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 Analysis of long-range chromatin interactions using Chromosome Conformation Capture

Methods ◽  
2012 ◽  
Vol 58 (3) ◽  
pp. 192-203 ◽  
Author(s):  
Natalia Naumova ◽  
Emily M. Smith ◽  
Ye Zhan ◽  
Job Dekker
Keyword(s):  
Long Range ◽  
Chromosome Conformation Capture ◽  
Chromosome Conformation ◽  
Chromatin Interactions

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 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 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.

Chromosome conformation capture-on-chip analysis of long-range cis-interactions of the SOX9 promoter

2013 ◽  
Vol 21 (8) ◽  
pp. 781-788 ◽  
Author(s):  
Marta Smyk ◽  
Przemyslaw Szafranski ◽  
Michał Startek ◽  
Anna Gambin ◽  
Paweł Stankiewicz
Keyword(s):  
Long Range ◽  
Chromosome Conformation Capture ◽  
Chromosome Conformation ◽  
On Chip ◽  
Chip Analysis

scholarly journals HIPPIE2: a method for fine-scale identification of physically interacting chromatin regions

2019 ◽  
Author(s):  
Pavel P. Kuksa ◽  
Alexandre Amlie-Wolf ◽  
Yih-Chii Hwang ◽  
Otto Valladares ◽  
Brian D. Gregory ◽  
...  
Keyword(s):  
High Resolution ◽  
Cell Line ◽  
Cell Lines ◽  
Dna Looping ◽  
Open Chromatin ◽  
Fine Scale ◽  
Long Distance ◽  
Chromosome Conformation ◽  
Chromatin Interactions ◽  
Distance Regulation

AbstractMost regulatory chromatin interactions are mediated by various transcription factors (TFs) and involve physically-interacting elements such as enhancers, insulators, or promoters. To map these elements and interactions, we developed HIPPIE2 which analyzes raw reads from high-throughput chromosome conformation (Hi-C) experiments to identify fine-scale physically-interacting regions (PIRs). Unlike standard genome binning approaches (e.g., 10K-1Mbp bins), HIPPIE2 dynamically calls physical locations of PIRs with better precision and higher resolution based on the pattern of restriction events and relative locations of interacting sites inferred from the sequencing readout.We applied HIPPIE2 to in situ Hi-C datasets across 6 human cell lines (GM12878, IMR90, K562, HMEC, HUVEC, NHEK) with matched ENCODE and Roadmap functional genomic data. HIPPIE2 detected 1,042,738 distinct PIRs across cell lines, with high resolution (average PIR length of 1,006bps) and high reproducibility (92.3% in GM12878 replicates). 32.8% of PIRs were shared among cell lines. PIRs are enriched for epigenetic marks (H3K27ac, H3K4me1) and open chromatin, suggesting active regulatory roles. HIPPIE2 identified 2.8M significant intrachromosomal PIR–PIR interactions, 27.2% of which were enriched for TF binding sites. 50,608 interactions were enhancer–promoter interactions and were enriched for 33 TFs (31 in enhancers/29 in promoters), several of which are known to mediate DNA looping/long-distance regulation. 29 TFs were enriched in >1 cell line and 4 were cell line-specific. These findings demonstrate that the dynamic approach used in HIPPIE2 (https://bitbucket.com/wanglab-upenn/HIPPIE2) characterizes PIR–PIR interactions with high resolution and reproducibility.

Sign in / Sign up

Export Citation Format

Share Document