Related Experiment Video
Updated: May 3, 2026
22:27
Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
Published on: May 6, 2010
414.5K
Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts
Ferhat Ay1, Timothy L Bailey2, William Stafford Noble3
1Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA;
Genome Research
|February 7, 2014
Summary
Fit-Hi-C models DNA contacts at the intermediate genomic scale, improving the identification of functional interactions between regulatory elements and gene promoters. This method enhances our understanding of genome organization and gene regulation.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Accurate modeling of DNA architecture at the intermediate scale (50 kb-10 Mb) is essential for understanding functional interactions.
- Current methods lack precision in identifying these mid-range genomic contacts.
Purpose of the Study:
- To introduce Fit-Hi-C, a novel method for statistically confident assignment of mid-range intra-chromosomal contacts.
- To improve the identification of functional genomic interactions.
Main Methods:
- Fit-Hi-C jointly models polymer looping and technical biases in Hi-C data.
- It computes empirical null models without distribution assumptions and corrects for binning artifacts.
- Statistical confidence estimates are assigned to intra-chromosomal contacts.
Main Results:
- Fit-Hi-C identifies high-confidence contacts linking promoters to active enhancers in human ESCs.
- It captures 77% of enhancer-promoter interactions from ChIA-PET data in mouse ESCs.
- Insulators and heterochromatin are identified as hubs for contacts, while promoters and enhancers are involved in fewer.
Conclusions:
- Fit-Hi-C provides improved statistical power for identifying functional genomic interactions.
- The method reveals insights into the roles of regulatory elements and genomic regions in DNA looping.
- High-confidence contacts correlate with replication timing and topological domain boundaries.
Related Concept Videos
02:36Chromatin Immunoprecipitation- ChIP
9.5K
Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
9.5K
02:38Heterochromatin
12.0K
The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at...
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at...
12.0K