scholarly journals Transcriptome profiling of developing testes and spermatogenesis in the Mongolian horse

2020 ◽  
Author(s):  
Bei LI ◽  
Xiaolong He ◽  
Yiping Zhao ◽  
Dongyi Bai ◽  
Ming Du ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Developmental Stages ◽  
Male Gamete ◽  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
Testicular Development ◽  
Testis Development ◽  
Oocyte Meiosis ◽  
Alternative Splicing Events ◽  
Mongolian Horse

Abstract Background: Horse testis development and spermatogenesis are complex physiological processes. Methods: To study these processes, three immature and three mature testes were collected from the Mongolian horse, and six libraries were established using high-throughput RNA sequencing technology (RNA-Seq) to screen for genes related to testis development and spermatogenesis. Results: A total of 16,237 upregulated genes and 8,641 downregulated genes were detected in the testis of the Mongolian horse. These genes play important roles in different developmental stages of spermatogenesis and testicular development. Five genes with alternative splicing events that may influence spermatogenesis and development of the testis were detected. GO (Gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses were performed for functional annotation of the differentially expressed genes. Pathways related to “spermatogenesis,” male gamete generation,” “spermatid development” and “oocyte meiosis” were significantly involved in different stages of testis development and spermatogenesis. Conclusion: Genes, pathways and alternative splicing events were identified with inferred functions in the process of spermatogenesis in the Mongolian horse. The identification of these differentially expressed genetic signatures improves our understanding of horse testis development and spermatogenesis.

scholarly journals Transcriptome profiling of developing testes and spermatogenesis in the Mongolian horse

2020 ◽  
Author(s):  
Bei LI ◽  
Xiaolong He ◽  
Yiping Zhao ◽  
Dongyi Bai ◽  
Ming Du ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Developmental Stages ◽  
Male Gamete ◽  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
Testicular Development ◽  
Testis Development ◽  
Oocyte Meiosis ◽  
Alternative Splicing Events ◽  
Mongolian Horse

Abstract Background: Horse testis development and spermatogenesis are complex physiological processes. Methods: To study these processes, three immature and three mature testes were collected from the Mongolian horse, and six libraries were established using high-throughput RNA sequencing technology (RNA-Seq) to screen for genes related to testis development and spermatogenesis. Results: A total of 16,237 upregulated genes and 8,641 downregulated genes were detected in the testis of the Mongolian horse. These genes play important roles in different developmental stages of spermatogenesis and testicular development. Five genes with alternative splicing events that may influence spermatogenesis and development of the testis were detected. GO (Gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses were performed for functional annotation of the differentially expressed genes. Pathways related to “spermatogenesis,” male gamete generation,” “spermatid development” and “oocyte meiosis” were significantly involved in different stages of testis development and spermatogenesis. Conclusion: Genes, pathways and alternative splicing events were identified with inferred functions in the process of spermatogenesis in the Mongolian horse. The identification of these differentially expressed genetic signatures improves our understanding of horse testis development and spermatogenesis.

scholarly journals Transcriptome profiling of developing testes and spermatogenesis in the Mongolian horse

2020 ◽  
Author(s):  
Bei LI ◽  
Xiaolong He ◽  
Yiping Zhao ◽  
Dongyi Bai ◽  
Ming Du ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Developmental Stages ◽  
Male Gamete ◽  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
Testicular Development ◽  
Testis Development ◽  
Oocyte Meiosis ◽  
Alternative Splicing Events ◽  
Mongolian Horse

Abstract Background: Horse testis development and spermatogenesis are complex physiological processes. Methods: To study these processes, three immature and three mature testes were collected from the Mongolian horse, and six libraries were established using high-throughput RNA sequencing technology (RNA-Seq) to screen for genes related to testis development and spermatogenesis. Results: A total of 16,237 upregulated genes and 8,641 downregulated genes were detected in the testis of the Mongolian horse. These genes play important roles in different developmental stages of spermatogenesis and testicular development. Five genes with alternative splicing events that may influence spermatogenesis and development of the testis were detected. GO (Gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses were performed for functional annotation of the differentially expressed genes. Pathways related to “spermatogenesis,” male gamete generation,” “spermatid development” and “oocyte meiosis” were significantly involved in different stages of testis development and spermatogenesis. Conclusion: Genes, pathways and alternative splicing events were identified with inferred functions in the process of spermatogenesis in the Mongolian horse. The identification of these differentially expressed genetic signatures improves our understanding of horse testis development and spermatogenesis.

scholarly journals Transcriptome profiling of developing testes and spermatogenesis in Mongolian horse

2019 ◽  
Author(s):  
Bei LI ◽  
Xiaolong He ◽  
Yiping Zhao ◽  
Dongyi Bai ◽  
Ming Du ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Male Gamete ◽  
Transcriptome Profiling ◽  
Testicular Development ◽  
Testis Development ◽  
Physiological Processes ◽  
Oocyte Meiosis ◽  
Mongolian Horse ◽  
Pathway Analyses ◽  
Upregulated Genes

