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Chromatin conformation dynamics during CD4+ Tcell activation implicates autoimmune disease associated genes and regulatory elements (HiC)

ABSTRACT: Chromatin conformation dynamics during CD4+ Tcell activation implicates autoimmune disease associated genes and regulatory elements (HiC)

PROVIDER: PRJNA960642 | ENA |

REPOSITORIES: ENA

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Chromatin conformation dynamics during CD4+ Tcell activation implicates autoimmune disease associated genes and regulatory elements (HiC)

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Chromatin conformation dynamics during CD4+ Tcell activation implicates autoimmune disease associated genes and regulatory elements (RNA-Seq)

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Chromatin conformation dynamics during CD4+ Tcell activation implicates autoimmune disease associated genes and regulatory elements (ATAC-Seq)

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Chromosome conformation analysis of N1E115 cells by HiC

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Project description:Neuronal nitric oxide synthase 1 (NOS1) produces the gaseous signaling molecule nitric oxide (NO), which plays important roles in the development and function of the nervous system. The regulation of Nos1 gene expression is incompletely understood. Here, we explored the role of physiological hypoxia in the control of Nos1 transcription and the underlying mechanisms using N1E115 mouse neuroblastoma cells as a model. N1E115 cells were cultured for 3 days at high (20%) and low (4%) oxygen levels. Following the verification of upregulation of Nos1 mRNA and protein levels in response to 4% oxygen, we analyzed 3-dimensional chromosome conformation by HiC.

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in situ HiC in Smchd1-GFP NSCs

Project description:in situ HiC to assess chromatin conformation in Smchd1-GFPMD43/MD43 and Smchd1-GFP+/+ neural stem cells.

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Long-range epigenetic concordance revealed by simultaneous profiling of DNA methylation and chromosomal conformation changes in bulk and single cell Methyl-HiC

Project description:Genomic sequences, as well as its covalent epigenetic modifications, are spatially organized into three-dimensional structures. Here, we developed Methyl-HiC by combining in situ Hi-C and whole genome bisulfite sequencing (WGBS) to simultaneously capture genome-wide chromosome conformation changes and DNA methylation within the same DNA molecule. Methyl-HiC generated consistent information compared with in situ Hi-C and WGBS from the same cell line. We detected long-range DNA methylation concordance in general but varied in different chromatin states. We extended Methyl-HiC to single cell level and applied it on 103 primed and 47 naïve mouse embryonic stem cells (mESCs). We revealed the heterogeneity of chromosomal conformation changes by grouping cells in their DNA methylation level alone. We also observed increases of DNA methylation stochasticity and decreases of contact frequency together in late replication timing regions. Our method here paves the road to evaluate the direct long-range effect of epigenetic alterations in different pathological and healthy conditions at genome-wide and single cell level.

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