scholarly journals Identification of Circular RNAs in the Anterior Pituitary in Rats Treated with GnRH

Animals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 2557
Author(s):  
Hai-Xiang Guo ◽  
Bao Yuan ◽  
Meng-Ting Su ◽  
Yi Zheng ◽  
Jin-Yu Zhang ◽  
...  

The pituitary gland, an important endocrine organ, can secrete a variety of reproductive hormones under the action of hypothalamus-secreted gonadotropin-releasing hormone (GnRH) and plays important roles in animal reproduction. Circular RNAs (circRNAs) are a class of RNA molecules with stable covalently closed circular structures. CircRNAs are equipped with miRNA response elements (MREs), which can regulate the expression of target genes by competitively binding miRNAs. However, whether the expression levels of circRNAs in the pituitary gland change under the action of GnRH and whether such changes can further affect the secretion of reproductive hormones are still unclear. In this study, we performed RNA sequencing (RNA-Seq) of GnRH-treated rats to identify differentially expressed circRNAs. The results revealed 1433 related circRNAs, 14 of which were differentially expressed. In addition, we randomly selected five differentially expressed circRNAs and tested their relative expression levels by RT-qPCR, the results of which were consistent with the RNA sequencing results. Finally, we predicted targeted relationships between the differentially expressed circRNAs and FSHb-LHb-associated miRNAs. In all, a total of 14 circRNAs were identified that may act on the secretion and regulation of reproductive hormones in GnRH-treated rats. Our expression profiles of circRNAs in the anterior pituitaries of rats treated with GnRH can provide insights into the roles of circRNAs in mammalian development and reproduction.

2020 ◽  
Author(s):  
Fangwei Li ◽  
Hong Wang ◽  
Hongyan Tao ◽  
Fanqi Wu ◽  
Dan Wang ◽  
...  

Abstract Background: Recent studies have found a regulatory role of circular RNAs (circRNAs) in the pathogenesis of idiopathic pulmonary fibrosis (IPF). However, the function and underlying molecular mechanism of circRNAs involved in IPF are uncertain and incomplete. This study aimed to further provide some critical information for the circRNA function in IPF using bioinformatic analysis. Methods: We searched in the NCBI (National Center for Biotechnology Information) Gene Expression Omnibus (GEO) database to find the circRNA expression profiles of human IPF. The microarray data GSE102660 was obtained and differentially expressed circRNAs were identified through R software. Results: 6 significantly up-regulated and 13 significantly down-regulated circRNAs were identified involved in the pathogenesis of IPF. The binding sites of miRNAs for each differentially expressed circRNA were also predicted and circRNA-miRNA-mRNA networks were constructed for the most up-regulated hsa_circ_0004099 and down-regulated hsa_circ_0029633. In addition, GO and KEGG enrichment analysis revealed the molecular function and enriched pathways of the target genes of circRNAs in IPF.Conclusion: These findings suggest that candidate circRNAs might serve an important role in the pathogenesis of IPF. Therefore, these circRNAs might be potential biomarkers for diagnosis and promising targets for treatment of IPF, which still need further verification in vivo and in vitro.


2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Xiaocong Yao ◽  
Minbo Liu ◽  
Fang Jin ◽  
Zhongxin Zhu

Aim. Circular RNAs (circRNAs) have been found to contribute to the regulation of many diseases and are abundantly expressed in various organisms. The present study is aimed at systematically characterizing the circRNA expression profiles in patients with senile osteoporotic vertebral compression fracture (OVCF) and predicting the potential functions of the regulatory networks correlated with these differentially expressed circRNAs. Methods. The circRNA expression profile in patients with senile OVCF was explored by using RNA sequencing. The prediction of the enriched signaling pathways and circRNA-miRNA networks was conducted by bioinformatics analysis. Real-time quantitative PCR was used to validate the selected differentially expressed circRNAs from 20 patients with senile OVCF relative to 20 matched healthy controls. Results. A total of 884 differentially expressed circRNAs were identified, of which 554 were upregulated and 330 were downregulated. The top 15 signaling pathways associated with these differentially expressed circRNAs were predicted. The result of qRT-PCR of the selected circRNAs was consistent with RNA sequencing. Conclusions. CircRNAs are differentially expressed in patients with senile OVCF, which might contribute to the pathophysiological mechanism of senile osteoporosis.


Author(s):  
Si Chen ◽  
Xiaofei Guo ◽  
Xiaoyun He ◽  
Ran Di ◽  
Xiaosheng Zhang ◽  
...  

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.


2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Yu Du ◽  
Haiyang Tang ◽  
Xia Gu ◽  
Yixin Shi ◽  
Ping Gong ◽  
...  