Abstract Introduction: The development of horse testis and spermatogenesis is a complex physiological process. Methods: To study those physiological processes, 3 immature and 3 mature testes of Mongolian horse were collected, and six libraries were established using a high-throughput RNA sequencing technology (RNA-Seq) to screen for genes that were related to Mongolian horse testis development and spermatogenesis.Results & Discussion: A total of 16,237 upregulated genes and 8,641 downregulated genes in the testis of Mongolian horse were detected. These genes play important roles in different developmental stages of spermatogenesis and testicular development. Five alternative splicing (AS) event genes were detected, and different AS events can also influence both spermatogenesis and developing of testis. GO (Gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses were performed for functional annotation of the differentially expressed genes during testis development and spermatogenesis. For example, oocyte meiosis pathways were significantly involved in different stages of testis development and spermatogenesis.Conclusion: These genes were associated with spermatogenesis, male gamete generation, spermatid development, and oocyte meiosis.The finding that gene is a vital element in horse testis development improves our understanding of horse testis development and spermatogenesis.

scholarly journals Comprehensive analysis of miRNA-mRNA/lncRNA during gonadal development of triploid female rainbow trout (Oncorhynchus mykiss)

2020 ◽  
Author(s):  
Tianqing Huang ◽  
Wei Gu ◽  
Enhui Liu ◽  
Xiulan Shi ◽  
Bingqian Wang ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Noncoding Rnas ◽  
Gonadal Development ◽  
Differentially Expressed ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Oocyte Meiosis ◽  
Non Coding Rna

Abstract Background: Chromosomal ploidy manipulation is one of the means to create excellent germplasm. Triploid fish could provide an ideal sterile model for the mechanism research of abnormality in meiosis. The complete understanding of the coding and noncoding RNAs regulating sterility caused by meiosis abnormality is still not well understood.Results: By high-throughput sequencing, we compared the expression profiles of gonadal mRNA, long non-coding RNA (lncRNA), and microRNA (miRNA) at different developmental stages [65 days post fertilisation (dpf), 180 dpf, and 600 dpf] between the diploid (XX) and triploid (XXX) female rainbow trout. A majority of differentially expressed (DE) RNAs were identified, and 22 DE mRNAs related to oocyte meiosis and homologous recombination were characterized. The predicted miRNA-mRNA/lncRNA networks of 3 developmental stages were constructed based on the target pairs of DE lncRNA-miRNA and DE mRNA-miRNA. According to the networks, meiosis-related gene of ccne1 was targeted by dre-miR-15a-5p_R+1, and 6 targeted DE lncRNAs were identified. Also, RT-qPCR was performed to validate the credibility of the network.Conclusions: This study explored the potential interplay between coding and noncoding RNAs during the gonadal development of polyploid fish. It provides full insights into polyploidy-associated effects on fertility of fish. These differentially expressed coding and noncoding RNAs provide a novel resource for studying genome diversity of polyploid induction.

Analysis of the miRNA transcriptome during testicular development and spermatogenesis of the Mongolian horse

2020 ◽  
Vol 32 (6) ◽  
pp. 582
Author(s):  
Bei Li ◽  
Xiaolong He ◽  
Yiping Zhao ◽  
Dongyi Bai ◽  
Dandan Li ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Profiles ◽  
Mammalian Species ◽  
Mature Mirnas ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
P Value ◽  
Testicular Development ◽  
Interaction Sites ◽  
Mongolian Horse

Numerous studies have shown that microRNAs (miRNAs) are essential for testicular development and spermatogenesis. In order to further characterise these physiological processes, three immature and three mature testes of the Mongolian horse were collected and six libraries were established. Using small RNA sequencing technology, 531 mature miRNAs were identified, including 46 novel miRNAs without previously ascribed functions. Among the 531 miRNAs, 421 were expressed in both immature and mature libraries, 65 miRNAs were found solely in immature testis libraries and 45 miRNAs were found solely in mature testis libraries. Furthermore, among the miRNAs that were identified in both immature and mature libraries, 107 were significantly differentially expressed (corrected P value (padj)<0.05). Among the miRNAs that were only expressed in immature testes, two miRNAs were differentially expressed, whereas among the miRNAs that were only expressed in mature testes, nine miRNAs were differentially expressed. Comprehensive analysis of miRNA and mRNA expression profiles predicted 107 miRNA–mRNA interaction sites. Gene ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis of the predicted target genes suggested roles of the differentially expressed miRNAs in testicular development and spermatogenesis. These findings identify miRNAs as key factors in the development of the testes and spermatogenesis in the Mongolian horse, which may also help us to understand the mechanisms of fertility in related mammalian species.

scholarly journals Integrated analysis of miRNA and mRNA expression profiles in testes of Duroc and Meishan boars

2019 ◽  
Author(s):  
Haisheng Ding ◽  
Min Liu ◽  
Changfan Zhou ◽  
Xiangbin You ◽  
Tao Su ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Male Gamete ◽  
Mirna Expression Profile ◽  
Mapk Signaling ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Testis Development ◽  
Differentially Expressed Mirnas

