Construction of N6 Methyladenosine Atlas in Yak Epididymis Reveals the Process of Sperm Maturation Modification
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ABSTRACT:
PROVIDER: PRJNA1101989 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28737077_1.fastq.gz | Fastqsanger.gz | |||
| SRR28737077_2.fastq.gz | Fastqsanger.gz | |||
| SRR28737078_1.fastq.gz | Fastqsanger.gz | |||
| SRR28737078_2.fastq.gz | Fastqsanger.gz | |||
| SRR28737079_1.fastq.gz | Fastqsanger.gz |
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Project description:The epididymis is an important component of the male reproductive system and a crucial site for sperm maturation. During the process of sperm maturation through the epididymis, the effective payload of SncRNA significantly changes, which may be related to epigenetic modifications. Unfortunately, the N6 Methyladenosine (m6A) modification profile of the epididymis has not yet been established. In this study, the MeRIP seq combined with RNA seq method was used to analyze the m6A modification levels in the head, body, and tail of yak epididymis. It was found that the level of m6A in the epididymis significantly increased, and differentially methylated RNAs (DMRs) in the proximal end of the epididymis were significantly enriched in Gap junction, ErbB signaling pathway, and mTOR signaling pathway, participating in cell communication and sperm maturation processes. In the distal epididymis, DMRs are enriched in Apoptosis, FoxO signaling pathway, PI3K Akt signaling pathway, and TNF signaling pathway, which are involved in sperm autophagy, oxidative stress, and sperm maturation. In addition, we identified key genes with significant changes in m6A levels but no differences in RNA levels, including YY1 associated factor 2 (YAF2), Fork head box J2 (FOXJ2), and Fork head box O1 (FOXO1), suggesting that these genes are modified by m6A to affect translation processes and participate in sperm maturation. In summary, our study established an m6A map of the epididymis, which is beneficial for further understanding the maturation process of sperm and revealing more information related to male infertility.
2024-06-01 | GSE264337 | GEO
Project description:N6-methyladenosine (m6A) is the most prominent mRNA modification in eukaryotes, and its potential regulatory role has recently been identified in mammals, plants, and yeast. However, how m6A methylation regulates spermatogenesis remains unknown. In this study, cattle-yak testis tissue was used as the experimental material, and the m6A map was generated through preliminary experiments and methylated RNA immunoprecipitation sequencing. Only spermatogonia and Sertoli cells were observed in cattle-yak testis tissue. Experiments examining the expression of methylation-related enzymes and the overall methylation level showed that the methylation level in the testis of the cattle-yak was slightly lower than that of the sexually mature yak, but significantly higher than that of the pre-sexually mature yak. Annotation analysis indicated that differentially methylated peaks were most frequently concentrated in exonic regions, followed by 3'UTR and finally 5'UTR regions. Through enrichment analysis of differentially expressed genes and differentially methylated corresponding genes, GO analysis of T-vs-Y group mainly involved spermatogenesis, including cytoskeleton, actin binding, etc. KEGG analysis showed that the differential genes were mainly enriched in actin cytoskeleton regulation and MAPK signaling pathway. GO analysis of the T-vs-M group mainly involved protein ubiquitination, ubiquitin ligase complexes, ubiquitin-dependent protein catabolism and endocytosis. KEGG analysis mainly involved apoptosis and Fanconi anemia pathways. This study will lay the foundation for elucidating the molecular mechanism of m6A in male sterility of cattle-yak.
2022-06-12 | GSE205649 | GEO
Project description:This study used yak and cattle-yak testes from different developmental stages as materials to construct a complete translation map of the testes, and integrated transcriptome and translation results to explore gene expression changes during the sexual maturation process of yak testes. This study utilized Ribo seq technology to construct a transcriptome map of yak testicular development, revealing that the expression of genes related to spermatogenesis is specifically translated and regulated at different developmental stages. In addition, many unknown open reading frames (ORFs) in the testes have been newly identified.
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Project description:Deep sequencing of mRNA from 6 organs of yak (Bos grunniens) Analysis of ploy(A)+ RNA of brain,heart,liver,lung,spleen, and stomach of yak (Bos grunniens)
2012-05-18 | E-GEOD-33300 | biostudies-arrayexpress
Project description:Cattle-yak is the hybrid offspring of yak and cattle. It has obvious heterosis in production performance, but the male sterility of cattle-yak has always been the focus of attention. Studies have shown that non-coding RNA is involved in the regulation of spermatogenesis. We comprehensively compared the testicular transcription profiles of cattle, yak and cattle-yak. More DEGs, DECs and DEMs were found in the intersection of the two comparison groups of cattle and cattle-yak, yak and cattle-yak, with 4,968, 360 and 59, respectively. The DEGs of cattle-yak, cattle and yak were mainly enriched in biological processes such as spermatogenesis, male gamete generation and sexual reproduction. At the same time, GO and KEGG analysis suggested that DECs host genes and DEMs source genes were also involved in the regulation of spermatogenesis. The construction of potential ceRNA networks found that some differentially expressed ncRNAs may be involved in the regulation of genes related to testicular spermatogenesis, including miR-423-5p, miR-449b, miR-34b/c, miR-15b, etc., as well as unreported miR-6123, miR-1306 and some miRNA and circRNA interaction pairs. This study provides a reference for further study on the mechanism of male sterility in cattle-yak.
