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Chromatin Immunoprecipitation- ChIP

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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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SMAdd-seq: probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing.

Gali Bai¹, Namrita Dhillon¹, Colette Felton¹

¹Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, United States.

Nucleic Acids Research

|July 19, 2025

Summary

We developed small-molecule adduct sequencing (SMAdd-seq) to map DNA accessibility in living cells. This nanopore sequencing method reveals chromatin structure and dynamics with high precision.

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Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC Crosslinking of Small Molecules to Isolate Chromatin

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Published on: January 20, 2016

Area of Science:

Genomics
Epigenetics
Molecular Biology

Background:

Current chromatin accessibility studies require purified nuclei and enzymatic treatments, limiting in vivo analysis.
Existing methods face challenges in profiling native chromatin dynamics and heterogeneity.

Purpose of the Study:

Introduce a novel nanopore sequencing technique, SMAdd-seq, for direct in vivo chromatin accessibility profiling.
Develop a computational tool (NEMO) to analyze sequencing data and map chromatin structure.
Assess the method's performance on both purified nuclei and intact cells.

Main Methods:

Small-molecule adduct sequencing (SMAdd-seq) using angelicin to label accessible DNA in intact cells or nuclei.
Nanopore sequencing to detect angelicin-modified DNA via distinct current signals.
Development and application of a neural network model (NEMO) for modification calling and chromatin analysis.

Main Results:

SMAdd-seq successfully detected angelicin modifications in DNA using nanopore signals.
NEMO accurately identified nucleosome occupancy patterns at transcription start sites.
Observed heterogeneity in chromatin structure at single-molecule and bulk levels.

Conclusions:

SMAdd-seq enables direct in vivo chromatin labeling and profiling of DNA accessibility.
The method accurately measures chromatin structure, dynamics, and heterogeneity.
SMAdd-seq offers a promising approach for studying native chromatin organization in various biological contexts.