Objectives. Radiotherapy is a common therapy in head and neck tumors, which may cause a side effect radiation bone injury (RBI). Furthermore, it has been investigated that microRNA (miRNA) expression levels were altered after radiotherapy. Exosomes play a role in bone formation as miRNA containers, while radiation affects exosomes composition, secretion, and function. So, our objective is to explore changes in miRNA levels during bone formation after radiotherapy and identify the differentially expressed miRNAs (DE-miRs) in plasma exosomes during the process of osteogenesis related to irradiation. Materials and Methods. In this study, we analyzed nine samples from three rabbits exposed twice to radiation (15 Gy each) and detected DE-miRs from irradiated plasma exosomes during the process of osteogenesis by RNA sequencing. Further, we identified DE-miRs with significant differences and predicted their target genes via the bioinformatics analysis tools Targetscan v7.2 and miRPathDB v2.0. Finally, we identified radiation-responsive miRNAs and predicted their target genes during osteogenesis. Results. Taken together, we have identified some DE-miRs in irradiated plasma exosomes, which were involved in several vital signaling pathways related to bone physiology, such as the Wnt pathway, MAPK cascade, and calcium modulating pathway. Conclusions. We have found that plasma exosomes are one of the ways by which radiation can affect bone metabolism and regeneration. However, the specific mechanisms of how these plasma exosomal miRNAs mediate the osteogenesis pathways must be further investigated. Clinical Relevance. Radiotherapy may cause radiation bone injury, and miRNA expression levels in rabbit plasma exosomes are altered after radiotherapy. High-throughput RNA sequencing can identify the differentially expressed miRNAs in irradiated plasma exosomes during the process of osteogenesis. These findings make sense to develop novel therapeutic strategies for treating radiation-induced bone injury disorders.


2021 ◽  
Author(s):  
Li-rong Yan ◽  
Ang Wang ◽  
Qian Xu ◽  
Ben-gang Wang

Abstract Background Recently, the incidence of cholangiocarcinoma (CCA) has gradually increased. As CCA has a poor prognosis, the ideal survival rate is scarce for patients. The abnormal expressed tsRNAs may regulate the progression of a variety of tumors, and tsRNAs is expected to become a new diagnostic biomarker of cancer. However, the expression of tsRNAs is obscure and should be elucidated in CCA. Methods High-throughput RNA sequencing technology (RNA-seq) was utilized to determine the overall expression profiles of tsRNAs in 3 pairs CCA and adjacent normal tissues and to screen the tsRNAs that were differentially expressed. The target genes of dysregulated tsRNAs were predicted and the biological effects and potential signaling pathways of these target genes were explored by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate 11 differentially expressed tRFs with 12 pairs CCA and adjacent normal tissues. Results High-throughput RNA-seq totally demonstrated 535 dysregulated tsRNAs, of which 241 tsRNAs were upregulated and 294 tsRNAs were downregulated in CCA compared with adjacent normal tissues (|log2 (fold change) |≥1 and P value < 0.05). GO and KEGG enrichment analyses indicated that the target genes of dysregulated tRFs (tRF-34-JJ6RRNLIK898HR, tRF-38-0668K87SERM492V and tRF-39-0668K87SERM492E2) were mainly enriched in the Notch signaling pathway, Hippo signaling pathway, cAMP signaling pathway and in growth hormone synthesis, secretion and action, etc. qRT-PCR result showed that tRF-34-JJ6RRNLIK898HR/tRF-38-0668K87SERM492V/tRF-39-0668K87SERM492E2 was down-regulated (P = 0.021) and tRF-20-LE2WMK81 was up-regulated in CCA (P = 0.033). Conclusion Differentially expressed tRFs in CCA are enriched in many pathways associated with neoplasms, which may impact the tumor progression and have potential to be diagnostic biomarkers and therapeutic targets of CCA.


2019 ◽  
Vol 2019 ◽  
pp. 1-14
Author(s):  
Maoxing Pan ◽  
Yuanjun Deng ◽  
Chuiyang Zheng ◽  
Huan Nie ◽  
Kairui Tang ◽  
...  

