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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.
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...

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Updated: Nov 17, 2025

Single-Cell Factor Localization on Chromatin using Ultra-Low Input Cleavage Under Targets and Release using Nuclease

Single-Cell Factor Localization on Chromatin using Ultra-Low Input Cleavage Under Targets and Release using Nuclease

Published on: February 1, 2022

Profiling Chromatin Accessibility at Single-cell Resolution.

Sarthak Sinha¹, Ansuman T Satpathy², Weiqiang Zhou³

¹Department of Comparative Biology & Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada.

Genomics, Proteomics & Bioinformatics

|February 13, 2021

Summary

This summary is machine-generated.

Understanding cellular heterogeneity requires examining the epigenome and chromatin accessibility. Single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) offers scalable insights into these regulatory elements.

Keywords:

Cis-regulatory elements Epigenetics Gene regulation Single-cell ATAC-seq Single-cell multi-omics

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Area of Science:

Molecular Biology
Genomics
Computational Biology

Background:

Cellular heterogeneity and plasticity are crucial for complex fate decisions.
The epigenome, specifically chromatin accessibility, governs distinct transcriptional programs.
Understanding gene regulation requires high-resolution insights into regulatory sequences.

Purpose of the Study:

To review molecular methods and bioinformatic tools for capturing cell-to-cell chromatin variation.
To discuss joint profiling of chromatin with other omics data.
To cover computational strategies for multi-omic data integration and prediction of chromatin accessibility.

Main Methods:

Single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) for scalable chromatin accessibility measurement.
Joint profiling techniques combining scATAC-seq with transcriptomic or proteomic data.
Bioinformatic tools for analyzing single-cell chromatin variation and integrating multi-omic datasets.

Main Results:

scATAC-seq enables scalable, single-cell resolution of chromatin accessibility.
Multi-omic approaches allow integrated analysis of chromatin, transcriptome, and proteome.
Predictive bioinformatic tools can infer chromatin accessibility from transcriptomic data.

Conclusions:

Methodological advancements in scATAC-seq enhance cell discovery through robust chromatin coverage.
Integration of multi-modal measurements deepens understanding of gene regulation.
These approaches are vital for studying gene regulation in both homeostasis and disease states.