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 HiCORE: Hi-C analysis for identification of core chromatin loops with higher resolution and reliability

2020 ◽  
Author(s):  
Hongwoo Lee ◽  
Pil Joon Seo
Keyword(s):  
High Resolution ◽  
High Throughput Sequencing ◽  
Stochastic Noise ◽  
3D Interaction ◽  
Chromosome Conformation ◽  
Genome Coverage ◽  
Chromatin Loops ◽  
Chromatin Interactions ◽  
Genome Wide ◽  
Physical Interactions

AbstractGenome-wide chromosome conformation capture (3C)-based high-throughput sequencing (Hi-C) has enabled identification of genome-wide chromatin loops. Because the Hi-C map with restriction fragment resolution is intrinsically associated with sparsity and stochastic noise, Hi-C data are usually binned at particular intervals; however, the binning method has limited reliability, especially at high resolution. Here, we describe a new method called HiCORE, which provides simple pipelines and algorithms to overcome the limitations of single-layered binning and predict core chromatin regions with 3D physical interactions. In this approach, multiple layers of binning with slightly shifted genome coverage are generated, and interacting bins at each layer are integrated to infer narrower regions of chromatin interactions. HiCORE predicts chromatin looping regions with higher resolution and contributes to the identification of the precise positions of potential genomic elements.Author SummaryThe Hi-C analysis has enabled to obtain information on 3D interaction of genomes. While various approaches have been developed for the identification of reliable chromatin loops, binning methods have been limitedly improved. We here developed HiCORE algorithm that generates multiple layers of bin-array and specifies core chromatin regions with 3D interactions. We validated our algorithm and provided advantages over conventional binning method. Overall, HiCORE facilitates to predict chromatin loops with higher resolution and reliability, which is particularly relevant in analysis of small genomes.

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.

Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions

2013 ◽  
Vol 8 (3) ◽  
pp. 509-524 ◽  
Author(s):  
Ralph Stadhouders ◽  
Petros Kolovos ◽  
Rutger Brouwer ◽  
Jessica Zuin ◽  
Anita van den Heuvel ◽  
...  
Keyword(s):  
High Resolution ◽  
Long Range ◽  
Chromosome Conformation Capture ◽  
Chromosome Conformation ◽  
Chromatin Interactions ◽  
Genome Scale ◽  
Capture Sequencing

scholarly journals Chromosome Conformation Capture with Nuclear Titrated Capture-C (NuTi Capture-C)

2021 ◽  
Author(s):  
Damien J. Downes ◽  
Jim R. Hughes
Keyword(s):  
High Resolution ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Chromosome Conformation Capture ◽  
Target Sequence ◽  
Sequence Specificity ◽  
Chromosome Conformation ◽  
Chromatin Interactions

Abstract NuTi Capture-C is a Chromosome Conformation Capture (3C) approach, which can very efficiently identify chromatin interactions at target viewpoints at high resolution. The addition of high-throughput sequencing adaptors prior to enrichment allows for multiplexing of replicates and comparison samples. This method is an improvement on the previous NG Capture-C1 method in that modifications have been made to the in situ 3C method to improve nuclear integrity (Nuclear 3C). Additionally, capture has been optimised to viewpoint complexity through titration, maximising on target sequence specificity. The experiment will take several weeks and provide reproducible interaction profiles for tens to thousands of viewpoints of interest.

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 SisterC: A novel 3C-technique to detect chromatin interactions between and along sister chromatids

2020 ◽  
Author(s):  
Marlies E. Oomen ◽  
Adam K. Hedger ◽  
Jonathan K. Watts ◽  
Job Dekker
Keyword(s):  
Cell Cycle ◽  
Single Strand ◽  
Chromosome Conformation Capture ◽  
Brdu Incorporation ◽  
Chromosome Conformation ◽  
Strand Breaks ◽  
Chromatin Interactions ◽  
Sister Chromatids ◽  
Single Strand Breaks ◽  
Capture Techniques

Abstract Current chromosome conformation capture techniques are not able to distinguish sister chromatids. Here we describe the protocol of SisterC1: a novel Hi-C technique that leverages BrdU incorporation and UV/Hoechst-induced single strand breaks to identify interactions along and between sister chromatids. By synchronizing cells, BrdU is incorporated only on the newly replicated strand, which distinguishes the two sister chromatids2,3. This is followed by Hi-C4 of cells that can be arrested in different stages of the cell cycle, e.g. in mitosis. Before final amplification of the Hi-C library, strands containing BrdU are specifically depleted by UV/Hoechst treatment. SisterC libraries are then sequenced using 50bp paired end reads, followed by mapping using standard Hi-C processing tools. Interactions can then be assigned as inter- or intra-sister interactions based on read orientation.

scholarly journals An integrative approach for fine-mapping chromatin interactions

2019 ◽  
Vol 36 (6) ◽  
pp. 1704-1711
Author(s):  
Artur Jaroszewicz ◽  
Jason Ernst
Keyword(s):  
Gene Regulation ◽  
High Resolution ◽  
Biological Significance ◽  
Computational Method ◽  
Supplementary Information ◽  
Integrative Approach ◽  
Genome Architecture ◽  
Open Chromatin ◽  
Chromatin Interactions ◽  
Genome Wide

Abstract Motivation Chromatin interactions play an important role in genome architecture and gene regulation. The Hi-C assay generates such interactions maps genome-wide, but at relatively low resolutions (e.g. 5-25 kb), which is substantially coarser than the resolution of transcription factor binding sites or open chromatin sites that are potential sources of such interactions. Results To predict the sources of Hi-C-identified interactions at a high resolution (e.g. 100 bp), we developed a computational method that integrates data from DNase-seq and ChIP-seq of TFs and histone marks. Our method, χ-CNN, uses this data to first train a convolutional neural network (CNN) to discriminate between called Hi-C interactions and non-interactions. χ-CNN then predicts the high-resolution source of each Hi-C interaction using a feature attribution method. We show these predictions recover original Hi-C peaks after extending them to be coarser. We also show χ-CNN predictions enrich for evolutionarily conserved bases, eQTLs and CTCF motifs, supporting their biological significance. χ-CNN provides an approach for analyzing important aspects of genome architecture and gene regulation at a higher resolution than previously possible. Availability and implementation χ-CNN software is available on GitHub (https://github.com/ernstlab/X-CNN). Supplementary information Supplementary data are available at Bioinformatics online.

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/.

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