- In recent years, an increasing number of long non-coding RNAs (lncRNAs) have been implicated in the regulation of mammal reproduction. - However, there are few studies on the function of lncRNAs in reproduction, particularly lncRNAs in the ovary.. - There were 115 /22 differential lncRNAs /TUCPs transcripts between the ovaries of the luteal phase and the follicular phase. - The results showed that lncRNAs /TUCPs, which are highly expressed in goat ovaries in the luteal phase, are mainly associated with the synthesis of progesterone, and we filtered the lncRNAs /TUCPs, such as XR and TUCP_001362, which may regulate the synthesis of progesterone. - lncRNAs /TUCPs, which are highly expressed in goat ovaries in the follicular phase, are mainly associated with oogenesis and the maturation of oocytes, and we filtered the lncRNAs /TUCPs that may regulate the oogenesis and maturation of oocyte, such as XR and TUCP_000849.. - There are two main functions of the goat ovary. - Subse- quently, the oocyte matures in the ovary and has the po- tential for fertilization in the ovary. - The goat ovaries in these two periods differ in the development of follicles, oogenesis and the maturation of oocytes, the formation of the corpus luteum, the maintenance of preg- nancy, and the secretion of gonadal hormone. - In the follicular phase, the follicles in the ovary grow, and the fol- licle development process is regulated by endocrine, para- crine and gene expression. - The amount of estrogen in the ovaries increases during this period, prompting the animals to become sexually aroused, and most mammals ovulate at the end of this period. - Ovaries in the luteal phase primarily secrete progesterone, which acts on the reproductive tract and the uterus, pro- moting embryo implantation and maintaining pregnancy.. - Xist is a lncRNA mol- ecule that plays a key role in the inactivation of the x chromosome in mammals [15]. - The discovery of Xist of- ficially prompted lncRNA research in the field of reproduction, and a growing number of lncRNA have been implicated in the regulation of mammalian ovary development [16, 17]. - Studies have shown that lncRNAs can regulate reproductive processes, such as the matur- ation and fertilization of oocytes and the embryonic de- velopment in the ovaries of female goats [18], and the maturation of oocytes is an important process that causes ovulation in goats [19]. - An increasing number of lncRNAs have also been implicated in the regulation of mamma- lian breeding. - In the present study, by using RNA-seq, we explored the genome-wide expression profiles of lncRNAs /TUCPs in goat ovaries at the follicular and lu- teal phases and predicted additional potential lncRNA /TUCP molecules. - The differential expression of lncRNAs /TUCPs in the ovaries at the follicular and lu- teal phases was explored. - We performed GO and KEGG enrichment analyses of the co-located and co-expressed genes of these different lncRNAs /TUCPs to investigate the role of these lncRNAs /TUCPs in goat reproduction.. - The ovaries in follicle and luteal stage of the Anhui white goat were selected as the animal tissues in the present study. - According to a model in the negative binomial distribution, Cuffdiff was used to determine the differential expression of the digital tran- scription or the gene expression data [29]. - The prediction of co-located and co-expressed genes In the present study, we predicted the co-expressed and co-located genes of lncRNA /TUCP to explore the func- tions of lncRNAs /TUCPs. - The GO enrichment analysis [30] of the related genes of differentially expressed lncRNAs or TUCPS was per- formed by the GOseq R package. - We examined the statistical enrichment of the related genes of differentially expressed lncRNAs or TUCPS in the KEGG pathway by using KOBAS [32] software.. - The genomic characteristics of lncRNA and TUCP in the goat ovaries. - In the present study, we collected five typical follicular phase and five typical luteal phase goat ovaries. - The expression levels in the ovaries in follicular and luteal phases were similar, and the expression level of lncRNA and TUCP was lower than that of mRNA (Fig. - The study also showed that most lncRNAs and TUCPs had fewer exons than did mRNAs: the average number of exons in the lncRNAs and TUCPs was ap- proximately 2, while that in mRNAs was 12. - In the present study, 115 lncRNAs were differentially expressed in goat ovaries for the luteal phase vs. - In total, 22 TUCPs were differentially expressed in the goat ovaries,. - According to the heat map analysis, the expression of the same gene in the same group is almost the same, indicating