Systematic Analysis of Long Non-Coding RNAs and mRNAs in the Ovaries of Duroc Pigs During Different Follicular Stages Using RNA Sequencing

Characterization and analysis of transcriptomes of multiple tissues from estrus and diestrus in pigs

A comprehensive understanding of the complex regulatory mechanisms governing estrus and ovulation across multiple tissues in mammals is imperative to improve the reproductive performance of livestock and mitigate ovulation-related disorders in humans. To comprehensively elucidate the regulatory landscape, we analyzed the transcriptome of protein-coding genes and long intergenic non-coding RNAs (lincRNAs) in 58 samples (including the hypothalamus, pituitary, ovary, vagina, and vulva) derived from European Large White gilts and Chinese Mi gilts during estrus and diestrus. We constructed an intricate regulatory network encompassing 358 hub genes across the five examined tissues. Furthermore, our investigation identified 85 differentially expressed lincRNAs that are predicted to target 230 genes associated with critical functions including behavior, receptors, and apoptosis. Importantly, we found that vital components of estrus and ovulation events involve "Apoptosis" pathway in the hypothalamus, "Autophagy" in the ovary, as well as "Hypoxia" and "Angiogenesis" in the vagina and vulva. We have identified several differentially expressed transcription factors (TFs), such as SPI1 and HES2, which regulate these pathways. SPI1 may suppress transcription in the autophagy pathway, promoting apoptosis and inhibiting the proliferation of ovarian granulosa cells. Our study provides the most comprehensive transcriptional profiling information related to estrus and ovulation events.

Integrative time-serial networks for genome-wide lncRNA-mRNA interactions reveal interferon-inducible antiviral and T-cell receptor regulations against PRRSV infection

Porcine reproductive and respiratory syndrome virus (PRRSV) infection severely affects the swine industry each year. Although the host mechanisms against PRRSV infection have been identified in key target tissues through whole transcriptome sequencing, specific molecular regulators have not been elucidated. Long non-coding RNA (lncRNA) expression is highly specific and could thus be used to effectively identify PRRSV-specific candidates. Here, we identified novel lncRNAs in lungs, bronchial lymph nodes, and tonsils after PRRSV infection and constructed phenotype-based integrative co-expression networks using time-series differentially expressed (DE) lncRNAs and mRNAs. After the analyses, a total of 309 lncRNA-mRNA interactions were identified. During early host innate signalling, interferon-inducible and interferon genes were positively regulated by specific lncRNA. Moreover, T-cell receptor genes in lung adaptive immune signalling were negatively regulated by specific lncRNA. Collectively, our findings provide insights into the genome-wide lncRNA-mRNA interactions and dynamic regulation of lncRNA-mediated mechanisms against PRRSV infection.

Genome-Wide Analysis of Long Noncoding RNAs in Porcine Intestine during Weaning Stress

Long noncoding RNAs (lncRNAs) play crucial roles in various biological processes, and they are considered to be closely associated with the pathogenesis of intestinal diseases. However, the role and expression of lncRNAs in intestinal damage during weaning stress remain unknown. Herein, we investigated the expression profiles of jejunal tissue from weaning piglets at 4 and 7 d after weaning (groups W4 and W7, respectively) and from suckling piglets on the same days (groups S4 and S7, respectively). Genome-wide analysis of lncRNAs was also performed using RNA sequencing technology. A total of 1809 annotated lncRNAs and 1612 novel lncRNAs were obtained from the jejunum of piglets. In W4 vs. S4, a total of 331 lncRNAs showed significant differential expression, and a total of 163 significantly differentially expressed lncRNAs (DElncRNAs) was identified in W7 vs. S7. Biological analysis indicated that DElncRNAs were involved in intestinal diseases, inflammation, and immune functions, and were mainly enriched in the Jak-STAT signaling pathway, inflammatory bowel disease, T cell receptor signaling pathway, B cell receptor signaling pathway and intestinal immune network for IgA production. Moreover, we found that lnc_000884 and target gene KLF5 were significantly upregulated in the intestine of weaning piglets. The overexpression of lnc_000884 also significantly promoted the proliferation and depressed apoptosis of IPEC-J2 cells. This result suggested that lnc_000884 may contribute to repairing intestinal damage. Our study identified the characterization and expression profile of lncRNAs in the small intestine of weaning piglets and provided new insights into the molecular regulation of intestinal damage during weaning stress.

Evaluation of Fatty Acid Distributions and Triacylglycerol Species in Sow Milk and Commercial Piglet Formulas: A Comparative Study Based on Fat Sources and Lactation Stages

Total fatty acid and sn-2 fatty acid compositions, and triacylglycerol (TAG) species in 130 sow colostrum, 100 sow milk, and 22 piglet formula samples were analyzed in the present study. Significant differences were found in concentrations of medium chain-saturated fatty acids (MC-SFAs) and distributions of palmitic acid (P) and oleic (O)/linoleic (L) acid. The levels of MC-SFAs in sow colostrum and sow milk fats (2.4-3.1%) were significantly lower than those in piglet formulas (7.9-27.2%). Approximately 63% of palmitic acid was located at the sn-2 position in both sow colostrum and milk fats, which was significantly higher than in piglet formula fats (21.1-39.1%). Correspondingly, only 17.8-28.3% of oleic and linoleic acids were at the sn-2 position in sow milk fats, contributing to their typical triacylglycerol structure in sow colostrum and milk, whose palmitic acid connected to the sn-2 position and unsaturated fatty acids located at the sn-1,3 positions. Sow colostrum, milk, and piglet formulas were notably distinguished into three groups based on their fatty acids and TAGs, among which triacylglycerols were the most differentiated index. A total of 51 TAG species (including their isomers) differed significantly between sow colostrum and milk and piglet formulas. OPL and OPO were the most important differentiating TAGs. The large amount of sn-2 esterified palmitic acid plays a key role in improving the absorption of fat and calcium. The results provide suggestions for design of sow milk fat equivalents.

