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HiChIP: Efficient and sensitive analysis of protein-directed genome architecture

ABSTRACT: HiChIP: Efficient and sensitive analysis of protein-directed genome architecture

PROVIDER: PRJNA320090 | ENA |

REPOSITORIES: ENA

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HiChIP: Efficient and sensitive analysis of protein-directed genome architecture

Project description:Three-dimensional genome structure is central to gene control, but current technologies are often impractical for many biological questions due to cell and read number requirements. Here we present HiChIP, a protein-centric chromatin conformation method. HiChIP improves the fraction of conformation-informative reads by over 10-fold and lowers input requirement greater than 100-fold to 1 million cells. HiChIP of cohesin reveals multi-scale genome architecture with greater signal to noise than in situ Hi-C. Thus, HiChIP will enable insight into the genome’s three-dimensional structure and regulation in once-inaccessible biological systems.

2016-08-31 | GSE80820 | GEO

HiChIP: efficient and sensitive analysis of protein-directed genome architecture.

Project description:Genome conformation is central to gene control but challenging to interrogate. Here we present HiChIP, a protein-centric chromatin conformation method. HiChIP improves the yield of conformation-informative reads by over 10-fold and lowers the input requirement over 100-fold relative to that of ChIA-PET. HiChIP of cohesin reveals multiscale genome architecture with greater signal-to-background ratios than those of in situ Hi-C.

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Genome wide SMC1A-mediated chromatin looping changes (HiChIP) in TAE684-sensitive, resistant, resistant shBORIS and resistant shGFP Kelly cells.

Project description:We performed SMC1A-mediated HiChIP analysis in sensitive, resistant, resistant shBORIS and resistant shGFP Kelly cells.

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RSC Defines MNase-sensitive Promoter Architecture in Yeast

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HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions [HiChIP]

Project description:We investigated the role of HSFA1a, a master regulator of heat stress response, in this reorganization through promotion of the formation of promoter/enhancer chromatin loops. To validate the presence of transcription factories we performed a HiChIP experiment, which is a sensitive and efficient method to analyze protein-centric chromosome conformation, using an anti-RNA polymerase II antibody.

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Polycomb-mediated genome architecture enables long-range spreading of H3K27 methylation [HiChIP]

Project description:Polycomb-mediated genome architecture enables long-range spreading of H3K27 methylation [HiChIP]

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TBX5 KO HiChIP

Project description:Understanding how the atrial and ventricular chambers of the heart maintain their distinct identity is a prerequisite for treating chamber-specific diseases. Here, we selectively inactivated the transcription factor Tbx5 in the atrial working myocardium of the neonatal mouse heart to show that it is required to maintain atrial identity. Atrial Tbx5 inactivation downregulated highly chamber specific genes such as Myl7 and Nppa, and increased expression of ventricular identity genes including Myl2. Using combined single nucleus transcriptome and open chromatin profiling, we assessed genomic accessibility changes underlying the altered atrial identity expression program, identifying 1846 genomic loci with greater accessibility in control atrial cardiomyocytes compared to KO aCMs. 69% of the control-enriched ATAC regions were bound by TBX5, demonstrating a role for TBX5 in maintaining genomic accessibility. These regions were associated with genes that had higher expression in control aCMs compared to KO aCMs, suggesting they act as TBX5-dependent enhancers. To confirm this hypothesis we analyzed chromatin looping of enhancers marked by H3K27Ac using HiChIP and found 510 chromatin loops that were sensitive to TBX5 dosage. Of the loops enriched in control aCMs, 73.7% contained anchors in control-enriched ATAC regions. Conversely, Tbx5 overexpression in the ventricular myocardium drove atrial gene expression. Together, these data demonstrate a role for TBX5 in maintaining the atrial gene expression program by binding to atrial enhancers to preserve tissue-specific chromatin architecture. We highlight this phenomenon at major atrial identity genes including Nppa, Bmp10 and Myl7. HiChIP for H3K27Ac from atria of TBX5KO and control animals

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The nuclear matrix protein SAFB maintains heterochromatin architecture through RNA-dependent phase separation [HiChIP]

Project description:The nuclear matrix protein SAFB maintains heterochromatin architecture through RNA-dependent phase separation [HiChIP]

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Arabidopsis MORC proteins function in the efficient establishment of RNA directed DNA methylation

Project description:Arabidopsis MORC proteins function in the efficient establishment of RNA directed DNA methylation

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Polycomb-mediated genome architecture enables long-range spreading of H3K27 methylation [HiChIP]

Project description:Polycomb-group proteins play critical roles in gene silencing through the deposition of histone H3 lysine 27 trimethylation (H3K27me3) and chromatin compaction. This process is essential for embryonic stem cells (ESCs) pluripotency, differentiation, and development. Polycomb repressive complex 2 (PRC2) can both read and write H3K27me3, enabling processive spread of H3K27me3 on linear genome and epigenetic memory. Long-range Polycomb-associated DNA contacts have also been described, but their regulation and role in gene silencing remains unclear. Here, we develop H3K27me3 HiChIP and apply optical reconstruction of chromatin architecture to reveal long-range Polycomb-associated DNA loops that span tens to hundreds of megabases and across multiple topological associated domains in mouse ESCs and human induced pluripotent stem cells. H3K27me3 loop anchors are enriched for Polycomb nucleation points and coincide with key developmental genes, such as Hmx1, Wnt6 and Hoxa. Genetic deletion of H3K27me3 loop anchors causes spatially proximal partner chromosomal loci to break apart, and alters H3K27me3 deposition, both locally and megabases away on the same chromosome. A selective EZH2 mutant deficient in RNA binding but intact H3K27me3 enzymatic activity leads to global alteration in H3K27me3 loops, decreased spatial proximity, and failure to spread Polycomb from PRC2 nucleation points to partner loci at developmental genes. Together, these results suggest PRC2 acts as a “genomic wormhole”, using RNA binding to enhance long range chromosome folding and H3K27me3 spreading. Developmental gene loci have novel roles in Polycomb spreading, emerging as key architectural elements of the epigenome.

2022-05-13 | GSE150906 | GEO

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