Objective. The purpose of present study was to investigate the potential mechanism underlying the protective effect of Shenling Baizhu San (SLBZS) on nonalcoholic fatty liver disease (NAFLD) by microRNA (miRNA) sequencing. Methods. Thirty male Wistar rats were randomly divided into a normal control (NC) group, a high-fat diet (HFD) group, and an SLBZS group. After 12 weeks, the biochemical parameters and liver histologies of the rats were assessed. The Illumina HiSeq 2500 sequencing platform was used to analyse the hepatic miRNA expression profiles. Representative differentially expressed miRNAs were further validated by qRT-PCR. The functions of the differentially expressed miRNAs were analysed by bioinformatics. Results. Our results identified 102 miRNAs that were differentially expressed in the HFD group compared with the NC group. Among those differentially expressed miRNAs, the expression levels of 28 miRNAs were reversed by SLBZS administration, suggesting the modulation effect of SLBZS on hepatic miRNA expression profiles. The qRT-PCR results confirmed that the expression levels of miR-155-5p, miR-146b-5p, miR-132-3p, and miR-34a-5p were consistent with those detected by sequencing. Bioinformatics analyses indicated that the target genes of the differentially expressed miRNAs reversed by SLBZS were mainly related to metabolic pathways. Conclusion. This study provides novel insights into the mechanism of SLBZS in protecting against NAFLD; this mechanism may be partly related to the modulation of hepatic miRNA expression and their target pathways.


2021 ◽  
Author(s):  
Luzheng Liu ◽  
Jiacheng Chen ◽  
Liang Chen ◽  
Cheng Chen ◽  
Dafeng Xu ◽  
...  

Abstract BACKGROUND Circular RNA (CircRNA) and HBx genes separately play essential roles in the occurrence and development of hepatitis B (HBV)-related hepatocellular carcinoma (HCC). However, whether HBx expression in HCC is co-related to differential circRNA patterns remains unknown. METHODS HCC cell lines with HBx overexpression (HepG2 H6679) and empty vector control (HepG2 H5298) were successfully constructed. The high-throughput second-generation transcriptome sequencing technology (RNA-seq) was employed to sequence the two cell lines, and the selected circRNAs were verified by qPCR (quantitative real-time PCR). The differentially expressed circRNAs were analyzed. Bioinformatics analyses, including clustering, differential expression, GO analysis, and KEGG pathway, were performed. Target Scan and Miranda software were employed to predict miRNAs corresponding with circRNAs. RESULTS We identified 1120 circRNAs upregulated and 1447 circRNAs downregulated in HepG2 cell lines with HBx overexpression compared to its control. We selected 36 circRNAs with significant differences (also consistent with log2fold change absolute value ≥ 1.0 or P ≤ 0.05) displayed by cluster analysis and then performed qPCR validation. Among them, 15 circRNAs (hsa_circ_0005603, hsa_circ_0004448, hsa_circ_0006845, hsa_circ_0064654, hsa_circ_0006460, hsa_circ_0045350, hsa_circ_0000824, hsa_circ_0005227, hsa_circ_0067991, hsa_circ_0064656, hsa_circ_0005224, circRNA11716, circRNA759, circRNA14848 and circRNA13751) are consistent with sequencing results. Hsa_circ_0005603 and hsa_circ_0006845 showed significant differences and were chosen for further study. GO analysis shows that many target genes are involved in biological processes, cellular components, and molecular functions. Nearly 193 target genes were enriched on KEGG pathways analysis. Actin cytoskeleton regulation, tight junction, and FoxO signaling pathway are among the top three pathways involved in most genes. We predicted that hsa_circ_0005603 might interact with micro-RNAs, including miR-182-5p, hsa-miR-27a-3p, hsa-miR-98-5p, and hsa-miR-198, that might thereby regulate downstream genes involved in tumor progression. Similarly, hsa_circ_0006845 was predicted to be referred to HBV-related HCC by acting as a sponge for hsa-miR-106a-3p and hsa-miR-198. Furthermore, we discovered two novel circular RNAs (circRNA11716 and circRNA13751) which might be involved in HCC occurrence. CONCLUSION In this study, we comprehensively explored the differentially expressed circRNAs in HepG2 cells with different HBx expression, and our results indicate that hsa_circ_0005603, hsa_circ_0006845, and novel circular RNAs (circRNA11716 and circRNA13751) might play an important role in HBV-related HCC, deserving further research.


Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1381
Author(s):  
Aqin Cao ◽  
Ruihua Wang ◽  
Jianbo Wang