Long noncoding RNA IRF1-AS is associated with peste des petits ruminants infection

Peste des petits ruminants (PPR) is an acute and highly contagious disease and has long been a significant threat to small ruminant productivity worldwide. However, the molecular mechanism underlying host-PPRV interactions remains unclear and the long noncoding RNAs (lncRNAs) regulation of PPR virus (PPRV) infection has rarely been reported so far. Here, we first demonstrated that PPRV infection can induce an obvious innate immune response in caprine endometrial epithelial cells (EECs) at 48 h post-infection (hpi) with an MOI of 3. Subsequently, we determined that PPRV infection is associated with 191 significantly differentially expressed (SDE) lncRNAs, namely, 137 upregulated and 54 downregulated lncRNAs, in caprine EECs compared with mock control cells at 48 hpi by using deep sequencing technology. Importantly, bioinformatics preliminarily analyses revealed that these DE lncRNAs were closely related to the immune response. Furthermore, we identified a system of lncRNAs related to the immune response and focused on the role of lncRNA 10636385 (IRF1-AS) in regulating the innate immune response. Interestingly, we found that IRF1-AS was a potent positive regulator of IFN-β and ISG production, which can significantly inhibit PPRV replication in host cells. In addition, our data revealed that IRF1-AS was positively correlated with its potential target gene, IRF1, which enhanced the activation of IRF3 and the expression of ISGs and interacted with IRF3. This study suggests that IRF1-AS could be a new host factor target for developing antiviral therapies against PPRV infection.

Identification, characterization and functional analysis of gonadal long noncoding RNAs in a protogynous hermaphroditic teleost fish, the ricefield eel (Monopterus albus)

Background

An increasing number of long noncoding RNAs (lncRNAs) have been found to play important roles in sex differentiation and gonad development by regulating gene expression at the epigenetic, transcriptional and posttranscriptional levels. The ricefield eel, Monopterus albus, is a protogynous hermaphroditic fish that undergoes a sequential sex change from female to male. However, the roles of lncRNA in the sex change is unclear.

Results

Herein, we performed RNA sequencing to analyse lncRNA expression patterns in five different stages of M. albus development to investigate the roles of lncRNAs in the sex change process. A total of 12,746 lncRNAs (1503 known lncRNAs and 11,243 new lncRNAs) and 2901 differentially expressed lncRNAs (DE-lncRNAs) were identified in the gonads. The target genes of the DE-lncRNAs included foxo1, foxm1, smad3, foxr1, camk4, ar and tgfb3, which were mainly enriched in signalling pathways related to gonadal development, such as the insulin signalling pathway, MAPK signalling pathway, and calcium signalling pathway. We selected 5 highly expressed DE-lncRNAs (LOC109952131, LOC109953466, LOC109954337, LOC109954360 and LOC109958454) for full length amplification and expression pattern verification. They were all expressed at higher levels in ovaries and intersex gonads than in testes, and exhibited specific time-dependent expression in ovarian tissue incubated with follicle-stimulating hormone (FSH) and human chorionic gonadotropin (hCG). The results of quantitative real-time PCR (qRT-PCR) analysis and a dual-luciferase assay showed that znf207, as the gene targeted by LOC109958454, was expressed in multiple tissues and gonadal developmental stages of M. albus, and its expression was also inhibited by the hormones FSH and hCG.

Conclusions

These results provide new insights into the role of lncRNAs in gonad development, especially regarding natural sex changes in fish, which will be useful for enhancing our understanding of sequential hermaphroditism and sex changes in the ricefield eel (M. albus) and other teleosts.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08679-2.

Integrative analysis of transcriptome complexity in pig granulosa cells by long-read isoform sequencing

Background

In intensive and large-scale farms, abnormal estradiol levels in sows can cause reproductive disorders. The high incidence rate of reproductive disturbance will induce the elimination of productive sows in large quantities, and the poor management will bring great losses to the pig farms. The change in estradiol level has an important effect on follicular development and estrus of sows. To solve this practical problem and improve the productive capacity of sows, it is significant to further clarify the regulatory mechanism of estradiol synthesis in porcine granulosa cells (GCs). The most important function of granulosa cells is to synthesize estradiol. Thus, the studies about the complex transcriptome in porcine GCs are significant. As for precursor-messenger RNAs (pre-mRNAs), their post-transcriptional modification, such as alternative polyadenylation (APA) and alternative splicing (AS), together with long non-coding RNAs (lncRNAs), may regulate the functions of granulosa cells. However, the above modification events and their function are unclear within pig granulosa cells.

Methods

Combined PacBio long-read isoform sequencing (Iso-Seq) was conducted in this work for generating porcine granulosa cells' transcriptomic data. We discovered new transcripts and possible gene loci via comparison against reference genome. Later, combined Iso-Seq data were adopted to uncover those post-transcriptional modifications such as APA or AS, together with lncRNA within porcine granulosa cells. For confirming that the Iso-Seq data were reliable, we chose four AS genes and analyzed them through RT-PCR.

Results

The present article illustrated that pig GCs had a complex transcriptome, which gave rise to 8,793 APA, 3,465 AS events, 703 candidate new gene loci, as well as 92 lncRNAs. The results of this study revealed the complex transcriptome in pig GCs. It provided a basis for the interpretation of the molecular mechanism in GCs.

