Single-cell multi-omics sequencing reveals the epigenomic landscapes in human spermatogenesis [STRT-seq scCOOL-seq]
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ABSTRACT:
PROVIDER: PRJNA985716 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Human spermatogenesis is a well-ordered dynamic process, which ensures the long-term production of functional spermatozoa; however, the roles of DNA methylation and chromatin accessibility in this process remain largely unknown. Here, by simultaneously investigating the chromatin accessibility, DNA methylome and transcriptome landscapes of human spermatogenesis using the modified single-cell chromatin overall omic-scale landscape sequencing approach (Modified scCOOL-seq), we revealed that the transcriptional changes throughout human spermatogenesis were correlated with the dynamic alternations of chromatin accessibility; particularly, several potential transcription factors and a set of regulatory elements involved in such process were identified. Remarkably, a round of DNA demethylation was uncovered upon meiosis initiation in human spermatogenesis, which was associated with male meiotic recombination and conserved between human and mouse. And aberrant DNA hypermethylation at recombination hotspots could be detected in leptotene spermatocytes of certain nonobstructive azoospermia patients. Functionally, the intervention of DNA demethylation affected male meiotic recombination. Collectively, this study provides multi-omics landscapes of human spermatogenesis at single-cell resolution, and offers insights into the association between DNA demethylation and male meiotic recombination.
2023-07-09 | GSE235321 | GEO
Project description:Human spermatogenesis is a well-ordered dynamic process, which ensures the long-term production of functional spermatozoa; however, the roles of DNA methylation and chromatin accessibility in this process remain largely unknown. Here, by simultaneously investigating the chromatin accessibility, DNA methylome and transcriptome landscapes of human spermatogenesis using the modified single-cell chromatin overall omic-scale landscape sequencing approach (Modified scCOOL-seq), we revealed that the transcriptional changes throughout human spermatogenesis were correlated with the dynamic alternations of chromatin accessibility; particularly, several potential transcription factors and a set of regulatory elements involved in such process were identified. Remarkably, a round of DNA demethylation was uncovered upon meiosis initiation in human spermatogenesis, which was associated with male meiotic recombination and conserved between human and mouse. And aberrant DNA hypermethylation at recombination hotspots could be detected in leptotene spermatocytes of certain nonobstructive azoospermia patients. Functionally, the intervention of DNA demethylation affected male meiotic recombination. Collectively, this study provides multi-omics landscapes of human spermatogenesis at single-cell resolution, and offers insights into the association between DNA demethylation and male meiotic recombination.
2023-07-09 | GSE235322 | GEO
Project description:Human spermatogenesis is a well-ordered dynamic process, which ensures the long-term production of functional spermatozoa; however, the roles of DNA methylation and chromatin accessibility in this process remain largely unknown. Here, by simultaneously investigating the chromatin accessibility, DNA methylome and transcriptome landscapes of human spermatogenesis using the modified single-cell chromatin overall omic-scale landscape sequencing approach (Modified scCOOL-seq), we revealed that the transcriptional changes throughout human spermatogenesis were correlated with the dynamic alternations of chromatin accessibility; particularly, several potential transcription factors and a set of regulatory elements involved in such process were identified. Remarkably, a round of DNA demethylation was uncovered upon meiosis initiation in human spermatogenesis, which was associated with male meiotic recombination and conserved between human and mouse. And aberrant DNA hypermethylation at recombination hotspots could be detected in leptotene spermatocytes of certain nonobstructive azoospermia patients. Functionally, the intervention of DNA demethylation affected male meiotic recombination. Collectively, this study provides multi-omics landscapes of human spermatogenesis at single-cell resolution, and offers insights into the association between DNA demethylation and male meiotic recombination.
2023-07-09 | GSE235323 | GEO
Project description:Single-cell multi-omics sequencing reveals the epigenomic landscapes in human spermatogenesis [Bisulfite-Seq]
| PRJNA985710 | ENA
Project description:Single-cell multi-omics sequencing reveals the epigenomic landscapes in human spermatogenesis [CUT&Tag]
| PRJNA985715 | ENA
Project description:Adult germline stem cells (AGSCs) are multifunctional - they must self renew, maintain genome pluripotency, and prepare for gametogenesis – which involves meiotic and chromatin repackaging phases. To better understand AGSCs and gametogenesis, we derived high-resolution profiles of transcription, DNA methylation, 5hmC, and multiple histone modifications at key stages. First, AGSCs display chromatin ‘poising’ of enhancers and promoters of genes utilized in embryo development. Second, the pluripotency network in AGSCs is remarkably distinct from ESCs - lacking Nanog, Sox2, or Prdm14 expression. Third, spermatogenesis involves stage-specific transcription and distinctive chromatin dynamics, but virtually no changes in DNAme. Surprisingly, we observe co-incidence of RNA polymerase II, high H3K4me3, and DNA methylation at 20-35% of genes transcribed during gametogenesis - including piRNA clusters - but often observe attendant promoter 5hmC. Our work reveals key differences between AGSCs and other germ/stem cells, and reveals both logical and unexpected chromatin-transcription relationships accompanying germline developmental transitions. Examination of 7 different histone modifications and 5hMC in 4 different cell types
2014-05-19 | E-GEOD-49621 | biostudies-arrayexpress
Project description:Adult germline stem cells (AGSCs) are multifunctional - they must self renew, maintain genome pluripotency, and prepare for gametogenesis – which involves meiotic and chromatin repackaging phases. To better understand AGSCs and gametogenesis, we derived high-resolution profiles of transcription, DNA methylation, 5hmC, and multiple histone modifications at key stages. First, AGSCs display chromatin ‘poising’ of enhancers and promoters of genes utilized in embryo development. Second, the pluripotency network in AGSCs is remarkably distinct from ESCs - lacking Nanog, Sox2, or Prdm14 expression. Third, spermatogenesis involves stage-specific transcription and distinctive chromatin dynamics, but virtually no changes in DNAme. Surprisingly, we observe co-incidence of RNA polymerase II, high H3K4me3, and DNA methylation at 20-35% of genes transcribed during gametogenesis - including piRNA clusters - but often observe attendant promoter 5hmC. Our work reveals key differences between AGSCs and other germ/stem cells, and reveals both logical and unexpected chromatin-transcription relationships accompanying germline developmental transitions. Methylation profiles of 8-week old wild type (WT) mice were generated by bisulfite sequencing using Illumina HiSeq 2000.
