Transcriptome analysis to identify long non coding RNA (lncRNA) and characterize their functional role in back fat tissue of pig

Kumar, Himansu; Srikanth, Krishnamoorthy; Park, Woncheol; Lee, Jun Young; Choi, Bong Hwan; Kim, Hana; Kim, Yong Min; Cho, Eun Seok; Kim, Jin Hyoung; Lee, Jang Hee; Jung, Ji Yeon; Go, Gyungchoon; Lee, Kyung Tai; Kim, Jun Mo; Lee, Jungjae; Lim, Dajeong

doi:10.1016/j.gene.2019.04.014

Cited by 27 publications

(19 citation statements)

References 84 publications

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“…Long noncoding RNAs (lncRNAs) are longer than 200 nucleotides and are transcribed from DNA, but they do not code for proteins ( Cai et al, 2018 ; Liu et al, 2013 ). However, lncRNAs can regulate the expression of protein-coding genes at various levels, including epigenetic regulation ( Du et al, 2020 ; Wei et al, 2020 ), transcriptional regulation ( Fei et al, 2020 ; Lauer et al, 2020 ; Yin et al, 2019 ) and posttranscriptional regulation ( Mangum et al, 2020 ; Zhang et al., 2020a ; Zhang et al., 2020b ), thereby influencing various biological processes, such as cell growth, cycle, development and gamete formation; epigenetics; and implantation ( Kumar et al, 2019 ). Recent studies have reported the mechanisms of lncRNA in hair growth and development in cashmere goats and sheep.…”

Section: Introductionmentioning

confidence: 99%

Integrated analysis of lncRNA and mRNA reveals novel insights into cashmere fineness in Tibetan cashmere goats

Zhao

Tian

et al. 2020

PeerJ

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Tibetan cashmere goats are famous for producing the finest, softest and lightest cashmere fiber in China. The growth and development of skin are closely related to fineness and are the key factors affecting the quality of cashmere. To investigate the specific role of long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) in regulating cashmere fineness of Tibetan Cashmere goats in the anagen phase, we conducted high-throughput RNA sequencing of fine-type and coarse-type skin tissues. We identified 2,059 lncRNA candidates (1,589 lncRNAs annotated, 470 lncRNAs novel), and 80 differentially expressed (DE) lncRNAs and their potential targets were predicted. We also identified 384 DE messenger RNAs (mRNAs) out of 29,119 mRNAs. Several key genes in KRT26, KRT28, KRT39, IFT88, JAK3, NOTCH2 and NOTCH3 and a series of lncRNAs, including ENSCHIT00000009853, MSTRG.16794.17, MSTRG.17532.2, were shown to be potentially important for regulating cashmere fineness. GO and KEGG enrichment analyses of DE mRNAs and DE lncRNAs targets significantly enriched in positive regulation of the canonical Wnt signaling pathway, regulation of protein processing and metabolism processes. The mRNA-mRNA and lncRNA-mRNA regulatory networks further revealed potential transcripts involved in cashmere fineness. We further validated the expression patterns of DE mRNAs and DE lncRNAs by quantitative real-time PCR (qRT-PCR), and the results were consistent with the sequencing data. This study will shed new light on selective cashmere goat breeding, and these lncRNAs and mRNAs that were found to be enriched in Capra hircus RNA database.

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Section: Introductionmentioning

confidence: 99%

Integrated analysis of lncRNA and mRNA reveals novel insights into cashmere fineness in Tibetan cashmere goats

Zhao

Tian

et al. 2020

PeerJ

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“…With the advent of omics technologies, many genes and pathways regulating the metabolism of porcine adipocytes have been identified [17][18][19]. Recently, the regulatory role of long noncoding RNAs (lncRNAs) in porcine adipogenesis has been reported by several groups [20,21].…”

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confidence: 99%

Comparative analysis of gene expression profiles in differentiated subcutaneous adipocytes between Jiaxing Black and Large White Pigs