Thyroid Transcriptomic Profiling Reveals the Follicular Phase Differential Regulation of lncRNA and mRNA Related to Prolificacy in Small Tail Han Sheep with Two FecB Genotypes

Long non-coding RNA (lncRNA) accounts for a large proportion of RNA in animals. The thyroid gland has been established as an important gland involved in animal reproduction, however, little is known of its gene expression patterns and potential roles in the sheep. Herein, RNA-Seq was used to detect reproduction-related differentially expressed lncRNAs (DELs) and mRNAs (DEGs) in the follicular phase (FT) FecBBB (MM) and FecB++ (ww) genotypes of Small Tail Han (STH) sheep thyroids. Overall, 29 DELs and 448 DEGs in thyroid between MM and ww sheep were screened. Moreover, GO and KEGG enrichment analysis showed that targets of DELs and DEGs were annotated in biological transitions, such as cell cycle, oocyte meiosis and methylation, which in turn affect reproductive performance in sheep. In addition, we constructed co-expression and networks of lncRNAs-mRNAs. Specifically, XLOC_075176 targeted MYB, XLOC_014695 targeted VCAN, 106991527 targeted CASR, XLOC_075176 targeted KIFC1, XLOC_360232 targeted BRCA2. All these differential lncRNAs and mRNAs expression profiles in the thyroid provide a new resource for elucidating the regulatory mechanism underlying STH sheep prolificacy.

Comprehensive Transcriptome Analysis of Follicles from Two Stages of the Estrus Cycle of Two Breeds Reveals the Roles of Long Intergenic Non-Coding RNAs in Gilts

Simple Summary

This study provides new perspectives about the roles of lincRNAs in the estrus expression of gilts, which is correlated with ovarian steroid hormone and follicular development. Follicular tissues from two stages of the estrus cycle of Large White and Mi gilts were used for RNA-seq. Some genes and lincRNAs related to estrus expression in pigs were discovered. PPI and ceRNA networks related to the estrus expression were constructed. These results suggest that the estrus expression may be affected by lincRNAs and their target genes.

Abstract

Visible and long-lasting estrus expression of gilts and sows effectively sends a mating signal. To reveal the roles of Long Intergenic Non-coding RNAs (lincRNAs) in estrus expression, RNA-seq was used to investigate the lincRNAs expression of follicular tissues from Large White gilts at diestrus (LD) and estrus (LE), and Chinese Mi gilts at diestrus (MD) and estrus (ME). Seventy-three differentially expressed lincRNAs (DELs) were found in all comparisons (LE vs. ME, LD vs. LE, and MD vs. ME comparisons). Eleven lincRNAs were differentially expressed in both LD vs. LE and MD vs. ME comparisons. Fifteen DELs were mapped onto the pig corpus luteum number Quantitative Trait Loci (QTL) fragments. A protein–protein interaction (PPI) network that involved estrus expression using 20 DEGs was then constructed. Interestingly, three predicted target DEGs (PTGs) (CYP19A1 of MSTRG.10910, CDK1 of MSTRG.10910 and MSTRG.23984, SCARB1 of MSTRG.1559) were observed in the PPI network. A competitive endogenous RNA (ceRNA) network including three lincRNAs, five miRNAs, and five genes was constructed. Our study provides new insight into the lincRNAs associated with estrus expression and follicular development in gilts.

Mechanisms of Oogenesis-Related Long Non-coding RNAs in Porcine Ovaries Treated With Recombinant Pig Follicle-Stimulating Hormone

Reproductive efficiency is of significant importance in pork production for it has a great impact on economic success. Ovulation rate is an early component of reproduction efficiency of pigs, and it contributes to the upper limit of litter size. In this study, we used the newly developed recombinant pig follicle stimulating hormone (rpFSH) instead of traditional PMSG to increase ovulation rate of pigs in order to achieve higher litter size, for it was better at stimulating ovulation, and showed more cheaper and greener. However, relatively little is known about the underlying genetic bases and molecular mechanisms. Consequently, an experiment was carried out in ovaries of replacement gilts to screen the key genes and lncRNAs that affect the fecundity of pigs by RNA-seq technology. Twenty gilts were divided into two groups, including 10 rpFSH treatment pigs and 10 control animals. After slaughtering and collecting the phenotypic data, ovaries of five pigs in each group were selected for RNA-seq. Total RNA was extracted to construct the library and then sequence on an Illumina Hiseq 4000 system. A comprehensive analysis of mRNAs and long non-coding RNAs (lncRNAs) from 10 samples was performed with bioinformatics. The phenotypic data showed that rpFSH treatment groups had the higher (P < 0.01) ovarian weight and more mature follicles. The RNA-seq results showed that a total of 43,499 mRNAs and 21,703 lncRNAs were identified, including 21,300 novel lncRNAs and 403 known lncRNAs, of which 585 mRNAs and 398 lncRNAs (P < 0.05) were significantly differentially expressed (DE) between the two groups of rpFSH treatment group and controlled group. GO and KEGG annotation analysis indicated that the target genes of DE lncRNAs and DE mRNAs were related to prolactin receptor activity, mitophagy by induced vacuole formation, and meiotic spindle. Moreover, we found that NR5A2 (nuclear receptor subfamily 5, group A, member 2), a target gene of lncRNA MSTRG.3902.1, was involved in regulating follicular development, ovulation, and estrogen production. Our study provided a catalog of lncRNAs and mRNAs associated with ovulation of rpFSH treatment, and they deserve further study to deepen the understanding of biological processes in the regulation of ovaries of rpFSH treatment pigs.

