Analysis of pituitary transcriptomics indicates that lncRNAs are involved in the regulation of sheep estrus

Li, Xiaoyue; Li, Cunyuan; Xu, Yuwen; Yao, Rui; Li, Huixiang; Ni, Wei; Quan, Renzhe; Zhang, Mengdan; Liu, Li; Yu, Shuting; Ullah, Yaseen; Hu, Ruirui; Li, Yaxin; Guo, Tao; Wang, Xiaokui; Hu, Shengwei

doi:10.1007/s10142-020-00735-y

Cited by 15 publications

(12 citation statements)

References 61 publications

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“…Ling-Ling Zheng et al used co-expression strategy to predict the putative function of lncRNAs [ 47 ]. Xiaoyue Li et al combined Gene ontology and an approach of identification of nearby genes (100 kb) that are potentially regulated by lncRNAs [ 48 ]. We have integrated three dimensional architecture of the genome (Hi-C), Gene enrichment analysis and nearby genes co-expression strategy to identify the potential functions of the lncRNAs.…”

Section: Resultsmentioning

confidence: 99%

Identification of the conserved long non-coding RNAs in myogenesis

et al. 2021

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Background Our understanding of genome regulation is ever-evolving with the continuous discovery of new modes of gene regulation, and transcriptomic studies of mammalian genomes have revealed the presence of a considerable population of non-coding RNA molecules among the transcripts expressed. One such non-coding RNA molecule is long non-coding RNA (lncRNA). However, the function of lncRNAs in gene regulation is not well understood; moreover, finding conserved lncRNA across species is a challenging task. Therefore, we propose a novel approach to identify conserved lncRNAs and functionally annotate these molecules. Results In this study, we exploited existing myogenic transcriptome data and identified conserved lncRNAs in mice and humans. We identified the lncRNAs expressing differentially between the early and later stages of muscle development. Differential expression of these lncRNAs was confirmed experimentally in cultured mouse muscle C2C12 cells. We utilized the three-dimensional architecture of the genome and identified topologically associated domains for these lncRNAs. Additionally, we correlated the expression of genes in domains for functional annotation of these trans-lncRNAs in myogenesis. Using this approach, we identified conserved lncRNAs in myogenesis and functionally annotated them. Conclusions With this novel approach, we identified the conserved lncRNAs in myogenesis in humans and mice and functionally annotated them. The method identified a large number of lncRNAs are involved in myogenesis. Further studies are required to investigate the reason for the conservation of the lncRNAs in human and mouse while their sequences are dissimilar. Our approach can be used to identify novel lncRNAs conserved in different species and functionally annotated them.

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Section: Resultsmentioning

confidence: 99%

Identification of the conserved long non-coding RNAs in myogenesis

et al. 2021

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“…That is, the FecB gene is closely related to sheep fertility. More and more evidence also indicates that lncRNAs function in the sheep reproductive process ( Miao et al, 2016 , 2017 ; Feng et al, 2018 ; Li et al, 2020 ). Nevertheless, the current research on lncRNA is principally centered on the ovary, ignoring the role of FecB response changes from folliculogenesis to ovulation, such as changes in hypothalamic GnRH secretion and its regulation of downstream hormones (FSH, LH, and PRL).…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Analysis Reveals Differentially Expressed Genes and Long Non-coding RNAs Associated With Fecundity in Sheep Hypothalamus With Different FecB Genotypes

Chen

Guo

et al. 2021

Front. Cell Dev. Biol.

