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Homo sapiens

ABSTRACT: Genome-wide profiling of chromatin accessibility during microRNA-mediated neuronal reprogramming [ATAC-seq]

PROVIDER: PRJNA396221 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5878910_1.fastq.gz	Fastqsanger.gz
	SRR5878910_2.fastq.gz	Fastqsanger.gz
	SRR5878911_1.fastq.gz	Fastqsanger.gz
	SRR5878911_2.fastq.gz	Fastqsanger.gz
	SRR5878912_1.fastq.gz	Fastqsanger.gz

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Project description:Genome-wide profiling of DNA methylation by MRE-seq during microRNA-mediated neuronal reprogramming [MRE-seq]

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Identification of chromatin accessibility during the early stage of pig SCNT embryo reprogramming by ATAC-seq

Project description:Somatic cell nuclear transplantation (SCNT) can transform highly differentiated donor nuclei into pluripotent nuclei through the large-scale reprogramming of chromatin. The reprogramming of chromatin has been documented to take place in the first few hours after SCNT embryo activation. Thus, studies that characterize dynamic changes in chromatin during the first few hours after embryo activation could provide insight into the mechanism and significance of genome-wide reprogramming. However, few studies have examined the epigenetic remodeling of reconstructed embryos during the early stage of reprogramming. Here, we conducted ATAC-seq on 50 porcine SCNT-HMC embryos and 50 parthenogenetic activation (PA) embryos 10 h after activation. Along with pig embryonic fibroblast (PEF) ATAC-seq data, we found low levels of chromatin accessibility and gene transcription in SCNT and PA embryos. Moreover, PEF genes and the X chromosome became inaccessible during embryo reprogramming. GO enrichment analysis revealed that the molecular functions related to accessible chromatin in embryos primarily included transcriptional regulatory activity and SMAD binding. The differentially accessible chromatin sites between SCNT and PEF were primarily related to transcriptional activity and histone modification. These results indicated that despite the tight chromatin structure during the early stage of embryo reprogramming, some accessible chromatin sites, which were primarily distributed in the intergenic region, were still detected. Dynamic changes in chromatin accessibility during reprogramming were primarily related to transcriptional activity and histone modification. Generally, this study provided new insight into the dynamics and importance of chromatin accessibility during the early stages of embryo reprogramming.

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Bulk ATAC-Sequencing of isolated spermatocytes from testis tissue from B6/CAST F1 hybrid mice

Project description:We performed profiling of allele-specific chromatin accessibility profiling in mouse spermatocytes. To this end, we isolated tetraploid spermatocytes using FACS-sorting from F1 crosses of the C57B6J and CAST/EiJ strains. We then performed ATAC-Seq (Corces et al. 2017) and analyzed allele-specific chromatin accessibility.

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Project description:Remodeling of chromatin accessibility is necessary for successful reprogramming of fibroblasts to neurons. However, it is still not fully known which transcription factors can induce a neuronal chromatin accessibility profile when overexpressed in fibroblasts. To identify such transcription factors, we here used ATAC-sequencing to generate differential chromatin accessibility profiles between human fibroblasts and iNeurons, an in vitro neuronal model system obtained by overexpression of Neurog2 in induced pluripotent stem cells (iPSCs). We found that the ONECUT transcription factor sequence motif was strongly associated with differential chromatin accessibility between iNeurons and fibroblasts. All three ONECUT transcription factors associated with this motif (ONECUT1, ONECUT2 and ONECUT3) induced neuronal morphology and expression of neuronal genes within two days of overexpression in fibroblasts. We observed widespread remodeling of chromatin accessibility; in particular, we found that chromatin regions that contain the ONECUT motif were in- or lowly accessible in fibroblasts and became accessible after the overexpression of ONECUT1, ONECUT2 or ONECUT3. There was substantial overlap with iNeurons, still, many regions that gained accessibility following ONECUT overexpression were not accessible in iNeurons. Our study highlights the potential of ONECUT transcription factors for direct neuronal reprogramming.

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