Differential expression of long non-coding RNAs under Peste des petits ruminants virus (PPRV) infection in goats

Peste des petits ruminants (PPR) characterized by fever, sore mouth, conjunctivitis, gastroenteritis, and pneumonia, is an acute, highly contagious viral disease of sheep and goats. The role of long non-coding RNAs (lncRNAs) in PPRV infection has not been explored to date. In this study, the transcriptome profiles of virulent Peste des petits ruminants virus (PPRV) infected goat tissues – lung and spleen were analyzed to identify the role of lncRNAs in PPRV infection. A total of 13,928 lncRNA transcripts were identified, out of which 170 were known lncRNAs. Intergenic lncRNAs (7625) formed the major chunk of the novel lncRNA transcripts. Differential expression analysis revealed that 15 lncRNAs (11 downregulated and 4 upregulated) in the PPRV infected spleen samples and 16 lncRNAs (13 downregulated and 3 upregulated) in PPRV infected lung samples were differentially expressed as compared to control. The differentially expressed lncRNAs (DElncRNAs) possibly regulate various immunological processes related to natural killer cell activation, antigen processing and presentation, and B cell activity, by regulating the expression of mRNAs through the cis- or trans-regulatory mechanism. Functional enrichment analysis of differentially expressed mRNAs (DEmRNAs) revealed enrichment of immune pathways and biological processes in concordance with the pathways in which correlated lncRNA-neighboring genes were enriched. The results suggest that a coordinated immune response is raised in both lung and spleen tissues of the goat through mRNA-lncRNA crosstalk.

Genetic Basis of Follicle Development in Dazu Black Goat by Whole-Transcriptome Sequencing

Simple Summary

The follicle development (FD) of a goat is precisely regulated by various noncoding RNAs (ncRNAs), especially by the regulatory mechanism of competing endogenous RNAs (ceRNAs). This study aimed to determine the expression patterns of messenger RNA (mRNA), long noncoding RNA, microRNA, and circular RNA during the FD of Dazhu black goats by whole-transcriptomic sequencing and analyze the regulatory mechanism of the ncRNA and ceRNA regulatory network. The results may lay a foundation for further research on FD and improving the reproductive performance of goats.

Abstract

The follicle development (FD) is an important factor determining litter size in animals. Recent studies have found that noncoding RNAs (ncRNAs) play an important role in FD. In particular, the role of the regulatory mechanism of competing endogenous RNAs (ceRNAs) that drive FD has attracted increasing attention. Therefore, this study explored the genetic basis of goat FD by obtaining the complete follicular transcriptome of Dazu black goats at different developmental stages. Results revealed that 128 messenger RNAs (mRNAs), 4 long noncoding RNAs (lncRNAs), 49 microRNAs (miRNAs), and 290 circular RNAs (circRNAs) were significantly differentially expressed (DE) between large and small follicles. Moreover, DEmRNAs were enriched in many signaling pathways related to FD, as well as GO terms related to molecular binding and enzyme activity. Based on the analysis of the ceRNA network (CRN), 34 nodes (1 DElncRNAs, 10 DEcircRNAs, 14 DEmiRNAs, and 9 DEmRNAs) and 35 interactions (17 DEcircRNAs–DEmRNAs, 2 DElncRNAs–DEmiRNAs, and 16 DEmRNA–DEmiRNAs) implied that the CRN could be involved in the FD of goats. In conclusion, we described gene regulation by DERNAs and lncRNA/circRNA–miRNA–mRNA CRNs in the FD of goats. This study provided insights into the genetic basis of FD in precise transcriptional regulation.

Follicular development in livestock: Influencing factors and underlying mechanisms

Livestock farming development has become increasingly important in recent years. It not only provides us with meat nutrition and pet feeding but also increases the economic value by providing numerous employment opportunities, which improves our life quality. The livestock farming development depends on successful animal reproduction. As a vital process in animal reproduction, folliculogenesis and its influencing factors as well as their underlying mechanisms need to be understood thoroughly. This review is aimed at summarizing the factors such as cellular processes, gene regulation, noncoding RNAs and other endocrine or paracrine regulatory factors that affect follicular development, and their underlying mechanisms of action in livestock in order to provide novel insights for future studies. The above factors were found as significant determinants influencing the follicular development in livestock through various signaling pathways.

Transcriptome analysis reveals that long noncoding RNAs contribute to developmental differences between medium-sized ovarian follicles of Meishan and Duroc sows

Ovulation rate is an extremely important factor affecting litter size in sows. It differs greatly among pig breeds with different genetic backgrounds. Long non-coding RNAs (lncRNAs) can regulate follicle development, granulosa cell growth, and hormone secretion, which in turn can affect sow litter size. In this study, we identified 3554 lncRNAs and 25,491 mRNAs in M2 follicles of Meishan and Duroc sows. The lncRNA sequence and open reading frame lengths were shorter than mRNAs, and lncRNAs had fewer exons, were less abundant, and more conserved than protein-coding RNAs. Furthermore, 201 lncRNAs were differentially expressed (DE) between breeds, and quantitative trait loci analysis of DE lncRNAs were performed. A total of 127 DE lncRNAs were identified in 119 reproduction trait-related loci. In addition, the potential target genes of lncRNAs in cis or trans configurations were predicted. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that some potential target genes were involved in follicular development and hormone secretion-related biological processes or pathways, such as progesterone biosynthetic process, estrogen metabolic process, ovarian steroidogenesis, and PI3K-Akt signaling pathway. Furthermore, we also screened 19 differentially expressed lncRNAs in the PI3K-Akt signaling pathway as candidates. This study provides new insights into the roles of lncRNAs in follicular growth and development in pigs.

