scholarly journals Targeted high-resolution chromosome conformation capture at genome-wide scale

2020 ◽  
Author(s):  
Damien J. Downes ◽  
Matthew E. Gosden ◽  
Jelena Telenius ◽  
Stephanie J. Carpenter ◽  
Lea Nussbaum ◽  
...  
Keyword(s):  
High Resolution ◽  
Fold Increase ◽  
Chromosome Conformation Capture ◽  
New Method ◽  
Entire Genome ◽  
Chromosome Conformation ◽  
Target Sequencing ◽  
Genome Wide ◽  
Technical Modifications ◽  
Wide Scale

ABSTRACTChromosome conformation capture (3C) provides an adaptable tool for studying diverse biological questions. Current 3C methods provide either low-resolution interaction profiles across the entire genome, or high-resolution interaction profiles at up to several hundred loci. All 3C methods are affected to varying degrees by inefficiency, bias and noise. As such, generation of reproducible high-resolution interaction profiles has not been achieved at scale. To overcome this barrier, we systematically tested and improved upon current methods. We show that isolation of 3C libraries from intact nuclei, as well as shortening and titration of enrichment oligonucleotides used in high-resolution methods reduces noise and increases on-target sequencing. We combined these technical modifications into a new method Nuclear-Titrated (NuTi) Capture-C, which provides a >3-fold increase in informative sequencing content over current Capture-C protocols. Using NuTi Capture-C we target 8,061 promoters in triplicate, demonstrating that this method generates reproducible high-resolution genome-wide 3C interaction profiles at scale.

scholarly journals High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Damien J. Downes ◽  
Robert A. Beagrie ◽  
Matthew E. Gosden ◽  
Jelena Telenius ◽  
Stephanie J. Carpenter ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Resolution ◽  
Regulatory Element ◽  
Gene Promoters ◽  
Entire Genome ◽  
Chromosome Conformation ◽  
Genome Wide ◽  
Wide Scale

AbstractChromosome conformation capture (3C) provides an adaptable tool for studying diverse biological questions. Current 3C methods generally provide either low-resolution interaction profiles across the entire genome, or high-resolution interaction profiles at limited numbers of loci. Due to technical limitations, generation of reproducible high-resolution interaction profiles has not been achieved at genome-wide scale. Here, to overcome this barrier, we systematically test each step of 3C and report two improvements over current methods. We show that up to 30% of reporter events generated using the popular in situ 3C method arise from ligations between two individual nuclei, but this noise can be almost entirely eliminated by isolating intact nuclei after ligation. Using Nuclear-Titrated Capture-C, we generate reproducible high-resolution genome-wide 3C interaction profiles by targeting 8055 gene promoters in erythroid cells. By pairing high-resolution 3C interaction calls with nascent gene expression we interrogate the role of promoter hubs and super-enhancers in gene regulation.

scholarly journals Hi-C 2.0: An Optimized Hi-C Procedure for High-Resolution Genome-Wide Mapping of Chromosome Conformation

2016 ◽  
Author(s):  
Houda Belaghzal ◽  
Job Dekker ◽  
Johan H. Gibcus
Keyword(s):  
High Resolution ◽  
Chromosome Conformation Capture ◽  
Digital Information ◽  
Dna Loops ◽  
Chromosome Conformation ◽  
Chromatin Interactions ◽  
Genome Wide

ABSTRACTChromosome conformation capture-based methods such as Hi-C have become mainstream techniques for the study of the 3D organization of genomes. These methods convert chromatin interactions reflecting topological chromatin structures into digital information (counts of pair-wise interactions). Here, we describe an updated protocol for Hi-C (Hi-C 2.0) that integrates recent improvements into a single protocol for efficient and high-resolution capture of chromatin interactions. This protocol combines chromatin digestion and frequently cutting enzymes to obtain kilobase (Kb) resolution. It also includes steps to reduce random ligation and the generation of uninformative molecules, such as unligated ends, to improve the amount of valid intra-chromosomal read pairs. This protocol allows for obtaining information on conformational structures such as compartment and TADs, as well as high-resolution conformational features such as DNA loops.

scholarly journals Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation

Methods ◽  
2017 ◽  
Vol 123 ◽  
pp. 56-65 ◽  
Author(s):  
Houda Belaghzal ◽  
Job Dekker ◽  
Johan H. Gibcus
Keyword(s):  
High Resolution ◽  
Chromosome Conformation ◽  
Genome Wide

scholarly journals epiTAD: a web application for visualizing chromosome conformation capture data in the context of genetic epidemiology

