Visualization and data exploration of chromosome conformation capture data using Voronoi diagrams with v3c-viz [PDF]
Scientific Reports, 2023 Chromosome conformation capture (3C) sequencing approaches, like Hi-C or micro-C, allow for an unbiased view of chromatin interactions. Most analysis methods rely on so-called interaction matrices, which are derived from counting read pairs in bins of ...
Alan M. Race, Alisa Fuchs, Ho-Ryun Chung
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The statistical-mechanics of chromosome conformation capture [PDF]
Nucleus, 2013 Since Jacob and Monod's characterization of the role of DNA elements in gene control, it has been recognized that the linear organization of genome structure is important for the regulation of gene transcription and hence the manifestation of phenotypes.
Jörg Langowski, Justin O'Sullivan
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Targeted Chromosome Conformation Capture (HiCap)
Methods in Molecular Biology, 2022 Targeted chromosome conformation capture (HiCap) is an experimental method for detecting spatial interactions of genomic features such as promoters and/or enhancers. The protocol first describes the design of sequence capture probes. After that, it provides details on the chromosome conformation capture adapted for next-generation sequencing (Hi-C ...
Pelin Sahlén
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Actual ligation frequencies in the chromosome conformation capture procedure. [PDF]
PLoS ONE, 2013 Chromosome conformation capture (3C) and derivative experimental procedures are used to estimate the spatial proximity between different genomic elements, thus providing information about the 3D organization of genomic domains and whole genomes within ...
Alexey A Gavrilov +2 more
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7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs [PDF]
BMC Genomics, 2019 Background Knowledge of the three-dimensional structure of the genome is necessary to understand how gene expression is regulated. Recent experimental techniques such as Hi-C or ChIA-PET measure long-range chromatin interactions genome-wide but are ...
Jonas Ibn-Salem +1 more
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Discovery of therapeutic targets in cardiovascular diseases using high-throughput chromosome conformation capture (Hi-C) [PDF]
Frontiers in GeneticsEpigenetic changes have been associated with several cardiovascular diseases. In recent years, epigenetic inheritance based on spatial changes has gradually attracted attention.
Quan Zheng +7 more
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Tethered Chromosome Conformation Capture Sequencing in Triticeae: A Valuable Tool for Genome Assembly [PDF]
Bio-Protocol, 2018 Chromosome conformation capture sequencing (Hi-C) is a powerful method to comprehensively interrogate the three-dimensional positioning of chromatin in the nucleus.
Axel Himmelbach +3 more
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Sequence-based multiscale modeling for high-throughput chromosome conformation capture (Hi-C) data analysis. [PDF]
PLoS ONE, 2018 In this paper, we introduce sequence-based multiscale modeling for biomolecular data analysis. We employ spectral clustering method in our modeling and reveal the difference between sequence-based global scale clustering and local scale clustering ...
Kelin Xia
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Chromosome conformation capture resolved near complete genome assembly of broomcorn millet [PDF]
Nature Communications, 2019 Broomcorn millet is one of the oldest crops cultivated by human that has strong abiotic stress tolerance. To facilitate genome assisted breeding of this and related species, the authors report its genome assembly and conduct comparative genome structure ...
Junpeng Shi +15 more
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Stable Chromosome Condensation Revealed by Chromosome Conformation Capture. [PDF]
Cell, 2015 Chemical cross-linking and DNA sequencing have revealed regions of intra-chromosomal interaction, referred to as topologically associating domains (TADs), interspersed with regions of little or no interaction, in interphase nuclei. We find that TADs and the regions between them correspond with the bands and interbands of polytene chromosomes of ...
Eagen KP, Hartl TA, Kornberg RD.
europepmc +4 more sources