Long non-coding RNA profile in banana shrimp, Fenneropenaeus merguiensis and the potential role of lncPV13 in vitellogenesis

The long non-coding RNAs (lncRNAs) have been known to play important roles in several biological processes as well as in reproduction. This study aimed to identify lncRNA in ovary female banana shrimp, Fenneropenaeus merguiensis, and investigate the potential role of lncPV13 in the vitellogenesis. After the in silico identification of the ovarian transcriptome, a total of 24,733 putative lncRNAs were obtained, and only 147 putative lncRNAs were significantly differentially expressed among the ovarian development stages. To validate the in silico identification of lncRNAs, the 16 lncRNAs with the highest differential expression in the transcriptome analysis were evaluated by RT-qPCR. The 6 lncRNAs showed higher expression levels in the mature stage than in the previtellogenic stage and were found in several tissues such as in eyestalks, brains, thoracic ganglia, gills, and muscle. Furthermore, most candidate lncRNAs were amplifiable in Litopenaeus vannamei's and Penaeus monodon's DNA but not in Macrobrachium rosenbergii's DNA, suggesting some lncRNAs are expressed in a species-specific manner among penaeid shrimp. In this study, the lncPV13 was investigated for its vitellogenin regulating function by RNA interference. The result indicates that the lncPV13 expression was suppressed in the ovary on day 7 after the injection of double-stranded RNA specific to lncPV13 (dslncPV13), while vitellogenin (Vg) expression was significantly decreased. In contrast, the gonad inhibiting hormone (GIH) expression was significantly increased in the lncPV13 knockdown shrimp. However, the oocyte proliferation was not significantly different between control and lncPV13 knockdown shrimp. This suggests that lncPV13 regulate Vg synthesis through GIH inhibition. Finally, our findings provide lncRNA information and potential lncRNAs involved in the vitellogenesis of female banana shrimp.

Integrated Analysis of Long Non-Coding RNA and mRNA Expression Profiles in Testes of Calves and Sexually Mature Wandong Bulls (Bos taurus)

The mRNAs and long non-coding RNAs axes are playing a vital role in the regulating of post-transcriptional gene expression. Thereby, elucidating the expression pattern of mRNAs and long non-coding RNAs underlying testis development is crucial. In this study, mRNA and long non-coding RNAs expression profiles were investigated in 3-month-old calves and 3-year-old mature bulls' testes by total RNA sequencing. Additionally, during the gene level analysis, 21,250 mRNAs and 20,533 long non-coding RNAs were identified. As a result, 7908 long non-coding RNAs (p-adjust < 0.05) and 5122 mRNAs (p-adjust < 0.05) were significantly differentially expressed between the distinct age groups. In addition, gene ontology and biological pathway analyses revealed that the predicted target genes are enriched in the lysine degradation, cell cycle, propanoate metabolism, adherens junction and cell adhesion molecules pathways. Correspondingly, the RT-qPCR validation results showed a strong consistency with the sequencing data. The source genes for the mRNAs (CCDC83, DMRTC2, HSPA2, IQCG, PACRG, SPO11, EHHADH, SPP1, NSD2 and ACTN4) and the long non-coding RNAs (COX7A2, COX6B2, TRIM37, PRM2, INHBA, ERBB4, SDHA, ATP6VOA2, FGF9 and TCF21) were found to be actively associated with bull sexual maturity and spermatogenesis. This study provided a comprehensive catalog of long non-coding RNAs in the bovine testes and also offered useful resources for understanding the differences in sexual development caused by the changes in the mRNA and long non-coding RNA interaction expressions between the immature and mature stages.

Photoperiod induced the pituitary differential regulation of lncRNAs and mRNAs related to reproduction in sheep

The pituitary is a vital endocrine organ that regulates animal seasonal reproduction by controlling the synthesis and secretion of the hormone. The change of photoperiod is the key factor affecting the function of the pituitary in animals, but the mechanism is unclear. Here, we studied the transcriptomic variation in pars distalis (PD) of the pituitary between short photoperiod (SP) and long photoperiod (LP) using RNA sequencing based on the OVX+E₂ sheep. 346 differentially expressed (DE) lncRNAs and 186 DE-mRNA were found in the PD. Moreover, function annotation analysis indicated that the reproductive hormones and photoperiod response-related pathways including aldosterone synthesis and secretion, insulin secretion, thyroid hormone synthesis, and circadian entrainment were enriched. The interaction analysis of mRNA-lncRNA suggested that MSTRG.240648, MSTRG.85500, MSTRG.32448, and MSTRG.304959 targeted CREB3L1 and DUSP6, which may be involved in the photoperiodic regulation of the PD. These findings provide resources for further study on the seasonal reproductive in ewes.

LncRNA lnc_13814 promotes the cells apoptosis in granulosa cells of duck by acting as apla-miR-145-4 sponge

Follicle development is a vital factor which determines the reproductive performance of poultry. Long noncoding RNAs (lncRNAs) have been reported to maintain animal reproductive function and play key roles in ovarian development and hormone secretion. But the regulatory mechanism of lncRNAs in duck follicle development has seldom been reported. In this study, to better explore the molecular mechanism of follicle development in ducks, the follicular lncRNA was sequenced and analyzed. A total of 9,551 lncRNAs were predicted in the duck follicles. Four hundred and forty-five lncRNAs were differentially expressed between the white follicles and yellow follicles. The results of our studies showed that lnc_13814 promoted cell apoptosis in duck GCs. Furthermore, the bioinformatics analysis results demonstrated that lnc_13814 was involved in a lncRNA-miRNA-mRNA coexpression network and it was observed to sponge two follicle-related miRNAs by a luciferase activity assay. Moreover, we found that overexpression of lnc_13814 significantly increased DNA damage inducible transcript 3 (DDIT3) expression and downregulated GCs apoptosis. Finally, we found that lnc_13814 directly binds to and inhibits apla-mir-145-4; then, lnc_13814 increases the expression of DDIT3 and up-regulates GCs apoptosis. Taken together, our findings demonstrate that lncRNAs have potential effects on duck ovarian follicles and lncRNAs may represent a new approach to understand follicular development.