Abstract Background: MicroRNAs (miRNAs) are small non-coding RNAs playing vital roles in regulating posttranscriptional gene expression. Elucidating the expression regulation of miRNAs underlying pig testis development will contribute to a better understanding of boar fertility and spermatogenesis. Results: In this study, miRNA expression profile was investigated in testes of Duroc and Meishan boars at 20, 75, and 270 days of age by high-throughput sequencing. Forty-five differentially expressed miRNAs were identified from testes of Duroc and Meishan boars before and after puberty. Integrated analysis of miRNA and mRNA profiles predicted many miRNA-mRNA pairs. Gene ontology and biological pathway analyses revealed that predicted target genes of ssc-mir-423-5p, ssc-mir-34c, ssc-mir-107, ssc-165 mir-196b-5p, ssc-mir-92a, ssc-mir-320, ssc-mir-10a-5p, and ssc-mir-181b were involved in sexual reproduction, male gamete generation, and spermatogenesis, and GnRH, Wnt, and MAPK signaling pathway. Four significantly differentially expressed miRNAs and their predicted target genes were validated by quantitative real-time polymerase chain reaction, and phospholipase C beta 1 ( PLCβ1) gene was verified to be a target of ssc-mir-423-5p . Conclusions: This study provides an insight into the functional roles of miRNAs in testis development and spermatogenesis and offers useful resources for understanding differences in sexual function development caused by the change in miRNAs expression between Duroc and Meishan boars.

scholarly journals Integrated analysis of miRNA and mRNA expression profiles in testes of Duroc and Meishan boars

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Haisheng Ding ◽  
Min Liu ◽  
Changfan Zhou ◽  
Xiangbin You ◽  
Tao Su ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Male Gamete ◽  
Mirna Expression Profile ◽  
Mapk Signaling ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Testis Development ◽  
Differentially Expressed Mirnas

Abstract Background MicroRNAs (miRNAs) are small non-coding RNAs playing vital roles in regulating posttranscriptional gene expression. Elucidating the expression regulation of miRNAs underlying pig testis development will contribute to a better understanding of boar fertility and spermatogenesis. Results In this study, miRNA expression profile was investigated in testes of Duroc and Meishan boars at 20, 75, and 270 days of age by high-throughput sequencing. Forty-five differentially expressed miRNAs were identified from testes of Duroc and Meishan boars before and after puberty. Integrated analysis of miRNA and mRNA profiles predicted many miRNA-mRNA pairs. Gene ontology and biological pathway analyses revealed that predicted target genes of ssc-mir-423-5p, ssc-mir-34c, ssc-mir-107, ssc-mir-196b-5p, ssc-mir-92a, ssc-mir-320, ssc-mir-10a-5p, and ssc-mir-181b were involved in sexual reproduction, male gamete generation, and spermatogenesis, and GnRH, Wnt, and MAPK signaling pathway. Four significantly differentially expressed miRNAs and their predicted target genes were validated by quantitative real-time polymerase chain reaction, and phospholipase C beta 1 (PLCβ1) gene was verified to be a target of ssc-mir-423-5p. Conclusions This study provides an insight into the functional roles of miRNAs in testis development and spermatogenesis and offers useful resources for understanding differences in sexual function development caused by the change in miRNAs expression between Duroc and Meishan boars.

scholarly journals Computer Analysis of Glioma Transcriptome Profiling: Alternative Splicing Events

2017 ◽  
Vol 14 (3) ◽  
Author(s):  
Vladimir N. Babenko ◽  
Natalya V. Gubanova ◽  
Anatoly O. Bragin ◽  
Irina V. Chadaeva ◽  
Gennady V. Vasiliev ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Culture ◽  
Alternative Splicing ◽  
Expression Profiles ◽  
Rna Extraction ◽  
Transcriptome Profiling ◽  
Laboratory Animals ◽  
Normal Brain ◽  
Computer Tools ◽  
Alternative Splicing Events

AbstractHere we present the analysis of alternative splicing events on an example of glioblastoma cell culture samples using a set of computer tools in combination with database integration. The gene expression profiles of glioblastoma were obtained from cell culture samples of primary glioblastoma which were isolated and processed for RNA extraction. Transcriptome profiling of normal brain samples and glioblastoma were done by Illumina sequencing. The significant differentially expressed exon-level probes and their corresponding genes were identified using a combination of the splicing index method. Previous studies indicated that tumor-specific alternative splicing is important in the regulation of gene expression and corresponding protein functions during cancer development. Multiple alternative splicing transcripts have been identified as progression markers, including generalized splicing abnormalities and tumor- and stage-specific events. We used a set of computer tools which were recently applied to analysis of gene expression in laboratory animals to study differential splicing events. We found 69 transcripts that are differentially alternatively spliced. Three cancer-associated genes were considered in detail, in particular: APP (amyloid beta precursor protein), CASC4 (cancer susceptibility candidate 4) and TP53. Such alternative splicing opens new perspectives for cancer research.

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