Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

By Borbála Mifsud, Filipe Tavares-Cadete, Alice N C Young, R. Sugar, Stefan Schoenfelder, Lauren Ferreira, Steven W. Wingett, Simon R. Andrews, W. Grey, Philip A. Ewels and 8 more. Nature Genetics, 2015

934 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/4c4617375a990a0ba1775e57e286198e2d4feace

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Citations in the corpus

Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data (2019, background): “Further work using promoter capture Hi-C [16] demonstrated that the interacting regions between enhancers and promoters, especially long-range interactions, are important to cell lineage and human diseases [17].”
Sequential regulatory activity prediction across chromosomes with convolutional neural networks (2017, methodology): “established gene regulation principles from inquiry into enhancer biology and 3D chromosomal contact domains has yet to be fully incorporated into expressive machine learning models (Dekker and Mirny 2016; Mifsud et al. 2015).”
Integrated single-cell analysis maps the continuous regulatory landscape of human hematopoietic differentiation (2018, methodology): “Integration of promoter capture Hi-C data Processed promoter-capture Hi-C loops for CD34+ (Mifsud et al., 2015) andmonocytes (Javierre et al., 2016) were downloaded from the supplemental resources associated with each of the original publications.”
GeneHancer: genome-wide integration of enhancers and target genes in GeneCards (2017, methodology): “The most direct approaches involve enhancer reporter assays, directed, for example, at non-coding DNA segments that show high interspecies sequence conservation (14, 15).”
HiCUP: pipeline for mapping and processing Hi-C data (2015, background): “Finally, four other research articles pioneered targeted Hi-C capture techniques, enriching for gene promoter-containing fragments to elucidate regulatory networks in mice 2,4,21 and humans 3 .”
Genome-wide mapping and analysis of chromosome architecture (2016, background): “Each pair of interacting loci has a unique local background model, which depends on the definition of its local neighbouring regions. coverage 54,92 .”
CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data (2015, methodology): “For GM12878 [3], the first replicate was not used for weight estimation as it led to unstable estimation.”
HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient (2017, background): “…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), and HiChIP (Mumbach et al. 2016).”
Ensembl 2016 (2015, background): “Capture Hi-C in the GM12878 lymphoblastoid cell line and displayed for the GRCh38 assembly (43).”