The Roles of the miRNAome and Transcriptome in the Ovine Ovary Reveal Poor Efficiency in Juvenile Superovulation

Simple Summary

Using the technology of juvenile superovulation, more follicles can be acquired in juvenile animals than in adult animals. However, oocytes derived from the follicles of juvenile animals are usually of poor quality, meaning that they have lower levels of subsequent maturation and embryonic development. In the present study, we used an exogenous hormone treatment to stimulate Hu sheep in order to compare the differences in ovarian superovulation effects and serum hormone secretion in juvenile and adult sheep. Differentially expressed microRNA (miRNA) and messenger RNA (mRNA) from the ovaries of juvenile and adult Hu sheep were then investigated using high-throughput sequencing technology to reveal the formation mechanism of large numbers of follicles and poor oocyte quality in juvenile ovaries under superovulation treatment. We found that molecules of oar-miR-143 and follicle-stimulating hormone receptor (FSHR), among others, might regulate follicle formation, while oar-miR-485-3p, oar-miR-377-3p, and pentraxin 3 (PTX3), among others, may be associated with oocyte quality. The results will help us to identify miRNAs and mRNAs that could be used to predict ovarian superovulation potential and oocyte quality in the future.

Abstract

Juvenile superovulation can provide a wealth of oocyte material for embryo production, animal cloning, and genetic modification research, but embryos derived from juvenile oocytes show poor efficiency in subsequent developmental capacity. In order to reveal the formation mechanism of large numbers of follicles and poor oocyte quality in juvenile ovaries under superovulation treatment, differentially expressed microRNAs (miRNAs) and messenger RNAs (mRNAs) were characterized and investigated in the ovaries of lambs and adult sheep using high-throughput sequencing technology. The majority of differentially expressed miRNAs (337/358) were upregulated in lamb libraries. The expression levels of mRNAs related to hormone receptors (follicle-stimulating hormone receptor, FSHR; luteinizing hormone/choriogonadotropin receptor, LHCGR; estrogen receptor 1, ESR1), steroid hormone secretion (cytochrome P450 family 11 subfamily A member 1, CYP11A1; cytochrome P450 family 17 subfamily A member 1, CYP17A1; cytochrome P450 family 19 subfamily A member 1, CYP19A1), and oocyte quality (pentraxin 3, PTX3; BCL2 apoptosis regulator, BCL2; caspase 3, CASP3) were significantly different between the lamb and adult libraries. The miRNA aor-miR-143, which targets FSHR, was highly and differentially expressed, and PTX3 was predicted to be targeted by oar-miR-485-3p and oar-miR-377-3p in the ovine ovary. A considerable number of miRNAs were predicted to inhibit ESR1 expression in lamb ovaries. In conclusion, oar-miR-143 and FSHR molecules, among others, might regulate follicle formation, and oar-miR-485-3p, oar-miR-377-3p, and PTX3, among others, may be associated with oocyte quality. These identified miRNAs and mRNAs will be beneficial for the prediction of ovarian superovulation potential and screening of oocytes.

Long non-coding RNA TCONS_00814106 regulates porcine granulosa cell proliferation and apoptosis by sponging miR-1343

Recent evidence shows that long non-coding RNAs (lncRNAs), a class of non-coding RNAs, are involved in the regulation of reproductive processes. In this study, we identified a lncRNA, TCONS_00814106, that was upregulated in high-fecundity sow ovarian tissues and influenced by reproductive hormones. Bioinformatics analyses and luciferase reporter assays showed that TCONS_00814106 is a miR-1343 target. Cell counting kit (CCK)-8 and apoptosis assays showed that TCONS_00814106 promotes proliferation and inhibits apoptosis in porcine granulosa cells (GCs), and that this could be reversed by miR-1343. Also, we observed that transforming growth factor-β receptor type I (TGFBR1) is a functional target of miR-1343 in GCs. TCONS_00814106 serves as a competing endogenous RNA to regulate TGFBR1 expression by sponging miR-1343, thereby exerting regulatory functions in GCs. Overall, these results provide new insights into the biological function of the lncRNA TCONS_00814106.

Integrated analysis of lncRNA, miRNA and mRNA reveals novel insights into the fertility regulation of large white sows

Background

Improving sow fertility is extremely important as it can lead to increased reproductive efficiency and thus profitability for swine producers. There are considerable differences in fertility rates among individual animals, but the underlying molecular mechanisms remain unclear. In this study, by using different types of RNA libraries, we investigated the complete transcriptome of ovarian tissue during the luteal (L) and follicular (F) phases of the estrous cycle in Large White pigs with high (H) and low (L) fecundity, and performed a comprehensive analysis of long noncoding RNAs (lncRNAs), mRNAs and micro RNAs (miRNAs) from 16 samples by combining RNA sequencing (RNA-seq) with bioinformatics.

