691 nt in length (consistent with GENCODE [26]), the putative novel lncRNA contigs were all below 400 nt in length. This is consistent with previous RNA-seqbased lncRNA studies which have tended to produce shorter contigs (less than 400 nt) even with genomeguided assembly [27,28].…”

Section: Length and Secondary Structure Characterization Of Known Andsupporting

confidence: 91%

Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis

et al. 2020

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Background: Long noncoding RNAs (lncRNAs) have roles in gene regulation, epigenetics, and molecular scaffolding and it is hypothesized that they underlie some mammalian evolutionary adaptations. However, for many mammalian species, the absence of a genome assembly precludes the comprehensive identification of lncRNAs. The genome of the American beaver (Castor canadensis) has recently been sequenced, setting the stage for the systematic identification of beaver lncRNAs and the characterization of their expression in various tissues. The objective of this study was to discover and profile polyadenylated lncRNAs in the beaver using high-throughput short-read sequencing of RNA from sixteen beaver tissues and to annotate the resulting lncRNAs based on their potential for orthology with known lncRNAs in other species. Results: Using de novo transcriptome assembly, we found 9528 potential lncRNA contigs and 187 high-confidence lncRNA contigs. Of the high-confidence lncRNA contigs, 147 have no known orthologs (and thus are putative novel lncRNAs) and 40 have mammalian orthologs. The novel lncRNAs mapped to the Oregon State University (OSU) reference beaver genome with greater than 90% sequence identity. While the novel lncRNAs were on average shorter than their annotated counterparts, they were similar to the annotated lncRNAs in terms of the relationships between contig length and minimum free energy (MFE) and between coverage and contig length. We identified beaver orthologs of known lncRNAs such as XIST, MEG3, TINCR, and NIPBL-DT. We profiled the expression of the 187 high-confidence lncRNAs across 16 beaver tissues (whole blood, brain, lung, liver, heart, stomach, intestine, skeletal muscle, kidney, spleen, ovary, placenta, castor gland, tail, toe-webbing, and tongue) and identified both tissuespecific and ubiquitous lncRNAs. Conclusions: To our knowledge this is the first report of systematic identification of lncRNAs and their expression atlas in beaver. LncRNAs-both novel and those with known orthologs-are expressed in each of the beaver tissues that we analyzed. For some beaver lncRNAs with known orthologs, the tissue-specific expression patterns were phylogenetically conserved. The lncRNA sequence data files and raw sequence files are available via the web supplement and the NCBI Sequence Read Archive, respectively.

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“…Fortunately, many studies have been performed to find their associated up/downstream mRNAs and antisense mRNAs related to lncRNAs. Functional annotation and enrichment are considered an effective way to reveal the biological significance and biological processes or functions of most enriched genes [28][29][30]. In this study, based on these basic principles, 2046 genes were scanned as apcGenes and antisense mRNAs for 883 lncRNAs, combined with the differentially expressed lncRNA, mRNAs and predicted pre-miRNA, as well as their interaction, and 1478 genes were detected and further served for GO enrichment and KEGG pathway analyses.…”

Section: Discussionmentioning

confidence: 99%

Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats

Chao

Liu

et al. 2020

BMC Genomics

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Background: The mammary gland is a unique organ for milk synthesis, secretion and storage, and it undergoes cyclical processes of development, differentiation, lactation and degeneration. At different developmental periods, the biological processes governing mammary gland physiology and internal environmental homeostasis depend on a complex network of genes and regulatory factors. Emerging evidence indicates that lncRNAs have arbitrarily critical functions in regulating gene expression in many organisms; however, the systematic characteristics, expression, and regulatory roles of lncRNAs in the mammary gland tissues of dairy goats have not been determined. Result: In the present study, we profiled long noncoding RNA (lncRNA) expression in the mammary gland tissues of Laoshan dairy goats (Capra hircus) from different lactation periods at the whole-genome level, to identify, characterize and explore the regulatory functions of lncRNAs. A total of 37,249 transcripts were obtained, of which 2381 lncRNAs and 37,249 mRNAs were identified, 22,488 transcripts, including 800 noncoding transcripts and 21,688 coding transcripts, differed significantly (p ≤ 0.01) among the different lactation stages. The results of lncRNA-RNA interaction analysis showed that six known lncRNAs belonging to four families were identified as the precursors of 67 known microRNAs; 1478 and 573 mRNAs were predicted as hypothetical cis-regulation elements and antisense mRNAs, respectively. GO annotation and KEGG analysis indicated that the coexpressed mRNAs were largely enriched in biological processes related to such activities as metabolism, immune activation, and stress,., and most genes were involved in pathways related to such phenomena as inflammation, cancer, signal transduction, and metabolism. Conclusions: Our results clearly indicated that lncRNAs involved in responses to stimuli, multiorganism processes, development, reproductive processes and growth, are closely related to mammary gland development and lactation.

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Systematic Analysis of Long Non-Coding RNAs and mRNAs in the Ovaries of Duroc Pigs During Different Follicular Stages Using RNA Sequencing

Cited by 35 publications

References 42 publications

Integrated Analysis of lncRNA, miRNA and mRNA Reveals Novel Insights into the Fertility Regulation of Large White Sows

Integrated Analysis of lncRNA, miRNA and mRNA Reveals Novel Insights into the Fertility Regulation of Large White Sows

Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis

Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats

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