that there is minimal difference between the samples in the same group. - analysis of the sample cluster showed that the five samples of the luteal phase are clustered together, and the five samples of the follicular phase are clustered to- gether, which indicates large differences between the samples in the different groups. - Analysis of the gene cluster shows that the differential lncRNAs are divided into two major categories. - There are 28 lncRNAs with high expression in the luteal stage and 87 lncRNAs with high expression in the follicular phase (Fig. - The heat map analysis showed that the expression of the same gene in the same group is ba- sically the same, indicating that there is little difference between the samples in the same group. - analysis of the sample cluster revealed five samples of the luteal phase that are clustered together. - The five samples of the. - a Screening of the candidate lncRNAs in goat ovaries. - Among them, 16 TUCPs show high expression in the luteal stage, and 6 TUCPs show high expression in the follicu- lar phase (Fig. - To study the relationship between chromosome length and the total number of total mapped reads, we calculated the density of total mapped reads against each chromosome (the positive and negative strands) in the genome. - The GO and KEGG analysis of the co-expression genes of differential lncRNAs. - The results of the GO enrichment analysis are shown in Fig. - X-axis is the relative position of the gene on the chromosome and Y-axis is foldchange (log2). - Therefore, in the luteal phase ovary, the highly expressed lncRNAs, such as XR XR and XR were related to the synthesis of steroid hormones.. - There were 87 highly expressed lncRNAs in the fol- licular phase ovary, and 86 of these molecules were used for co-expression analysis. - Therefore, the highly expressed lncRNAs in the follicular phase ovary, such as XR XR and XR were related to gene expression.. - A total of 28 lncRNAs showed higher expression levels in the luteal phase ovaries than those in the follicular phase ovaries, and 24 of these molecules could be used for co-location analysis. - In summary, in the luteal phase ovary, the highly expressed lncRNAs, such as XR LNC_002673, and XR may be associated with the formation of the transcription initiation complex.. - There were 87 lncRNAs with higher expression in the follicular phase ovaries, and 63 of these molecules could be used for co-location analysis. - In sum- mary, in the follicle phase ovaries, the highly expressed lncRNA XR was related to gene expression.. - There were 16 TUCPs showing higher expression levels in the luteal phase ovaries than those in the follicular phase ovaries. - In the steroid biosynthesis signaling pathway, the related genes, such as EBP, DHCR24, and SQLE, were differentially expressed, and the TUCPs co-expressed with related genes include TUCP_001362, TUCP_001032, and TUCP_000183 (Additional file 6: Table S1). - In summary, as the steroids belong to the isoprenoids, we conclude that in the luteal phase ovary, the highly expressed TUCPs, such as. - There were 6 TUCPs showing higher expression in the follicular phase ovary, and all of these molecules could be used for co-expression analysis. - In the three terms, many related genes, such as AR, HMGB1 and CREM, were differentially expressed. - In summary, in the follicle phase ovaries, the highly expressed TUCPs, such as TUCP_000849, TUCP_000249 and TUCP_001109, were related to gene expression.. - There were 16 TUCPs showing higher localization in the luteal phase ovaries than in the follicular phase ovaries, and 11 of these molecules could be used for co-location ana- lysis. - In the two signal pathways, many related genes, such as LOC102178850, FUT1 and LOC102185028, were differentially expressed. - In summary, in the luteal phase ovary, the highly expressed TUCPs, TUCP_000751 and TUCP_000882, are related to the bio- synthesis of lipid (Additional file 6: Table S1). - The increase in lipid amount in the luteal phase ovary was beneficial to the synthesis of steroids.. - There were 6 TUCPs showing higher localization in the follicular phase ovary, and all of these molecules could be used for co-location analysis. - In the three terms, many re- lated genes, such as MCM7, TAF6 and ZSCAN2, were differentially expressed. - In summary, in the follicle phase ovary, the highly expressed TUCPs, such as TUCP_000849, TUCP_000249, and TUCP_001109, were related to gene expression.. - In the present study, we. - To our knowledge, the present study is the first systematic study of the lncRNAs and TUCPs in the goat ovaries. - In the present study, the goat ovary