Results

In total, 24,447 lncRNAs, 27,370 mRNAs, and 216 known miRNAs were identified in ovarian tissues. The genomic features of lncRNAs, such as length distribution and number of exons, were further analyzed. We selected a threshold of P < 0.05 and |log₂ (fold change)| ≥ 1 to obtain the differentially expressed lncRNAs, miRNAs and mRNAs by pairwise comparison (LH vs. LL, FH vs. FL). Bioinformatics analysis of these differentially expressed RNAs revealed multiple significantly enriched pathways (P < 0.05) that were closely involved in the reproductive process, such as ovarian steroidogenesis, lysosome, steroid biosynthesis, and the estrogen and GnRH signaling pathways. Moreover, bioinformatics screening of differentially expressed miRNAs that share common miRNA response elements (MREs) with lncRNAs and their downstream mRNA targets were performed. Finally, we constructed lncRNA–miRNA–mRNA regulation networks. The key genes in these networks were verified by Reverse Transcription Real-time Quantitative PCR (RT-qRCR), which were consistent with the results from RNA-Seq data.

Conclusions

These results provide further insights into the fertility of pigs andcan contribute to further experimental investigation of the functions of these genes.

Comprehensive Identification and Characterization of Long Non-coding RNAs Associated With Rice Black-Streaked Dwarf Virus Infection in Laodelphax striatellus (Fallén) Midgut

Long non-coding RNAs (lncRNAs) are involved in a variety of biological functions through transcriptional and post-transcriptional regulation. However, little is known about their functions in the process of insect mediated virus transmission. In the present study, we analyzed using RNA-Seq, the lncRNAs that were differentially expressed in response to Rice black-streaked dwarf virus (RBSDV) infection in Laodelphax striatellus (Fallén) midgut. A total of 13,927 lncRNAs were identified and over 69% were assigned to intergenic regions. Among them, 176 lncRNAs were differentially expressed and predicted to target 168 trans-regulatory genes. Ten differentially expressed lncRNAs were selected and their expression changes were validated by RT-qPCR. KEGG analysis showed that these target genes were enriched in the essential biological process, such as Purine metabolism, Valine, leucine and isoleucine degradation, and Fatty acid elongation. The expression levels of the differentially expressed lncRNAs and the predicted target genes that were significantly enriched in the Human papillomavirus infection pathway were analyzed by RT-qPCR. The results showed that several lncRNAs were co-expressed with their target genes. One of the lncRNAs called MSTRG15394 and its target gene, encoding a secreted protease inhibitor (PI), were up-regulated at the transcriptional level after RBSDV infection. Knockdown of MSTRG15394 could down-regulate the PI expression at mRNA level. Inhibition of either MSTRG15394 or PI expression by RNA interference promoted RBSDV accumulation in L. striatellus midgut. Our finding provides new insights into the function of lncRNAs in regulating virus infection in an important insect vector.

Comprehensive analysis of miRNAs, lncRNAs, and mRNAs reveals potential players of sexually dimorphic and left-right asymmetry in chicken gonad during gonadal differentiation

Despite thousands of sex-biased genes being found in chickens, the genetic control of sexually dimorphic and left-right asymmetry during gonadal differentiation is not yet completely understood. This study aimed to identify microRNAs (miRNAs), long noncoding RNAs (lncRNAs), messenger RNAs (mRNAs), and signaling pathways during gonadal differentiation in chick embryos (day 6/stage 29). The left and right gonads were collected for RNA sequencing. Sex-biased, side-biased miRNAs, lncRNAs, mRNAs, and shared differentially expressed miRNAs (DEmiRNA)–differentially expressed mRNAs (DEmRNA)–differentially expressed lncRNAs (DElncRNA) interaction networks were performed. A total of 8 DEmiRNAs, 183 DElncRNAs, and 123 DEmRNAs were identified for the sex-biased genes, and 7 DEmiRNAs, 189 DElncRNAs, and 183 DEmRNAs for the side-biased genes. The results of quantitative real-time PCR were generally consistent with the RNA-sequencing results. The study suggested that miRNAs and lncRNAs regulation were novel gene-specific dosage compensation mechanism and they could contribute to left-right asymmetry of chicken, but sex-biased and side-biased miRNAs, lncRNAs, and mRNAs were independent of each other. The competing endogenous RNA (ceRNA) networks showed that 17 target pairs including miR-7b (CYP19A1, FSHR, GREB1, STK31, CORIN, and TDRD9), miR-211 (FSHR, GREB1, STK31, CORIN, and TDRD9), miR-204 (FSHR, GREB1, CORIN, and TDRD9), and miR-302b-5p (CYP19A1 and TDRD9) may play crucial roles in ovarian development. These analyses provide new clues to uncover molecular mechanisms and signaling networks of ovarian development.

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

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.

Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis

BACKGROUND

Long noncoding RNAs (lncRNAs) have roles in gene regulation, epigenetics, and molecular scaffolding and it is hypothesized that they underlie some mammalian evolutionary adaptations. However, for many mammalian species, the absence of a genome assembly precludes the comprehensive identification of lncRNAs. The genome of the American beaver (Castor canadensis) has recently been sequenced, setting the stage for the systematic identification of beaver lncRNAs and the characterization of their expression in various tissues. The objective of this study was to discover and profile polyadenylated lncRNAs in the beaver using high-throughput short-read sequencing of RNA from sixteen beaver tissues and to annotate the resulting lncRNAs based on their potential for orthology with known lncRNAs in other species.

RESULTS

Using de novo transcriptome assembly, we found 9528 potential lncRNA contigs and 187 high-confidence lncRNA contigs. Of the high-confidence lncRNA contigs, 147 have no known orthologs (and thus are putative novel lncRNAs) and 40 have mammalian orthologs. The novel lncRNAs mapped to the Oregon State University (OSU) reference beaver genome with greater than 90% sequence identity. While the novel lncRNAs were on average shorter than their annotated counterparts, they were similar to the annotated lncRNAs in terms of the relationships between contig length and minimum free energy (MFE) and between coverage and contig length. We identified beaver orthologs of known lncRNAs such as XIST, MEG3, TINCR, and NIPBL-DT. We profiled the expression of the 187 high-confidence lncRNAs across 16 beaver tissues (whole blood, brain, lung, liver, heart, stomach, intestine, skeletal muscle, kidney, spleen, ovary, placenta, castor gland, tail, toe-webbing, and tongue) and identified both tissue-specific and ubiquitous lncRNAs.

