Chromosome conformation capture methods

Current computational methods on Hi-C analysis focused on identifying Mb-size domains often failed to unveil the underlying functional and mechanistic relationship of chromatin structure and gene regulation. We developed a novel computational method HiSIF to identify genome-wide interacting loci.

13p vibransone 28-03-2024 7 2   Download

The three-dimensional (3D) organization of chromosomes can be probed using methods like Capture-C. However, it is unclear how such population-level data relate to the organization within a single cell, and the mechanisms leading to the observed interactions are still largely obscure. We present a polymer modeling scheme based on the assumption that chromosome architecture is maintained by protein bridges, which form chromatin loops.

16p viaristotle 29-01-2022 17 1   Download

Chromosome conformation capture methods are being increasingly used to study three-dimensional genome architecture in multiple cell types and species. An important challenge is to examine changes in three-dimensional architecture across cell types and species. We present Arboretum-Hi-C, a multi-task spectral clustering method, to identify common and context-specific aspects of genome architecture.

18p viaristotle 29-01-2022 7 0   Download

Chromosome conformation capture (3C)-based techniques have revolutionized the field of nuclear organization, partly replacing DNA FISH as the method of choice for studying three-dimensional chromosome architecture. Although DNA FISH is commonly used for confirming 3C-based findings, the two techniques are conceptually and technically different and comparing their results is not trivial. Here, we discuss both 3C-based techniques and DNA FISH approaches to highlight their similarities and differences.

9p viaristotle 29-01-2022 11 0   Download

The three-dimensional conformation of a genome can be profiled using Hi-C, a technique that combines chromatin conformation capture with high-throughput sequencing. However, structural variations often yield features that can be mistaken for chromosomal interactions.

15p viarchimedes 26-01-2022 11 0   Download

An important unanswered question in chromatin biology is the extent to which long-range looping interactions change across developmental models, genetic perturbations, drug treatments, and disease states. Computational tools for rigorous assessment of cell type-specific loops across multiple biological conditions are needed.

44p viarchimedes 26-01-2022 10 1   Download

Deciphering the 3D structure of the genome is essential for elucidating the regulatory mechanisms of gene expression in detail. Existing methods, such as chromosome conformation capture (3C) and Hi-C have enabled the identification of novel aspects of chromatin structure.

6p visilicon2711 20-08-2021 16 1   Download

Hi-C is a molecular biology technique to understand the genome spatial structure. However, data obtained from Hi-C experiments is biased. Therefore, several methods have been developed to model Hi-C data and identify significant interactions.

10p vijeeni2711 24-07-2021 8 0   Download

Normalization is essential to ensure accurate analysis and proper interpretation of sequencing data, and chromosome conformation capture data such as Hi-C have particular challenges. Although several methods have been proposed, the most widely used type of normalization of Hi-C data usually casts estimation of unwanted effects as a matrix balancing problem, relying on the assumption that all genomic regions interact equally with each other.

16p viconnecticut2711 28-10-2020 10 1   Download