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Small-tailed Han sheep, with different FecB genotypes, manifest distinct ovulation rates and fecundities, which are due to differences in reproductive hormones secreted by the hypothalamic–pituitary–ovarian axis. Nevertheless, the function of the hypothalamus against a FecB mutant background on increasing ovulation rate is rarely reported. Therefore, we determined the expression profiles of hypothalamus tissue collected from six wild-type (WW) and six FecB mutant homozygous (BB) ewes at the follicular and luteal phases by whole-transcriptome sequencing. We identified 53 differentially expressed mRNAs (DEGs) and 40 differentially expressed long non-coding RNAs (DELs) between the two estrus states. Functional annotation analysis revealed that one of the DEGs, PRL, was particularly enriched in the hypothalamic function, hormone-related, and reproductive pathways. The lncRNA–target gene interaction networks and KEGG analysis in combination suggest that the lncRNAs LINC-676 and WNT3-AS cis-acting on DRD2 and WNT9B in different phases may induce gonadotropin-releasing hormone (GnRH) secretion. Furthermore, there were differences of regulatory elements and WNT gene family members involved in the follicular–luteal transition in the reproductive process between wild-type (WNT7A) and FecB mutant sheep (WNT9B). We combined the DEG and DEL data sets screened from different estrus states and genotypes. The overlap of these two sets was identified to select the mRNAs and lncRNAs that have major effects on ovulation. Among the overlapping molecules, seven DEGs and four DELs were involved in the follicular–luteal transition regulated by FecB mutation. Functional annotation analysis showed that two DEGs (FKBP5 and KITLG) were enriched in melanogenesis, oxytocin, and GnRH secretion. LINC-219386 and IGF2-AS were highly expressed in the BB ewes compared with WW ewes, modulating their target genes (DMXL2 and IGF2) to produce more GnRH during follicular development, which explains why mutated ewes produced more mature follicles. These results from expression profiling of the hypothalamus with the FecB mutation at different estrus states provide new insights into how the hypothalamus regulates ovulation under the effect of the FecB mutation.

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“…The involvement of lncRNAs in seasonal estrus was also examined in sheep pituitaries and 995 lncRNAs were identified, of which 335 were DE during estrus and anestrus ( 136 ). Prediction of the target genes of these lncRNAs, together with the function of the encoded proteins in hormone synthesis and metabolism, led the authors to suggest possible functions for some of these lncRNAs in estrous ( 136 ). The same group profiled also the circRNAs expressed in estrus and anestrus sheep pituitary ( 137 ) and those expressed in prenatal and postnatal sheep pituitaries ( 138 ).…”

Section: Screening For Functional Pituitary Lncrnas Associated With Sexual Maturation and Reproductive Functionmentioning

confidence: 99%

Enhancing Gonadotrope Gene Expression Through Regulatory lncRNAs

Refael

Melamed

2021

Endocrinology

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The world of long non-coding RNAs (lncRNAs) has opened up massive new prospects in understanding the regulation of gene expression. Not only are there seemingly almost infinite numbers of lncRNAs in the mammalian cell, but they have highly diverse mechanisms of action. In the nucleus, some are chromatin-associated, transcribed from transcriptional enhancers (eRNAs) and/or direct changes in the epigenetic landscape with profound effects on gene expression. The pituitary gonadotrope is responsible for activation of reproduction through production and secretion of appropriate levels of the gonadotropic hormones. As such, it exemplifies a cell whose function is defined through changes in developmental and temporal patterns of gene expression, including those that are hormonally-induced. Roles for diverse distal regulatory elements and eRNAs in gonadotrope biology have only just begun to emerge. Here, we will present an overview of the different kinds of lncRNAs that alter gene expression, and what is known about their roles in regulating some of the key gonadotrope genes. We will also review various screens that have detected differentially expressed pituitary lncRNAs associated with changes in reproductive state, and those whose expression is found to play a role in gonadotrope-derived non-functioning pituitary adenomas. We hope to shed light on this exciting new field, emphasize the open questions, and encourage research to illuminate the roles of lncRNAs in various endocrine systems.

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Analysis of pituitary transcriptomics indicates that lncRNAs are involved in the regulation of sheep estrus

Cited by 15 publications

References 61 publications

Identification of the conserved long non-coding RNAs in myogenesis

Identification of the conserved long non-coding RNAs in myogenesis

Transcriptome Analysis Reveals Differentially Expressed Genes and Long Non-coding RNAs Associated With Fecundity in Sheep Hypothalamus With Different FecB Genotypes

Enhancing Gonadotrope Gene Expression Through Regulatory lncRNAs

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