What is chromosome conformation capture used for?
Chromosome conformation capture (3C) is a technique used to detect the spatial organization of chromosomal DNA in fixed cells.
What is Hi-C technique?
The classical Hi-C technique involves restriction digestion of a formaldehyde cross-linked genome with sequence specific restriction enzymes, followed by fill in and repair of digested ends with the incorporation of biotin-linked nucleotides. The repaired ends are then re-ligated.
What is Hi-C sequencing used for?
Today, Hi-C is the most widely used and well-known 3C variant. Using next-generation sequencing strategies such as high-throughput and parallel sequencing, Hi-C enables researchers to profile read-pair interactions on an all-versus-all basis—that is, to profile interactions for all read pairs in an entire genome.
What are Hi-C maps?
The high-throughput chromosome conformation capture (Hi-C) technique has enabled genome-wide mapping of chromatin interactions. However, high-resolution Hi-C data requires costly, deep sequencing; therefore, it has only been achieved for a limited number of cell types.
How do I visualize Hi-C data?
A heat map is perhaps the most straightforward visualization method for a Hi-C contact matrix. Contact matrices are by definition symmetric around the diagonal, and the number of rows and columns is equal to the length of the genome divided by the bin size.
How are chromosomal rearrangements detected?
Read-pair method Sequence read pairs are short sequences from both ends of each of the millions of DNA fragments (‘inserts’) generated by library preparation. Clustering of at least two discordant pairs of reads, either by size or by orientation, is suggestive of a chromosome rearrangement.
What is Hi-C genomics?
Arima Hi-C is a proximity ligation method that captures the organizational structure of chromatin in three dimensions, where genomic sequences that are distal to each other in linear distance can be closer to each other in the 3D space.
What is on a chromosome?
A chromosome is made up of proteins and DNA organized into genes. Each cell normally contains 23 pairs of chromosomes.
How does Gro seq work?
GRO-Seq maps the binding sites of transcriptionally active RNA polymerase II (RNAPII). In this method, active RNAPII is allowed to run on in the presence of 5-bromouridine 5′-triphosphate (Br-UTP). RNAs are hydrolyzed and purified using beads coated with antibodies to 5-bromo-2-deoxyuridine (BrdU).
Why is Hi-C important?
Hi-C allows the analysis of non-random 3d-genome structures, chromatin domains, of which topologically-associating-domains (TADs) are thought to be the most important ones: “TADs have been shown to be a fundamental component of the 3D organization of the genome in the nuclear space, restraining and facilitating …
What is Hi-C sequencing?
Hi-C sequencing is high‐throughput chromosome conformation capture technique to analyze spatial genome organization and map higher‐order chromosome folding and topological associated domains.
What is Bionano optical mapping?
In contrast to reference-based methods like sequencing or comparative methods like aCGH, optical mapping is a de novo assembly-based method that enables better realization of true genomic structure.
What’s new in Chromosome Conformation Capture?
Advances in the study of chromosome conformation capture technologies, such as Hi-C technique – capable of capturing chromosomal interactions in a genome-wide scale – have led to the development of three-dimensional chromosome and genome structure reconstruction methods from Hi-C data.
What are the methods for chromosome 3D structure reconstruction from 3C?
Many methods have been developed for chromosome 3D structure reconstruction from chromosome conformation capture (3C) such as the Hi-C data. Generally, these data-driven methods can be grouped into three classes [ 31] based on how the IF is used for 3D structure construction: distance-based, contact-based and probability-based.
What does iterative correction of Hi-C data reveal about chromosome organization?
Iterative correction of hi-C data reveals hallmarks of chromosome organization. Nat Methods. 2012;9 (10):999. Hu M, Deng K, Selvaraj S, Qin Z, Ren B, Liu JS.
What is chromosome3d?
Adhikari B, Trieu T, Cheng J. Chromosome3D: reconstructing three-dimensional chromosomal structures from hi-C interaction frequency data using distance geometry simulated annealing. BMC Genomics. 2016;17 (1):886.