2014-05-19 | E-GEOD-49623 | biostudies-arrayexpress
Project description:Adult germline stem cells (AGSCs) are multifunctional - they must self renew, maintain genome pluripotency, and prepare for gametogenesis – which involves meiotic and chromatin repackaging phases. To better understand AGSCs and gametogenesis, we derived high-resolution profiles of transcription, DNA methylation, 5hmC, and multiple histone modifications at key stages. First, AGSCs display chromatin ‘poising’ of enhancers and promoters of genes utilized in embryo development. Second, the pluripotency network in AGSCs is remarkably distinct from ESCs - lacking Nanog, Sox2, or Prdm14 expression. Third, spermatogenesis involves stage-specific transcription and distinctive chromatin dynamics, but virtually no changes in DNAme. Surprisingly, we observe co-incidence of RNA polymerase II, high H3K4me3, and DNA methylation at 20-35% of genes transcribed during gametogenesis - including piRNA clusters - but often observe attendant promoter 5hmC. Our work reveals key differences between AGSCs and other germ/stem cells, and reveals both logical and unexpected chromatin-transcription relationships accompanying germline developmental transitions. Methylation profiles of human sperm were generated by bisulfite sequencing using Illumina HiSeq 2000.
2014-05-19 | E-GEOD-57097 | biostudies-arrayexpress
Project description:Adult germline stem cells (AGSCs) are multifunctional - they must self renew, maintain genome pluripotency, and prepare for gametogenesis – which involves meiotic and chromatin repackaging phases. To better understand AGSCs and gametogenesis, we derived high-resolution profiles of transcription, DNA methylation, 5hmC, and multiple histone modifications at key stages. First, AGSCs display chromatin ‘poising’ of enhancers and promoters of genes utilized in embryo development. Second, the pluripotency network in AGSCs is remarkably distinct from ESCs - lacking Nanog, Sox2, or Prdm14 expression. Third, spermatogenesis involves stage-specific transcription and distinctive chromatin dynamics, but virtually no changes in DNAme. Surprisingly, we observe co-incidence of RNA polymerase II, high H3K4me3, and DNA methylation at 20-35% of genes transcribed during gametogenesis - including piRNA clusters - but often observe attendant promoter 5hmC. Our work reveals key differences between AGSCs and other germ/stem cells, and reveals both logical and unexpected chromatin-transcription relationships accompanying germline developmental transitions. Examination of 3 different histone modifications in human sperm
2014-05-19 | E-GEOD-57095 | biostudies-arrayexpress
Project description:Adult germline stem cells (AGSCs) are multifunctional - they must self renew, maintain genome pluripotency, and prepare for gametogenesis – which involves meiotic and chromatin repackaging phases. To better understand AGSCs and gametogenesis, we derived high-resolution profiles of transcription, DNA methylation, 5hmC, and multiple histone modifications at key stages. First, AGSCs display chromatin ‘poising’ of enhancers and promoters of genes utilized in embryo development. Second, the pluripotency network in AGSCs is remarkably distinct from ESCs - lacking Nanog, Sox2, or Prdm14 expression. Third, spermatogenesis involves stage-specific transcription and distinctive chromatin dynamics, but virtually no changes in DNAme. Surprisingly, we observe co-incidence of RNA polymerase II, high H3K4me3, and DNA methylation at 20-35% of genes transcribed during gametogenesis - including piRNA clusters - but often observe attendant promoter 5hmC. Our work reveals key differences between AGSCs and other germ/stem cells, and reveals both logical and unexpected chromatin-transcription relationships accompanying germline developmental transitions. mRNA and small RNA profiles of human sperm generated by deep sequencing using Illumina HiSeq 2000 and Illumina Genome Analyzer II.
2014-05-19 | E-GEOD-57096 | biostudies-arrayexpress