Zhang

Huang

et al. 2020

Preprint

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Background: Chinese domestic pig breeds are reputed for pork quality, but their low ratio of lean-to-fat carcass weight decreases production efficiency. A better understanding of the genetic regulation network of SC fat tissue is necessary for the rational selection of Chinese domestic pig breeds. In the present study, SC adipocytes were isolated from Jiaxing Black pigs (a Chinese indigenous pig breed with redundant SC fat deposition) and Large White pigs (a lean-type pig breed with relatively low SC fat deposition) and the expression profiles of mRNAs and lncRNAs were compared by RNA-seq analysis to identify biomarkers correlated with the differences of SC fat deposition between the two breeds.Results: A total of 3,371 differentially expressed genes (DEGs) and 1,182 differentially expressed lncRNAs (DELs) were identified in SC adipocytes between Jiaxing Black (JX) and Large White (LW) pigs, which included 797 upregulated mRNAs, 2,574 downregulated mRNAs, 461 upregulated lncRNAs and 721 downregulated lncRNAs. Gene Ontology and KEGG pathway analyses revealed that the DEGs and DELs were mainly involved in the immune response, cell fate determination, PI3K-Akt signaling pathway and MAPK signaling pathway, which are known to be related to adipogenesis and lipid metabolism. The expression levels of DEGs and DELs according to the RNA-seq data were verified by quantitative PCR, which showed 81.8% consistency. The differences in MAPK pathway activity between JX and LW pigs was confirmed by western blot analysis, with <100-fold elevated p38 phosphorylation in JX pigs.Conclusions: This study offers a detailed characterization of mRNAs and lncRNAs in fat- and lean-type pig breeds. The activity of the MAPK signaling pathway was found to be associated with subcutaneous adipogenesis. These results greatly enhance our understanding of the molecular mechanisms regulating SC fat deposition in pigs.

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“…To remove the possibility of getting housekeeping genes (including tRNA, rRNA, snRNAs, and snoRNAs etc. ), the transcripts were also cross-checked against the Rfam database (http://rfam.xfam.org/: using INFERNAL) and rRNA database (https:// www.arb-silva.de/; Kang & Liu, 2015, Kumar et al, 2019.…”

Section: Identification Of Long Non-coding Rnas and Their Annotationmentioning

confidence: 99%

Drought responsiveness in black pepper (Piper nigrum L.): Genes associated and development of a web‐genomic resource

Negi

Kokkat

Jasrotia

et al. 2020

Physiologia Plantarum

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Black pepper (Piper nigrum L.; 2n = 52; Piperaceae), the king of spices, is a perennial, trailing woody flowering vine and has global importance with widespread dietary, medicinal, and preservative uses. It is an economically important germplasm cultivated for its fruit and the major cash crop in >30 tropical countries. Crop production is mainly affected by drought stress. The present study deals with the candidate gene identification from drought-affected black pepper leaf transcriptome generated by Illumina Hiseq2000. It also aims to mine putative molecular markers (namely SSRs, SNPs, and InDels) and generate primers for them. The identification of transcription factors and pathways involved in drought tolerance is also reported here. De novo transcriptome assembly was performed with trinity assembler. In total, 4914 differential expressed genes, 2110 transcriptional factors, 786 domains and 1137 families, 20,124 putative SSR markers, and 259,236 variants were identified. At2g30105 (unidentified gene containing leucine-rich repeats and ubiquitin-like domain), serine threonine protein kinase, Mitogen-activated protein kinase, Nucleotide Binding Site-Leucine Rich Repeat, Myeloblastosis-related proteins, basic helix-loop-helix are all found upregulated and are reported to be associated with plant tolerance against drought condition. All these information are catalogued in the Black Pepper Drought Transcriptome Database (BPDRTDb), freely accessible for academic use at http:// webtom.cabgrid.res.in/bpdrtdb/. This database is a good foundation for the genetic improvement of pepper plants, breeding programmes, and mapping population of this crop. Putative markers can also be a reliable genomic resource to develop droughttolerant variety for better black pepper productivity.

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Transcriptome analysis to identify long non coding RNA (lncRNA) and characterize their functional role in back fat tissue of pig

Cited by 27 publications

References 84 publications

Integrated analysis of lncRNA and mRNA reveals novel insights into cashmere fineness in Tibetan cashmere goats

Integrated analysis of lncRNA and mRNA reveals novel insights into cashmere fineness in Tibetan cashmere goats

Comparative analysis of gene expression profiles in differentiated subcutaneous adipocytes between Jiaxing Black and Large White Pigs

Drought responsiveness in black pepper (Piper nigrum L.): Genes associated and development of a web‐genomic resource

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