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Chromatin Immunoprecipitation- ChIP

Chromatin Immunoprecipitation- ChIP

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.
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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...

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

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Updated: Aug 12, 2025

Capturing Chromosome Conformation Across Length Scales

Capturing Chromosome Conformation Across Length Scales

Published on: January 20, 2023

HiCLift: A fast and efficient tool for converting chromatin interaction data between genome assemblies.

Xiaotao Wang, Feng Yue

Biorxiv : the Preprint Server for Biology

|January 30, 2023

Summary

HiCLift efficiently converts chromatin contact data between genome assemblies, including the T2T genome. This tool is faster than re-mapping reads and can process patient data without raw sequencing reads.

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Last Updated: Aug 12, 2025

Capturing Chromosome Conformation Across Length Scales

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Published on: January 20, 2023

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Published on: October 14, 2022

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

Area of Science:

Genomics
Epigenetics
Bioinformatics

Background:

Accurate genomic coordinate conversion is vital for comparative genomics and understanding 3D genome organization.
Existing tools are insufficient for chromatin interaction data, hindering studies on gene regulation and disease.

Approach:

Developed HiCLift, a novel tool for converting chromatin contact data (e.g., Hi-C, Micro-C) between genome assemblies.
HiCLift supports the latest T2T human reference genome assembly.

Key Points:

HiCLift significantly outperforms read re-mapping, achieving an average speedup of 42x (hours vs. days).
The tool generates highly comparable contact matrices to direct re-mapping.
Crucially, HiCLift bypasses the need for raw sequencing reads, enabling analysis of patient samples where data may be inaccessible.

Conclusions:

HiCLift provides a fast, efficient, and accessible solution for converting chromatin interaction data across genome assemblies.
This facilitates large-scale comparative and integrative genomic studies, particularly those involving personal genomes and clinical samples.