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Project description:Transcriptome-wide dynamics of m6A mRNA methylation during porcine spermatogenesis
| PRJNA596208 | ENA
Project description:Purpose: To understand the overall transcriptional profile changes in porcine spermatogenesis.
2021-12-15 | GSE174782 | GEO
Project description:Spermatogenesis is precisely controlled at the transcriptional, posttranscriptional, and translational levels. Here we report that N6-methyladenosine (m6A), an epitranscriptomic mark regulating gene expression, plays essential roles during spermatogenesis. We present comprehensive m6A mRNA methylomes of mouse spermatogenic cells from five developmental stages: undifferentiated spermatogonia, type A1 spermatogonia, preleptotene spermatocytes, pachytene/diplotene spermatocytes, and round spermatids. Germ cell-specific inactiva- tion of the m6A RNA methyltransferase Mettl3 or Mettl14 with Vasa-Cre causes loss of m6A and depletion of SSCs. m6A depletion dysregulates translation of transcripts that are required for SSC proliferation/differentiation. Com- bined deletion of Mettl3 and Mettl14 in advanced germ cells with Stra8-GFPCre disrupts spermiogenesis, whereas mice with single deletion of either Mettl3 or Mettl14 in advanced germ cells show normal spermatogenesis. The sper- matids from double-mutant mice exhibit impaired translation of haploid-specific genes that are essential for spermio- genesis. This study highlights crucial roles of mRNA m6A modification in germline development, potentially ensuring coordinated translation at different stages of spermatogenesis.
2020-11-11 | GSE161059 | GEO
Project description:We profile transcriptome-wide m6A in porcine liver of three developmental stages: newborn, suckling and adult. Approximately one-third of the transcribed genes are modified by m6A, with a frequency of 1.47 to 1.56 m6A peaks per mRNA. m6A was distributed predominantly around stop codon. Consensus motif sequence ‘RRm6ACH’ has been observed in most m6A peaks. A negative correlation rate (average Pearson’s r = -0.450) was found between m6A methylation level and gene expression. Gene ontology analysis of transcripts persistently modified in three stages showed m6A modified genes relevant to critical functions, including regulation of growth and development, regulation of metabolic process and protein catabolic process. Genes with higher m6A methylation and lower expression of one certain stage are associated with the biological processes required for or unique to this stage. These results will provide a source for identifying adenosine methylation modified mRNA of porcine liver and extended our knowledge of the role of m6A in development and growth of mammalian organ.
2016-09-25 | GSE87327 | GEO
Project description:Studies on the epigenetic regulation of gene expression during germ cell development are still at the beginning stage. In the present study, we used our highly specific 5hmC-labeling and enrichment technique coupled with DNA deep-sequencing to profile the global 5hmC distribution in 8 serial stages of male germ cells during spermatogenesis, as well as in the the Sertoli cells (SE) which are the only somatic cell type inside seminiferous tubules. We analyzed the genomic distribution and dynamic changes of 5hmC during spermatogenesis. Moreover, to dissect the functional significance of 5hmC modifications for transcriptional regulation of gene expression, we also performed RNA-Seq transcriptome analysis in all of the 8 corresponding stages of male germ cells and found that 5hmC is positively correlated with gene expression. RNA-seq: Examination of the transcriptomes during mouse spermatogenesis. 5hmC-seq: Identification of 5hmC enriched genmoic regions in mouse germ cell.
2012-03-12 | E-GEOD-35005 | biostudies-arrayexpress
Project description:We performed m6A sequencing to compare N6 transcriptome methylation profiles of the longissimus dorsi muscles (LDMs) between Landrace pigs (a Danish pig breed) and Jinhua (a Chinese pig breed with higher levels of intramuscular fat). The results show m6A is widely spread and highly conserved in pig mRNA. m6A occurs in the conserved sequence motif of GGACU and exhibits a unique topology in pig.Transcriptome-wide m6A profiling revealed that about 20% of transcribed genes were modified by m6A, with the consensus sequence GGACU appearing highly in m6A-modified genes. Functional enrichment analysis showed that genes differentially methylated in LDMs of the two porcine breeds were related to gene regulation and muscle development and differentiation,suggesting that the m6A modification is tissue-specific and influences mRNA stability or translation.
2019-05-26 | GSE113237 | GEO
Project description:m6A profiling in two accessions of Arabidopsis thaliana (Can-0 and Hen-16) using the m6A-targeted antibody coupled with high-throughput sequencing m6A-seq in two accessions of Arabidopsis, two replicates for each sample
2014-11-06 | E-GEOD-59154 | biostudies-arrayexpress
Project description:In this experiment, m6A-seq sequencing technology was used to study the functional role of methylated molecules in the process of CPB2 processing porcine small intestinal epithelial cells. In this experiment, an IP library and an input library were built together. The IP library was enriched with m6A specific antibodies to generate methylated RNA, and the influence of m6A methylation modification on its expression was analyzed by bioinformatics. We finally concluded that m6A methylation modification may play a very important role after CPB2 toxin treats small intestinal epithelial cells.
2021-10-05 | GSE167267 | GEO
Project description:N6-methyladenosine (m6A) is the most abundant internal modification on mRNA which influences most steps of mRNA metabolism and is involved in several biological functions. The E3 ubiquitin ligase Hakai was previously found in complex with components of the m6A methylation machinery in plants and mammalian cells but its precise function remained to be investigated. Here we show that Hakai is a conserved component of the methyltransferase complex in Drosophila and human cells. In Drosophila, its depletion results in reduced m6A levels and altered m6A-dependent functions including sex determination. We show that its ubiquitination domain is required for dimerisation and interaction with other members of the m6A machinery, while its catalytic activity is dispensable. Finally, we demonstrate that the loss of Hakai destabilizes several subunits of the methyltransferase complex, resulting in impaired m6A deposition. Our work adds new functional and molecular insights into the mechanism of the m6A mRNA writer complex.
2021-04-29 | PXD022294 | Pride
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