transcriptome of lncRNAs and TUCPs were provided. - What are the main functions of lncRNAs and TUCPs that are highly expressed in the luteal phase ovary? Ac- cording to the functional analysis of higher expressed lncRNA (co-expressing genes) in the luteal phase ovary, the terms coenzyme binding and cofactor binding are the most significant GO terms. - For example, the cytochrome P450c17 protein encoded by the CYP17A1 (all called cytochrome P450c17α) gene is a cytochrome P450 enzyme expressed in the ovary and testis. - P450c17 has both 17 α -hydroxylase and 17,20-lyase activities and is a typical membrane- bound bifunctional monooxygenase that plays a key role in the synthesis of steroid hormones [41] and plays an im- portant role in maintaining the synthesis of sex hormones [42]. - Therefore, the lncRNAs that are highly expressed in the luteal phase may be mainly related to the synthesis of steroid hormones. - According to the functional analysis of more highly expressed TUCPs (co-expressing genes) in the luteal phase ovary, the term isoprenoid is the most sig- nificant GO term. - Steroids are a general term for a large class of cyclopentadiene-perhydrophenanthrene deriva- tives widely distributed in the biosphere. - According to the functional analysis of more highly expressed lncRNAs (co-location genes) in the luteal phase ovary, the term lipid synthesis was the most significant GO term. - The for- mation and accumulation of lipid droplets in the luteal cells may be important for the production of steroids [43]. - Ovarian function is associated with decreased lipid levels, particularly in the luteal phase [44. - Through the above functional analysis of co-expressed and co-localized genes of TUCPs, we propose that TUCPs and lncRNAs highly expressed in the luteal phase ovary may be related to the synthesis of steroid hormone. - In summary, the present re- sults indicate that the high expression of lncRNA and TUCP in the luteal phase ovary may be mainly related to the synthesis of steroid hormones. - During pregnancy, estrogen plays a role in the initiation of labor and is conducive to childbirth. - In the luteal phase of the goat ovary, the follicle ruptures and forms a corpus luteum after ovulation. - The above results can provide evidence that lncRNAs /TUCPs regulate the synthesis of progester- one in the luteal phase and influence the reproductive per- formance of animals.. - What are the major functions of lncRNA and TUCP that are highly expressed in the follicular phase ovarian?. - According to the functional analysis of more highly expressed lncRNAs (co-expressing genes) in the follicular phase ovary, the terms ribosomes and translation were the most significant GO terms. - The genetic information stored in the DNA sequence is transcribed and translated into biologic- ally active protein molecules that enable organisms to ex- hibit corresponding traits. - According to the functional analysis of more highly expressed TUCPs (both co-expressed and co-localized genes) in the follicular phase ovary, the terms transcription, DNA-dependent, and RNA biosynthetic processes are the common GO terms, with significant differences. - In summary, analyses with co-expression or co-location methods show that highly expressed lncRNAs /TUCPs in the follicular phase ovary are mainly associated with gene expression. - In the follicular phase goat ovaries, the follicles continue developing, and the oocytes continue growing and achieve maturation. - Studies have shown that gene expression is an in- dispensable step in the oogenesis and maturation of oo- cyte [48–50]. - One of the main functions of lncRNAs is to regulate gene. - In the present study, we conducted genome-wide RNA-seq for follicular and luteal ovaries in goat and provided the transcriptome profile of the lncRNAs and TUCPs in the goat ovaries. - The distribution of exon number in the lncRNAs and mRNAs. - The distribution of average length in the lncRNAs and mRNAs. - The distribution of ORF in the lncRNAs and mRNAs. - The distribution of exon number in the TUCPs and mRNAs. - The distribution of average length in the TUCPs and mRNAs. - The distribution of ORF in the TUCPs and mRNAs. - The pathway to femaleness: current knowledge on embryonic development of the ovary. - Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. - Long non-coding RNAs: a new frontier in the study of human diseases. - The landscape of long noncoding RNAs in the human transcriptome. - Screening and evaluating of long noncoding RNAs in the puberty of goats.. - Long non-coding RNAs as regulators of the endocrine system
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