High-throughput sequencing was used to distinguish the gene and miRNA expression profiles in the leaves of three progenies from a rice backcross introgression line (BC2F12) and their parents (Oryza sativa and wild rice, O. longistaminata). A total of 33,419 genes and 513 miRNAs were identified in two parents and three lines, and the majority of the genes and miRNAs were commonly expressed. The results show that 10.23% to 17.94% of the genes were differentially expressed genes (DEGs) in the progenies compared with those of the two parents, and the majority of them were up-regulated. Of the miRNAs, 12.56% to15.43% were differentially expressed in the progeny/O. sativa comparisons and the majority of which were up-regulated, while 42.02% to 45.21% of miRNAs were differentially expressed in the progeny/O. longistaminata comparisons, of which nearly half were down-regulated. Most of the DEGs and differentially expressed miRNAs showed expression levels close to that of O. sativa, indicating that the expression of genes and miRNAs in progenies was closely related to their chromosome complements and that the miRNAs were more susceptible than the genes to the effects of genomic composition. Furthermore, a larger number of target genes were predicted in the progeny/O. longistaminata comparisons. Finally, we found that the expression of some genes and miRNAs might increase the possibility for abiotic stress responses and adaptation in progenies. Together, our findings increase the understanding of the molecular mechanisms of hybridization and backcrossing on the expression levels of genes and miRNAs in rice leaves.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Samina Shabbir ◽  
Prerona Boruah ◽  
Lingli Xie ◽  
Muhammad Fakhar-e-Alam Kulyar ◽  
Mohsin Nawaz ◽  
...  

AbstractOvary development is an important determinant of the procreative capacity of female animals. Here, we performed genome-wide sequencing of long non-coding RNAs (lncRNAs) and mRNAs on ovaries of 1, 3 and 8 months old Hu sheep to assess their expression profiles and roles in ovarian development. We identified 37,309 lncRNAs, 45,404 messenger RNAs (mRNAs) and 330 novel micro RNAs (miRNAs) from the transcriptomic analysis. Six thousand, seven hundred and sixteen (6716) mRNAs and 1972 lncRNAs were significantly and differentially expressed in ovaries of 1 month and 3 months old Hu sheep (H1 vs H3). These mRNAs and target genes of lncRNAs were primarily enriched in the TGF-β and PI3K-Akt signalling pathways which are closely associated with ovarian follicular development and steroid hormone biosynthesis regulation. We identified MSTRG.162061.1, MSTRG.222844.7, MSTRG.335777.1, MSTRG.334059.16, MSTRG.188947.6 and MSTRG.24344.3 as vital genes in ovary development by regulating CTNNB1, CCNA2, CDK2, CDC20, CDK1 and EGFR expressions. A total of 2903 mRNAs and 636 lncRNAs were differentially expressed in 3 and 8 months old ovaries of Hu sheep (H3 vs H8); and were predominantly enriched in PI3K-Akt, progesterone-mediated oocyte maturation, estrogen metabolism, ovulation from the ovarian follicle and oogenesis pathways. These lncRNAs were also found to regulate FGF7, PRLR, PTK2, AMH and INHBA expressions during follicular development. Our result indicates the identified genes participate in the development of the final stages of follicles and ovary development in Hu sheep.


Author(s):  
Han-Wen Chen ◽  
Xiao-Xia Zhang ◽  
Zhu-Ding Peng ◽  
Zu-Min Xing ◽  
Yi-Wen Zhang ◽  
...  

AbstractTreatment of bone cancer pain (BCP) caused by bone metastasis in advanced cancers remains a challenge in clinical oncology, and the underlying mechanisms of BCP are poorly understood. This study aimed to investigate the pathogenic roles of circular RNAs (circRNAs) in regulating cancer cell proliferation and BCP development. Eight differentially expressed circRNAs in the rat spinal cord were validated by agarose gel electrophoresis and Sanger sequencing. Expression of circRNAs and mRNAs was detected by quantitative RT-PCR. MTS assay and flow cytometry were performed to analyze cell proliferation and apoptosis, respectively. Differentially expressed mRNA profiles were characterized by deep RNA sequencing, hierarchical clustering, and functional categorization. The interactions among circRNAs, microRNAs (miRNAs), and mRNAs were predicted using TargetScan. Additionally, western blot was performed to determine the protein levels of Pax8, Isg15, and Cxcl10. Multiple circRNAs were differentially expressed in the spinal cords of BCP model rats; of these, circSlc7a11 showed the greatest increase in expression. The overexpression of circSlc7a11 significantly promoted cell proliferation and repressed apoptosis of LLC-WRC 256 and UMR-106 cells, whereas circSlc7a11 silencing produced the opposite effects. Altered expression of circSlc7a11 also induced substantial changes in the mRNA expression profiles of LLC-WRC 256 cells; these changes were linked to multiple apoptotic processes and signaling pathways, such as the chemokine signaling pathway, and formed a complex circRNA/miRNA/mRNA network. Additionally, Pax8, Isg15, and Cxc110 protein level in LLC-WRC 256 cells was consistent with the mRNA results. The circRNA circSlc7a11 regulates rat BCP development by modulating LLC-WRC 256 cell proliferation and apoptosis through multiple-signaling mechanisms.


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