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Chromatin accessibility-based epigenetic landscape in osteoclastogenesis [ATAC-seq]

ABSTRACT: Chromatin accessibility-based epigenetic landscape in osteoclastogenesis [ATAC-seq]

PROVIDER: PRJNA876291 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21408984_1.fastq.gz	Fastqsanger.gz
	SRR21408984_2.fastq.gz	Fastqsanger.gz
	SRR21408985_1.fastq.gz	Fastqsanger.gz
	SRR21408985_2.fastq.gz	Fastqsanger.gz
	SRR21408986_1.fastq.gz	Fastqsanger.gz

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Chromatin accessibility-based epigenetic landscape in osteoclastogenesis [ATAC-seq]

Project description:In this study, we showed chromatin accessibility-based epigenetic landscape in osteoclastogenesis. To reveal chromatin accessibility landscape throughout osteoclastogenesis, we conducted Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) with BMM (D0), OC precursors day 1 (D1), OC precursor day 2 (D2), and OC (D3).

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Chromatin accessibility-based epigenetic landscape in osteoclastogenesis [RNA-seq]

Project description:In this study, we showed chromatin accessibility-based epigenetic landscape in osteoclastogenesis. To reveal the affected genes by alteration in histone acetylation states after RANKL stimulation, we supplemented sodium acetate, which increased histone acetylation, to OC precursors. Then we conducted RNA-seq with BMM (D0), OC precursors (D1), and OC precursors treaed with sodium acetate (ACD1).

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Chromatin accessibility-based epigenetic landscape in osteoclastogenesis [RNA-seq]

Project description:Chromatin accessibility-based epigenetic landscape in osteoclastogenesis [RNA-seq]

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Function of BRD9 during osteoclastogenesis [ATAC-seq]

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TGFβ reprograms TNF stimulation of macrophages towards osteoclastogenesis [ATAC-seq]

Project description:TNF plays a key role in inflammation and bone resorption. However, the mechanisms regulating TNF-mediated osteoclastogenesis remain largely unclear because its direct osteoclastogenic ability is weak. Here, we found that TGFβ priming enables TNF to effectively induce osteoclastogenesis from macrophages, independently of the osteoclastogenic action of RANKL. Lack of TGFβ signaling in macrophages suppresses inflammatory, but not physiological, osteoclastogenesis and bone resorption in vivo. Mechanistically, TGFβ priming reprograms macrophage response to TNF towards osteoclastogenesis by remodeling chromatin accessibility and histone modification. TGFβ and TNF induce an unconventional osteoclastogenic program, which includes the suppression of the TNF-induced IRF1-IFNβ-IFN stimulated gene (ISG) axis, promotion of IRF8 degradation and B-Myb induction. These mechanisms are present in RA, in which TGFβ level is elevated and correlated with osteoclast activity. Our findings identify a function and mechanism of action for TGFβ in TNF-mediated inflammatory osteoclastogenesis, and open avenues for selective treatment of inflammatory bone loss.

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Single-cell chromatin accessibility data using scATAC-seq

Project description:Cell-to-cell variation is a universal feature of life that impacts a wide range of biological phenomena, from developmental plasticity to tumor heterogeneity. While recent advances have improved our ability to document cellular phenotypic variation the fundamental mechanisms that generate variability from identical DNA sequences remain elusive. Here we reveal the landscape and principles of cellular DNA regulatory variation by developing a robust method for mapping the accessible genome of individual cells via assay of transposase accessible chromatin sequencing (ATAC-seq). Single-cell ATAC-seq (scATAC-seq) maps from hundreds of single-cells in aggregate closely resemble accessibility profiles from tens of millions of cells and provides insights into cell-to-cell variation. Accessibility variance is systematically associated with specific trans-factors and cis-elements, and we discover combinations of trans-factors associated with either induction or suppression of cell-to-cell variability. We further identify sets of trans-factors associated with cell-type specific accessibility variance across 6 cell types. Targeted perturbations of cell cycle or transcription factor signaling evoke stimulus-specific changes in this observed variability. The pattern of accessibility variation in cis across the genome recapitulates chromosome topological domains de novo, linking single-cell accessibility variation to three-dimensional genome organization. All together, single-cell analysis of DNA accessibility provides new insight into cellular variation of the “regulome.” Profiles of single cell epigenomes, assayed using scATAC-seq, across 8 cell types and 4 targeted cell manipulations. The complete data set contains a total of 1,632 assayed wells.

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Project description:Current genome-wide detection of chromatin accessibility uses the assay for transposase-accessible chromatin (ATAC-seq). To a provide panoramic view of the chromatin accessibility landscape in prostate cancer and normal prostate, we performed ATAC-seq in 20 pairs of prostate cancer tissues and matched adjacent tissues. Assay of transposase accessible chromatin with high-throughput sequencing (ATAC-seq) for 20 pairs of prostate cancer tissues and matched adjacent tissues.

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Project description:In mammals, extensive chromatin reorganization is essential for reprogramming terminally committed gametes to a totipotent state during preimplantation development. However, the global chromatin landscape and its dynamics in this period remain unexplored. Here we report a genome-wide map of accessible chromatin in mouse preimplantation embryos using an improved assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) approach with CRISPR/Cas9-assisted mitochondrial DNA depletion. We show that despite extensive parental asymmetry in DNA methylomes, the chromatin accessibility between the parental genomes is globally comparable after major zygotic genome activation (ZGA). Accessible chromatin in early embryos is widely shaped by transposable elements and overlaps extensively with putative cis-regulatory sequences. Unexpectedly, accessible chromatin is also found near the transcription end sites of active genes. By integrating the maps of cis-regulatory elements and single-cell transcriptomes, we construct the regulatory network of early development, which helps to identify the key modulators for lineage specification. Finally, we find that the activities of cis-regulatory elements and their associated open chromatin diminished before major ZGA. Surprisingly, we observed many loci showing non-canonical, large open chromatin domains over the entire transcribed units in minor ZGA, supporting the presence of an unusually permissive chromatin state. Together, these data reveal a unique spatiotemporal chromatin configuration that accompanies early mammalian development. Mouse preimplantation embryos were obtained from crosses of C57BL/6N and DBA/2N. ATAC-seq was performed in these embryos at various stages in preimplantation development.

2016-06-15 | E-GEOD-66581 | biostudies-arrayexpress

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