Suchergebnisse
Suchergebnisse:
An overview of the Hi-C workflow and its applications in research. Figure made using BioRender. Hi-C is a high-throughput genomic and epigenomic technique to capture chromatin conformation.
We describe a method, Hi-C, to comprehensively detect chromatin interactions in the mammalian nucleus. This method is based on Chromosome Conformation Capture, in which chromatin is crosslinked with formaldehyde, then digested, and re-ligated in such a way that only DNA fragments that are covalently ….
- Jon-Matthew Belton, Rachel Patton McCord, Johan Harmen Gibcus, Natalia Naumova, Ye Zhan, Job Dekker
- 2012
Hi-C is a chromosome conformation capture (3C)-based technology to detect pair-wise chromatin interactions genome-wide, and has become a benchmark tool to study genome organization. In Hi-C, chromatin conformation is first captured by chemical cross-linking of cells.
- Denis L. Lafontaine, Liyan Yang, Job Dekker, Job Dekker, Johan H. Gibcus, Johan H. Gibcus
- 2021
The Hi-C approach extends 3C-Seq to map chromatin contacts genome-wide, and it has also been applied to studying in situ chromatin interactions. In this method, DNA-protein complexes are crosslinked with formaldehyde.
- Tools to Call Compartments
- Tad Callers
- Interaction Callers
Compartments are the first level of chromatin organization which was derived from the analysis of Hi-C data in (Lieberman-Aiden et al. 2009). They clearly emerged in the Hi-C map as a plaid pattern after calculating Pearson correlation of the distance normalized map. To define active (“A”) and inactive (“B”) compartments, the authors used the sign ...
As with compartments, TADs were first identified by visual inspection of the interaction maps. Here, they appear along the diagonal of the contact matrix as blocks of highly self-interacting regions. This observed pattern guided the design of TAD-calling algorithms. Only subsequently to their observation, their biological properties, putative funct...
Interactions are specific points of contact between distant chromatin regions, such as those occurring between promoters and enhancers. The computational identification of interactions requires the definition of a background model in order to discern contacts with an interaction frequency higher than expected. The background can be estimated using ...
- Koustav Pal, Mattia Forcato, Francesco Ferrari
- 2019
In Hi-C, a biotin-labeled nucleotide is incorporated at the ligation junction, making it possible to enrich for chimeric DNA ligation junctions when modifying the DNA molecules for deep sequencing. The compatibility of Hi-C with next generation sequencing platforms makes it possible to detect chromatin interactions on an unprecedented scale ...
The aim of this paper is to provide guidelines for analyzing and interpreting data obtained with genome-wide 3C methods such as Hi-C and 3C-seq that rely on deep sequencing to detect and quantify pairwise chromatin interactions genome-wide.
