Screening and evaluating of long noncoding RNAs in the puberty of goats

Gao, Xiaoxiao; Ye, Jing; Yang, Chen; Zhang, Kaifa; Li, Xiumei; Luo, Lei; Ding, Jianping; Li, Yunsheng; H, Cao; Ling, Yinghui; Zhang, Xiaorong; Liu, Ya; Fang, Fugui; Zhang, Yunhai

doi:10.1186/s12864-017-3578-9

Cited by 45 publications

(49 citation statements)

References 57 publications

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“…To date, many studies have been performed to study ncRNAs (noncoding RNAs) of dairy goat mammary and have revealed a landscape of transcriptomics, miRomics, and proteomics [7][8][9]. However, to the best of our knowledge, studies of lncRNAomics of dairy goats have been reported only in ovary, hair follicle, skeletal muscle, hypothalamus, and skin pigmentation tissue [10][11][12][13][14][15][16], and there are no studies of the lncRNAomics of dairy goat mammary gland tissues in different lactating periods.…”

Section: Introductionmentioning

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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Section: Introductionmentioning

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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“…Therefore, it is possible that DNA methylation affects the initiation of puberty via lncRNA. The lncRNAs which participated in regulation of puberty in goats were screened as our previous research (Gao et al, ). In this study, we detected different methylation expression levels of the lncRNA.…”

Section: Discussionmentioning

confidence: 99%

“…Transcriptome assembly was done according to the description by Gao et al (2017). Briefly, we used the following GTF file (https:// www.ncbi.nlm.nih.gov/genome/?term=Capra_hircus) to annotate the goat genome.…”

Section: Transcriptome Assemblymentioning

confidence: 99%

“…Altogether, these studies highlight the important role of lncRNA in reproduction. Our previous research had measured differentially expressed lncRNAs in hypothalamus from pubertal and pre-pubertal goats; then, a number of lncRNAs involved in the regulation of puberty and reproduction were screened (Gao et al, 2017). Recently, many studies have reported that DNA methylation plays an essential role in the regulation of lncRNAs.…”

Section: Introductionmentioning

confidence: 99%

“…Both lncRNA and methylation are important factors in epigenetics, playing an essential role in regulating the onset of puberty (Gao et al, 2017;Yang et al, 2016). In this study, we performed whole-genome bisulphite sequencing (WGBS) and RNA-sequencing (RNA-seq) to examine the interrelationship between lncRNA and methylation and further understand the epigenetic mechanisms involved in goat puberty initiation for the first time.…”

Section: Introductionmentioning

confidence: 99%

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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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A novel lncRNA LOC105613571 binding with BDNF in pituitary promotes gonadotropin secretion by AKT/ERK‐mTOR pathway in sheep associated with prolificacy

et al. 2023

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The pituitary is a vital endocrine organ for synthesis and secretion of gonadotropic hormones (FSH and LH), and the gonadotropin showed fluctuations in animals with different fecundity. Long non‐coding RNAs (lncRNAs) have been identified as regulatory factors for the reproductive process. However, the profiles of lncRNAs and their roles involved in sheep fecundity remains unclear. In this study, we performed RNA‐sequencing for the sheep pituitary gland associated with different fecundity, and identified a novel candidate lncRNA LOC105613571 targeting BDNF related to gonadotropin secretion. Our results showed that expression of lncRNA LOC105613571 and BDNF could be significantly upregulated by GnRH stimulation in sheep pituitary cells in vitro. Notably, either lncRNA LOC105613571 or BDNF silencing inhibited cell proliferation while promoted cell apoptosis. Moreover, lncRNA LOC105613571 knockdown could also downregulate gonadotropin secretion via inactivation AKT, ERK and mTOR pathway. In addition, co‐treatment with GnRH stimulation and lncRNA LOC105613571 or BDNF knockdown showed the opposite effect on sheep pituitary cells in vitro. In summary, BDNF‐binding lncRNA LOC105613571 in sheep regulates pituitary cell proliferation and gonadotropin secretion via the AKT/ERK‐mTOR pathway, providing new ideas for the molecular mechanisms of pituitary functions.

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Screening and evaluating of long noncoding RNAs in the puberty of goats

Cited by 45 publications

References 57 publications

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

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

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

A novel lncRNA LOC105613571 binding with BDNF in pituitary promotes gonadotropin secretion by AKT/ERK‐mTOR pathway in sheep associated with prolificacy

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