Metagenomic Chromosome Conformation Capture (3C): techniques, applications, and challenges [version 1; referees: 2 approved] [PDF]
F1000Research, 2015 We review currently available technologies for deconvoluting metagenomic data into individual genomes that represent populations, strains, or genotypes present in the community. An evaluation of chromosome conformation capture (3C) and related techniques
Michael Liu, Aaron Darling
doaj +7 more sources
Quantitative Chromosome Conformation Capture (3C-qPCR)
Methods in Molecular Biology, 2022 Many population-based methods investigating chromatin dynamics and organization in eukaryotes are based on the chromosome conformation capture (3C) method. Here, we provide an updated version of the quantitative 3C (3C-qPCR) protocol for improved and simplified quantitative analyses of intra-chromosomal contacts.
Thierry Forné
exaly +5 more sources
Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C) [PDF]
PeerJ, 2016 Background Chromosome conformation capture, coupled with high throughput DNA sequencing in protocols like Hi-C and 3C-seq, has been proposed as a viable means of generating data to resolve the genomes of microorganisms living in naturally occuring ...
Matthew Z. DeMaere, Aaron E. Darling
doaj +6 more sources
High-resolution analysis of chromosome conformation in hyperthermophilic archaea
STAR Protocols, 2021 Summary: Chromosome conformation capture (3C) techniques are emerging as promising approaches to study genome organization in Archaea, the least understood domain of life in terms of chromosome biology. Here, we describe a 3C technique combined with deep
Naomichi Takemata, Stephen D. Bell
doaj +2 more sources
Quantitative analysis of chromosome conformation capture assays (3C-qPCR) [PDF]
Nature Protocols, 2007 Chromosome conformation capture (3C) technology is a pioneering methodology that allows in vivo genomic organization to be explored at a scale encompassing a few tens to a few hundred kilobase-pairs. Understanding the folding of the genome at this scale is particularly important in mammals where dispersed regulatory elements, like enhancers or ...
Hagège, Hélène +7 more
openaire +5 more sources
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
doaj +2 more sources
3D genome organization and epigenetic regulation in autoimmune diseases
Frontiers in Immunology, 2023 Three-dimensional (3D) genomics is an emerging field of research that investigates the relationship between gene regulatory function and the spatial structure of chromatin.
Yueqi Qiu +13 more
doaj +1 more source
Investigation of the Basic Steps in the Chromosome Conformation Capture Procedure
Frontiers in Genetics, 2021 A constellation of chromosome conformation capture methods (С-methods) are an important tool for biochemical analysis of the spatial interactions between DNA regions that are separated in the primary sequence.
Oleg V. Bylino +5 more
doaj +1 more source
Chromosome Conformation Capture (3C) in Budding Yeast [PDF]
Cold Spring Harbor Protocols, 2015 Chromosome conformation capture (3C) is a method for studying chromosomal organization that takes advantage of formaldehyde cross-linking to measure the spatial association of two pieces of chromatin. The 3C method begins with whole-cell formaldehyde fixation of chromatin.
Belton, Jon-Matthew, Dekker, Job
openaire +3 more sources
Application of the 3C Method to Study the Developmental Genes in Drosophila Larvae
Frontiers in Genetics, 2022 A transition from one developmental stage to another is accompanied by activation of developmental programs and corresponding gene ensembles. Changes in the spatial conformation of the corresponding loci are associated with this activation and can be ...
Oleg V. Bylino +6 more
doaj +1 more source