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

By Maxwell R Mumbach, Adam J. Rubin, Ryan A. Flynn, Chao Dai, P. Khavari, W.J. Greenleaf, Howard Y. Chang. Nature Methods, 2016

971 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/672b967ca72ad0cfd9e6b23d631679be4e4e019c

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In Molecular Biology

Citations in the corpus

Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization (2017, positive): “Out of the 188 genes down-regulated after 1 day of depletion only 53 (28%) overlap an anchor for SMC1a HiChIP loops (Mumbach et al., 2016) and 19 Nora et al.”
HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient (2017, positive): “A progression of high-throughput methods based on chromatin conformation capture (3C) (Dekker 2002) has emerged, including 4C (Simonis et al. 2006), 5C (Dostie et al. 2006), Hi-C (Lieberman-Aiden et al. 2009), ChIA-PET (Li et al. 2010), Capture Hi-C (Hughes et al. 2014; Mifsud et al.2015), andHiChIP”
Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II, and Pol III (2020, methodology): “H3K27Ac HiChIP maps chromatin loops-associated with active promoters and enhancers [52, 53] and Ocean-C, a recently developed antibody free chromosome conformation capture technique, combines FAIRE-seq with HiC to map hubs of open chromatin interactions [54].”
The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions (2017, background): “Along with ChIA-PET, data from other chip-based technologies, such as HiChIP and PLAC-Seq are displayed together with DHS-linkage in this browser mode.”
Targeted in situ genome-wide profiling with high efficiency for low cell numbers (2018, neutral): “31| Incubate at 0 °C for the desired digestion time (default is 30 min).”
YY1 Is a Structural Regulator of Enhancer-Promoter Loops (2017, positive): “To determine whether YY1 is associated with sites of enhancer-promoter interactions in human cells, we conducted YY1 HiChIP experiments (Mumbach et al., 2016) in three different cell types.”
Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data (2017, neutral): “…variety of contact mapping experiments, such as dilution Hi-C (Lieberman-Aiden et al., 2009), in situ Hi-C (Rao et al., 2014), single-cell Hi-C (Nagano et al., 2013), Hi-C 2 (Sanborn et al., 2015), ChIA-PET (Fullwood et al., 2009), HiChIP (Mumbach et al., 2016), and SPRITE (Quinodoz et al., 2017).”