CONCLUSIONS

To our knowledge this is the first report of systematic identification of lncRNAs and their expression atlas in beaver. LncRNAs-both novel and those with known orthologs-are expressed in each of the beaver tissues that we analyzed. For some beaver lncRNAs with known orthologs, the tissue-specific expression patterns were phylogenetically conserved. The lncRNA sequence data files and raw sequence files are available via the web supplement and the NCBI Sequence Read Archive, respectively.

Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms

Next-generation sequencing technologies and the availability of an increasing number of mammalian and other genomes allow gene expression studies, particularly RNA sequencing, in many non-model organisms. However, incomplete genome annotation and assignments of genes to functional annotation databases can lead to a substantial loss of information in downstream data analysis. To overcome this, we developed Mammalian Annotation Database tool (MAdb, https://madb.ethz.ch) to conveniently provide homologous gene information for selected mammalian species. The assignment between species is performed in three steps: (i) matching official gene symbols, (ii) using ortholog information contained in Ensembl Compara and (iii) pairwise BLAST comparisons of all transcripts. In addition, we developed a new tool (AnnOverlappeR) for the reliable assignment of the National Center for Biotechnology Information (NCBI) and Ensembl gene IDs. The gene lists translated to gene IDs of well-annotated species such as a human can be used for improved functional annotation with relevant tools based on Gene Ontology and molecular pathway information. We tested the MAdb on a published RNA-seq data set for the pig and showed clearly improved overrepresentation analysis results based on the assigned human homologous gene identifiers. Using the MAdb revealed a similar list of human homologous genes and functional annotation results regardless of whether starting with gene IDs from NCBI or Ensembl. The MAdb database is accessible via a web interface and a Galaxy application.

Genome-Wide Differential Expression Profiling of Ovarian circRNAs Associated With Litter Size in Pigs

Circular RNAs (circRNAs) have been emerging as an important regulator in mammalian reproduction via acting as miRNA sponges. However, the circRNAs in porcine ovaries related with litter size remains largely unknown. In this study, porcine ovaries with smaller or larger litter size (LLS) were subjected to high-throughput RNA sequencing. In total, 38,722 circRNAs were identified, of which 1,291 circRNAs were commonly expressed in all samples. There were 56 circRNAs significantly down-regulated and 54 circRNAs up-regulated in LLS pig (|log2 (fold change) | > 1, FDR < 0.05). Bioinformatics predicted that most of circRNAs harbored miRNA binding sites, and the expression patterns of circRNAs and their putative binding miRNAs were validated by qPCR. Moreover, the expression of circ-TCP11/miR-183 was significantly reversely correlated and their direct interaction was confirmed by dual-luciferase assay. Our study indicates that circRNAs may play potential effects on modulating porcine litter size.

Potential of epigenetic events in human thyroid cancer

Thyroid cancer remains the highest prevailing endocrine malignancy, and its incidence rate has progressively increased in the previous years. Above 95% of thyroid tumor are follicular cells types of carcinoma in which are considered invasive type of tumor. The pathogenesis and molecular mechanism of thyroid tumors are yet remains elucidated, in spite of activating RET, RAS and BRAF carcinogenesis have been well introduced. Nemours molecular alterations have been defined and have revealed promise for their diagnostic, prognostic and therapeutic capacity but still need further confirmation. Among different types of mechanisms, the current article reviews the importance of epigenetic modifications in thyroid cancer. Increasing data from previous reports demonstrate that acquired epigenetic abnormalities together with genetic changes plays an important role in alteration of gene expression patterns. Aberrant DNA methylation has been well known in the CpG regions and profile of microRNAs (mi-RNAs) expression also involved in cancer development. In addition, the gene expression through epigenetic control contribution to thyroid cancer is analyzed and it is semi considered in the clinic. However the epigenetic of the thyroid cancer is yet remains in its early stages, and it carries encouraging potential thyroid cancer detections in its early stages, assessment of prognosis and targeted cancer treatment.

Identification and characterization of long non-coding RNAs involved in embryo development of Ginkgo biloba

Long non-coding RNAs (lncRNAs) are important regulatory factors for plant growth and development. Despite this, little is known about the regulatory interactions of lncRNAs with mRNA during embryo development. Here, we used a bioinformatics genome-wide approach to identify lncRNAs involved in embryo development of Ginkgo biloba, based on RNA sequencing datasets from G. biloba embryos during early, middle, late developmental stages. In total, 2326 lncRNAs were identified in the G. biloba embryos, of which 1307 and 1019 could be classified as long intergenic non-coding RNAs and antisense lncRNAs, respectively. Among them, a total of 657 differentially expressed lncRNAs were identified in the different developmental stages of the G. biloba embryos. Based on the functional annotation of potential target genes of lncRNAs, 50, 33, and 76 lncRNAs were predicted to target genes involved in plant hormone signal transduction, plant hormone biosynthesis, and circadian rhythm regulation, respectively. A lncRNA (17)-miRNA (25)-PCgene (52) network was constructed for the G. biloba embryo. Three lncRNAs (lnc000823, lnc002072, lnc000866) were predicted as target mimics of miR159, which targeted two transcription factors with variety of functions, Gb_11536 (MYB33) and Gb_23921 (MYB101). The data generated in this study provide a better understanding of the roles of lncRNAs in embryo development of G. biloba and plants in general.