Genome-wide identification and characterization of long non-coding RNAs expressed during sheep fetal and postnatal hair follicle development

Sulayman, Ablat; Tian, Kechuan; Huang, Xixia; Tian, Yuezhen; Xu, Xinming; Fu, Xuefeng; Zhao, Bi; Wu, Weiwei; Wang, Dan; Yasin, Aynur; Tulafu, Hanikezi

doi:10.1038/s41598-019-44600-w

Cited by 35 publications

(36 citation statements)

References 90 publications

(95 reference statements)

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“…The vast majority of putative lncRNAs were intronic or intergenic in our study, which confirmed that intragenic and intergenic regions were the major sources of non-coding RNAs (Mattick and Makunin 2006;Xu, Bai, et al 2017). lncRNAs are known to be shorter transcript lengths and fewer exon numbers than mRNAs (Wang et al 2018;Sulayman et al 2019). Approximately 80.51% of our 4155 lncRNAs was shorter than 2800 bp and 87.32% of them had 2-4 exons, which was in agreement with previous studies in cattle (Billerey et al 2014;Liu et al 2017;Choi et al 2019;Yue et al 2019).…”

Section: Discussionsupporting

confidence: 92%

“…With the development of genetic array and high throughput sequencing technology, more and more lncRNAs have been discovered in human, rat and mouse (Zhao et al 2016). Recently, lncRNAs have also been identified in pig (Yang et al 2017;Jin et al 2018;Kern et al 2018), chicken (Muret et al 2017;Kern et al 2018;Li et al 2019), sheep (Ren et al 2016;Ling et al 2017;Bush et al 2018;Sulayman et al 2019) and cattle (Billerey et al 2014;Koufariotis et al 2015;Tong et al 2017;Bush et al 2018;Kern et al 2018;Weikard et al 2018;Yang et al 2018;Choi et al 2019;Wang et al 2019;Yue et al 2019).…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide identification and characterisation of long non-coding RNAs in two Chinese cattle breeds

Jia

Chen

et al. 2020

Italian Journal of Animal Science

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Long non-coding RNAs (lncRNAs) have been essentially involved in all kinds of important biological processes, such as cell differentiation and development. In this study, we comprehensively profiled genome-wide lncRNAs of bovine skeletal muscle in two Chinese cattle breeds using RNAseq approach. The longissimus dorsi samples were collected from three Charolais (CH) and three Tongjiang (TJ) adult cattle, respectively. Approximately 80 million reads were obtained per library, and by which we assembled 31,009 unique transcripts. We successfully identified a total of 4155 different lncRNAs in six muscle samples, consisting of 3204 intronic lncRNAs, 737 intergenic lncRNAs, 113 sense lncRNAs and 101 antisense lncRNAs. Among them, 32 lncRNAs were differentially expressed (Fold Change >1.0, FDR < 0.05) between CH and TJ. Among these lncRNAs, 1744 identified bovine lncRNAs were located adjacent to 1146 protein-coding genes (<100 kb upstream and downstream) and functionally enriched in organ development, gene regulation and signal transduction. Our results provide a catalogue of bovine skeletal muscle-related lncRNAs, which will complement the list of bovine lncRNAs and contribute to understanding of the molecular mechanism of underpinning muscle development in cattle. HIGHLIGHTS The first study to compare specialised beef cattle breed with Chinese local beef cattle breed on long non-coding RNA (lncRNA). The 4155 different lncRNAs in beef cattle genome were identified to complement the list of bovine lncRNAs. The 1146 protein-coding genes were found maybe in cis-regulatory relationships with lncRNAs to understand the molecular mechanism underpinning muscle development in cattle.

