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Genomic profiling of HIV-1 integration in microglia cells links viral integration to the topologically associated domains

ABSTRACT: Genomic profiling of HIV-1 integration in microglia cells links viral integration to the topologically associated domains

PROVIDER: PRJNA927003 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23209940_1.fastq.gz	Fastqsanger.gz
	SRR23209940_2.fastq.gz	Fastqsanger.gz
	SRR23209941_1.fastq.gz	Fastqsanger.gz
	SRR23209941_2.fastq.gz	Fastqsanger.gz

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Genomic profiling of HIV-1 integration in microglia cells links viral integration to the topologically associated domains

Project description:HIV-1 encounters the hierarchically organized host chromatin to stably integrate and persist in anatomically distinct latent reservoirs. The contribution of genome organization in HIV-1 infection has been largely understudied across different HIV-1 targets. Here we determine HIV-1 integration sites (IS), associate them to chromatin and expression signatures at different genomic scales in a microglia cell model and profile them together with the primary T cell reservoir. HIV-1 insertions into introns of actively transcribed genes with IS hotspots in genic- and super-enhancers, characteristic of blood cells, are maintained in the microglia cell model. Genome organization analysis reveals dynamic CCCTC-binding factor (CTCF) clusters in cells with active and repressed HIV-1 transcription, while CTCF removal impairs viral integration. We identify CTCF-enriched topologically associated domain (TAD) boundaries with signatures of transcriptionally active chromatin as HIV-1 integration determinant in microglia and CD4+ T cells, highlighting the importance of the host genome organization in HIV-1 infection.

2023-01-24 | GSE223638 | GEO

Topologically Associated Domains Delineate Susceptibility to Somatic Hypermutation

Project description:Topologically Associated Domains Delineate Susceptibility to Somatic Hypermutation

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Glucocorticoid stimulation induces regionalized gene responses within topologically associating domains

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Identification of topologically associated domains (TADs) in peripheral blood CD34+ cells

Project description:We performed a Hi-C experiment on CD34+ cells isolated from peripheral blood and identifed topologically associated domains (TADs).

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Identification of topologically associated domains (TADs) in peripheral blood CD34+ cells

Project description:Identification of topologically associated domains (TADs) in peripheral blood CD34+ cells

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HIV-1 integration in microglia (ChIP-seq)

Project description:We performed ChIP-seq in a microglia cell line (C20) to understand integration patterns of HIV-1. We characterised the uninfected epigenetic cellular landscape in order to assess how integration is affected by distinct chromatin states and to understand the features defining integration-permissible regions.

2023-02-20 | GSE205914 | GEO

HIV-1 integration in microglia (LM-PCR)

Project description:We performed LM-PCR in an infected microglia cell line (C20) to map HIV-1 integration sites. Our aim was to compare the IS obtained through this method with ChIP-seq, ATAC-seq, and RNA-seq data obtained in the uninfected cells, allowing the assessment of integration preferences.

2023-02-20 | GSE206255 | GEO

Escape from X chromosome inactivation occurs within topologically associated domains

Project description:The spatial proximity between regulatory elements and their target genes has a profound affect on gene expression. X Chromosome Inactivation (XCI) is an epigenetic process by which an entire chromosome is rendered, for the most part, transcriptionally silent. A few genes are known to escape XCI and the mechanism for this escape remains unclear. Here, using mouse trophectodermal stem cells, we address whether specific chromosomal interactions facilitate escape from XCI by bringing escape-specific regulatory elements in close proximity to gene promoters. Our results suggest a model where escape from XCI occurs within topologically associated domains. As such, escaping genes and the regulatory sequences required for their escape are likely located within close linear proximity to each other. The datasets provided include those generated from allele-specific 4C-Seq of genes escaping XCI, genes subject to XCI, and non-genic regions of the X chromosome. FASTQ files, text files containing genomic coordiantes, and BED aligmnets are provided. All sequences were mapped relative to mouse genome build mm9. Deep sequencing of circular chromosome conformation capture (4C-Seq) of genes escaping X inactivation in mouse trophoblast stem cells

2014-03-26 | E-GEOD-49111 | biostudies-arrayexpress

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