2019 ◽  
Vol 35 (21) ◽  
pp. 4462-4464
Author(s):  
Jordan H Creed ◽  
Garrick Aden-Buie ◽  
Alvaro N Monteiro ◽  
Travis A Gerke
Keyword(s):  
Genetic Epidemiology ◽  
In Silico ◽  
Web Application ◽  
Large Scale ◽  
Source Code ◽  
Chromosome Conformation Capture ◽  
Chromosome Conformation ◽  
Web Based ◽  
Genome Wide ◽  
Public Data

Abstract Summary Complementary advances in genomic technology and public data resources have created opportunities for researchers to conduct multifaceted examination of the genome on a large scale. To meet the need for integrative genome wide exploration, we present epiTAD. This web-based tool enables researchers to compare genomic 3D organization and annotations across multiple databases in an interactive manner to facilitate in silico discovery. Availability and implementation epiTAD can be accessed at https://apps.gerkelab.com/epiTAD/ where we have additionally made publicly available the source code and a Docker containerized version of the application.

scholarly journals epiTAD: a web application for visualizing high throughput chromosome conformation capture data in the context of genetic epidemiology

2018 ◽  
Author(s):  
Jordan H. Creed ◽  
Garrick Aden-Buie ◽  
Alvaro N. Monteiro ◽  
Travis A. Gerke
Keyword(s):  
High Throughput ◽  
Genetic Epidemiology ◽  
In Silico ◽  
Web Application ◽  
Chromosome Conformation Capture ◽  
Chromosome Conformation ◽  
Web Based ◽  
Genome Wide ◽  
Public Data ◽  
Complex Scale

AbstractThe increasing availability of public data resources coupled with advancements in genomic technology has created greater opportunities for researchers to examine the genome on a large and complex scale. To meet the need for integrative genome wide exploration, we present epiTAD. This web-based tool enables researchers to compare genomic structures and annotations across multiple databases and platforms in an interactive manner in order to facilitate in silico discovery. epiTAD can be accessed at https://apps.gerkelab.com/epiTAD/.

scholarly journals Systematic evaluation of statistical methods for identifying looping interactions in 5C data

2017 ◽  
Author(s):  
Thomas G. Gilgenast ◽  
Jennifer E. Phillips-Cremins
Keyword(s):  
High Resolution ◽  
Statistical Methods ◽  
Variance Estimation ◽  
Chromosome Conformation Capture ◽  
Systematic Evaluation ◽  
High Coverage ◽  
Method Performance ◽  
Chromosome Conformation ◽  
Trade Offs ◽  
Carbon Copy

SummaryChromosome-Conformation-Capture-Carbon-Copy (5C) is a molecular technology based on proximity ligation that enables high-resolution and high-coverage inquiry of long-range chromatin looping interactions. Computational pipelines for analyzing 5C data involve a series of inter-dependent normalization procedures and statistical methods that markedly influence downstream biological results. A detailed analysis of the trade-offs inherent to all stages of 5C analysis has not been reported, but is essential for understanding the biological basis of looping. Here, we provide a comparative assessment of method performance at each step in the 5C analysis pipeline, including sequencing depth and library complexity correction, bias mitigation, spatial noise reduction, distance-dependent expected and variance estimation, modeling, and loop detection. We present a detailed discussion of methodological advantages/disadvantages at each step and provide a full suite of algorithms, lib5C, to allow investigators to test the range of approaches on their own high-resolution 5C data. Principles learned from our comparative analyses will have broad impact on many other forms of Chromosome-Conformation-Capture-based data, including Hi-C, 4C, and Capture-C.

scholarly journals No kissing in the nucleus: Unbiased analysis reveals no evidence of trans chromosomal regulation of mammalian immune development

2017 ◽  
Author(s):  
Timothy M. Johanson ◽  
Hannah D. Coughlan ◽  
Aaron T.L. Lun ◽  
Naiara G. Bediaga ◽  
Gaetano Naselli ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Fate ◽  
Immune Cells ◽  
Chromosome Conformation Capture ◽  
Chromosome Conformation ◽  
Immune Development ◽  
Regulate Gene Expression ◽  
Genome Wide ◽  
Capture Technique ◽  
Regulate Gene

SummaryIt has been proposed that interactions between mammalian chromosomes, or transchromosomal interactions (also known as kissing chromosomes), regulate gene expression and cell fate determination. Here we aimed to identify novel transchromosomal interactions in immune cells by high-resolution genome-wide chromosome conformation capture. Although we readily identified stable interactions in cis, and also between centromeres and telomeres on different chromosomes, surprisingly we identified no gene regulatory transchromosomal interactions in either mouse or human cells, including previously described interactions. We suggest that advances in the chromosome conformation capture technique and the unbiased nature of this approach allow more reliable capture of interactions between chromosomes than previous methods. Overall our findings suggest that stable transchromosomal interactions that regulate gene expression are not present in mammalian immune cells and that lineage identity is governed by cis, not trans chromosomal interactions.

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