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Section: Discussionsupporting

confidence: 92%

Section: Introductionmentioning

confidence: 99%

Genome-wide identification and characterisation of long non-coding RNAs in two Chinese cattle breeds

Jia

Chen

et al. 2020

Italian Journal of Animal Science

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“…Moreover, GO enrichment analysis revealed that several co-expressed genes were enriched in MAPK and PI3K signaling, both of which are known to participate in oocyte meiotic resumption and maturation (Schmitt and Nebreda, 2002;Liang et al, 2007). In addition, lncRNA has previously been reported to be involved in cAMP and MAPK signaling pathways (Sulayman et al, 2019;Wang, 2019). Thus, we suggested that many lncRNAs might participate in oocyte maturation via trans-regulation.…”

Section: Discussionmentioning

confidence: 74%

Genome-Wide Network of lncRNA–mRNA During Ovine Oocyte Development From Germinal Vesicle to Metaphase II in vitro

et al. 2020

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Long non-coding RNA (lncRNA) is involved in many biological processes, and it has been closely investigated. However, research into the role of lncRNA in ovine ovarian development is scant and poorly understood, particularly in relation to the molecular mechanisms of ovine oocyte maturation. In the current study, RNA sequencing was performed with germinal vesicle (GV) and in vitro matured metaphase II (MII) stage oocytes, isolated from ewes. Through the use of bioinformatic analysis, abundant candidate lncRNAs in stage-specific ovine oocytes were identified, and their trans-and cis-regulatory effects were deeply dissected using computational prediction software. Functional enrichment analysis of these lncRNAs revealed that they were involved in the regulation of many key signaling pathways during ovine oocyte development, which was reflected by their targeted genes. From this study, multiple lncRNA-mRNA networks were presumed to be involved in key signaling pathways regarding ovine oocyte maturation and meiotic resumption. In particular, one novel lncRNA (MSTRG.17927) appeared to mediate the regulation of phosphatidylinositol 3-kinase signaling (PI3K) signaling during ovine oocyte maturation. Therefore, this research offers novel insights into the molecular mechanisms underlying ovine oocyte meiotic maturation regulated by lncRNA-mRNA networks from a genome-wide perspective.

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“…NF-kappa B regulates the WNT pathway and acts as a signal mediator by upregulating Shh ligand expression [ 44 , 45 ]. Moreover, WNT10A plays an important role in hair follicle development [ 46 ]. Thomas et al [ 47 ] demonstrated that a primary WNT ( WNT3 ) and secondary WNTs ( WNT0A and WNT10B ) are essential for hair follicle initiation, morphogenesis and development.…”

Section: Discussionmentioning

confidence: 99%

Genetic Signatures of Selection for Cashmere Traits in Chinese Goats

Jin

Lü

Fei

et al. 2020

Animals

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Inner Mongolia and Liaoning cashmere goats in China are well-known for their cashmere quality and yield. Thus, they are great models for identifying genomic regions associated with cashmere traits. Herein, 53 Inner Mongolia cashmere goats, Liaoning cashmere goats and Huanghuai goats were genotyped, and 53,347 single-nucleotide polymorphisms (SNPs) were produced using the Illumina Caprine 50K SNP chip. Additionally, we identified some positively selected SNPs by analyzing Fst and XP-EHH. The top 5% of SNPs had selection signatures. After gene annotation, 222 and 173 candidate genes were identified in Inner Mongolia and Liaoning cashmere goats, respectively. Several genes were related to hair follicle development, such as TRPS1, WDR74, LRRC14, SPTLC3, IGF1R, PADI2, FOXP1, WNT10A and CSN3. Gene enrichment analysis of these cashmere trait-associated genes related 67 enriched signaling pathways that mainly participate in hair follicle development and stem cell pluripotency regulation. Furthermore, we identified 20 overlapping genes that were selected in both cashmere goat breeds. Among these overlapping genes, WNT10A and CSN3, which are associated with hair follicle development, are potentially involved in cashmere production. These findings may improve molecular breeding of cashmere goats in the future.

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Genome-wide identification and characterization of long non-coding RNAs expressed during sheep fetal and postnatal hair follicle development

Cited by 35 publications

References 90 publications

Genome-wide identification and characterisation of long non-coding RNAs in two Chinese cattle breeds

Genome-wide identification and characterisation of long non-coding RNAs in two Chinese cattle breeds

Genome-Wide Network of lncRNA–mRNA During Ovine Oocyte Development From Germinal Vesicle to Metaphase II in vitro

Genetic Signatures of Selection for Cashmere Traits in Chinese Goats

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