2024-02-06 | GSE254886 | GEO
Project description:Characterization of N6-methyladenosine in the testis tissue of cattle-yak
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Project description:Short-reading long RNA sequencing technology has been used to study the transcriptome of skeletal muscle of yak and cattle-yak, but it cannot accurately define full-length transcripts and alternative splicing isoforms. In this study, based on Oxford Nanopore Technologies ( ONT ) full-length sequencing technology, the longissimus dorsi transcription profiles of yak and cattle-yak were obtained. A total of 20323 new genes and 172870 new transcripts were identified, and 159700 new transcripts were successfully annotated. A total of 157812 AS events, 58073 SSRs, 57468 complete ORFs, 2296 transcription factors and 20404 lncRNAs were detected. The analysis found that different structural variations have specific functions, which contribute to the coordination of muscle development and the diversity of gene expression. In addition, the differentially expressed transcripts in longissimus dorsi muscle of yak and cattle-yak were involved in MAPK and JAK-STAT signaling pathway related to muscle development and growth. PPI analysis of differentially expressed transcripts suggested that TNNI2 may play a prominent role in the differences in muscle growth and meat quality traits between yak and cattle-yak. Our study enriched the transcriptome data of yak dorsal muscle and provided a reference for the production of yaks with higher meat yield and better meat quality.
2025-06-02 | GSE269050 | GEO
Project description:BackgroundDuring maturation, spermatozoa acquire motility and fertilizing capacity as they transit through the epididymis. In recent years, two-dimensional gel electrophoresis has been employed in proteomics studies conducted in rat, boar and human. However, there has not been a complete information regarding the proteins associated with sperm maturation in the epididymis. In this study, we employed iTRAQ proteomics to investigate proteins associated with sperm maturation between yak and cattleyak epididymis.ResultsAfter a successful sampling and protein extraction, the iTRAQ coupled with LC-MS/MS mass spectrometry and bioinformatics analysis were performed. We identified 288 differentially abundant proteins (DAPs) between yak and cattleyak epididymis; 151 were up-regulated while 137 were down-regulated in cattleyak relative to yak. Gene Ontology analysis identified that down-regulated DAPs in cattleyak were mostly enriched in the acetylation of protein component, along with negative and positive regulatory activities. iTRAQ proteomics data showed that the top up-regulated DAPs were mainly enriched in cell communication, cell adhesion, cytoskeleton organization, stress response, post-translational modifications and metabolic functions while the down-regulated DAPs were predominantly associated with sperm maturation, long-term sperm storage, sperm forward motility, sperm-oocyte fusion and regulatory functions.ConclusionThese results provide insight into the molecular mechanisms underlying male cattleyak sterility.
| S-EPMC8314601 | biostudies-literature
Project description:The yak estrus is a seasonal phenomenon, probably involving the epigenetic regulation of the synthesis and secretion of sex hormones as well as the growth and development of follicles. In this study, we collected the yak ovarian tissues at the three different states of anestrus, estrus, and pregnancy, and obtained the full transcriptome m6A map in yak by MeRIP-seq. The RT-qPCR showed that the expression of METTL3, METTL14, FTO, YTHDC1 were significantly different across different periods in the ovaries. Next, we identified 20174, 19747 and 13523 m6A peaks in the three ovarian samples of YO-A, YO-F and YO-P using the methylated RNA immunoprecipitation sequencing (MeRIP-seq). The m6A peaks are highly enriched in the coding sequence (CDS) region and 3′untranslated region (3′UTR) as well as the conserved sequence of “RRACH.” Functional analysis revealed the involvement of m6A in many physiological activities of the yak’s ovary during estrus and pregnancy. The association analysis found that some genes such as BNC1, HOMER1, BMP15, BMP6, GPX3, and WNT11 were related to ovarian functions. The comparison of the distribution patterns of methylation peaks in the ovarian tissues across different periods further explored the m6A markers related to the regulation of ovarian ovulation and follicular development in the yak ovary. This comprehensive map provides a solid foundation for revealing the potential function of the mRNA m6A modification in the yak ovary.
2021-07-22 | GSE180401 | GEO
Project description:Studying spermatogenesis is the key to understanding the development mechanism of the yak reproductive system. Although N6-methyladenosine (m6A) RNA modification has been reported to regulate spermatogenesis and reproductive function in mammals, the molecular mechanism of m6A in yak testis development and spermatogenesis remains largely unknown. Therefore, we collected testicular tissue from junile and adult yaks, and found that the m6A level significantly increased after sexual maturity in yak. In MeRIP-seq, 1,702 hypermethylated peaks and 724 hypomethylated peaks were identified. The hypermethylated differentially methylated RNAs (DMRs) (CIB2, AK1, FOXJ2, PKDREJ, SLC9A3, and TOPAZ1) mainly regulated spermatogenesis, while the hypomethylated DMRs (BCL6, USP25, CD96, EPHA2, and TAF12) mainly participated in immune response. Functional enrichment analysis showed that DMRs were significantly enriched in the adherens junction, gap junction, and Wnt, PI3K, and mTOR signaling pathways, regulating cell development, spermatogenesis, and testicular endocrine function. The functional analysis of differentially expressed genes showed that they were involved in the biological processes of mitosis, meiosis, and flagellated sperm motility during sexual maturity of yak testis. We also screened the key regulatory factors of testis development and spermatogenesis by combined analysis, which included BRCA1, CREBBP, STAT3, and SMAD4. This study has important research value and practical guiding significance for yak genetic improvement, particularly in understanding the molecular mechanism and evolutionary dynamics of the progression of testis developmental stages in yaks.
2023-04-15 | GSE229363 | GEO