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(2025)", "display_title": "Buka K et al. (2025) PMID:40082674", "ID": "PMID:40082674", "date_published": "2025-03-14", "@type": ["Publication", "Item"], "@id": "/publications/b65676d0-556f-4e4e-a8bb-ce0ca10e2d64/", "status": "current", "abstract": "Chromosome Conformation Capture (3 C) methods, including Hi-C (a high-throughput  variation of 3 C), detect pairwise interactions between DNA regions, enabling the  reconstruction of chromatin architecture in the nucleus. HiChIP is a modification  of the Hi-C experiment that includes a chromatin immunoprecipitation (ChIP) step,  allowing genome-wide identification of chromatin contacts mediated by a protein  of interest. In mammalian cells, cohesin protein complex is one of the major  players in the establishment of chromatin loops. We present an improved cohesin  HiChIP experimental protocol. Using comprehensive bioinformatic analysis, we show  that a dual chromatin fixation method compared to the standard formaldehyde-only  method, results in a substantially better signal-to-noise ratio, increased ChIP  efficiency and improved detection of chromatin loops and architectural stripes.  Additionally, we propose an automated pipeline called nf-HiChIP (  https://github.com/SFGLab/hichip-nf-pipeline ) for processing HiChIP samples  starting from raw sequencing reads data and ending with a set of significant  chromatin interactions (loops), which allows efficient and timely analysis of  multiple samples in parallel, without requiring additional ChIP-seq experiments.  Finally, using advanced approaches for biophysical modelling and stripe calling  we generate accurate loop extrusion polymer models for a region of interest and  provide a detailed picture of architectural stripes, respectively.", "uuid": "b65676d0-556f-4e4e-a8bb-ce0ca10e2d64", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"@id": "/publications/b65676d0-556f-4e4e-a8bb-ce0ca10e2d64/", "authors": ["Buka K", "Parteka-Tojek Z", "Agarwal A", "Denkiewicz M", "Korsak S", "Chilinski M", "Banecki KH", "Plewczynski D"], "ID": "PMID:40082674", "date_published": "2025-03-14", "display_title": "Buka K et al. (2025) PMID:40082674", "abstract": "Chromosome Conformation Capture (3 C) methods, including Hi-C (a high-throughput  variation of 3 C), detect pairwise interactions between DNA regions, enabling the  reconstruction of chromatin architecture in the nucleus. HiChIP is a modification  of the Hi-C experiment that includes a chromatin immunoprecipitation (ChIP) step,  allowing genome-wide identification of chromatin contacts mediated by a protein  of interest. In mammalian cells, cohesin protein complex is one of the major  players in the establishment of chromatin loops. We present an improved cohesin  HiChIP experimental protocol. Using comprehensive bioinformatic analysis, we show  that a dual chromatin fixation method compared to the standard formaldehyde-only  method, results in a substantially better signal-to-noise ratio, increased ChIP  efficiency and improved detection of chromatin loops and architectural stripes.  Additionally, we propose an automated pipeline called nf-HiChIP (  https://github.com/SFGLab/hichip-nf-pipeline ) for processing HiChIP samples  starting from raw sequencing reads data and ending with a set of significant  chromatin interactions (loops), which allows efficient and timely analysis of  multiple samples in parallel, without requiring additional ChIP-seq experiments.  Finally, using advanced approaches for biophysical modelling and stripe calling  we generate accurate loop extrusion polymer models for a region of interest and  provide a detailed picture of architectural stripes, respectively.", "@type": ["Publication", "Item"], "journal": "Communications biology", "short_attribution": "Buka K et al. 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