Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Epigenetic conditioning improves sequence-based modeling of gene regulation across cell types and alleles.

bioRxiv : the preprint server for biology·2026

Same author

Single-molecule variation in telomeric sequence and structure across humans.

bioRxiv : the preprint server for biology·2026

Same author

Haplotype-resolved centromeric chromatin organization from a complete diploid human genome.

bioRxiv : the preprint server for biology·2026

Same author

In vitro reconstitution of heterochromatin compartments reveals the spontaneous formation of tunable liquid-liquid interfaces.

Nucleic acids research·2026

Same author

Phosphorylation of Xenopus M18BP1 governs centromeric localization and CENP-A nucleosome assembly.

EMBO reports·2026

Same author

Author Correction: Heterochromatin boundaries maintain centromere position, size and number.

Nature structural & molecular biology·2026

Same journal

An assay to quantify sexual commitment and stage conversion in the human malaria parasite Plasmodium falciparum.

Nature protocols·2026

Same journal

Author Correction: Direct inoculation of bioreactor-controlled stirred suspension culture with cryopreserved human pluripotent stem cells.

Nature protocols·2026

Same journal

High-throughput measurements of protein domain functions using magnetic separation.

Nature protocols·2026

Same journal

Inducing physiological polarity and performing gene editing using CRISPR-Cas9 in human trophoblast organoids.

Nature protocols·2026

Same journal

Photocatalytic low-temperature defluorination of PTFE.

Nature protocols·2026

Same journal

Multimodal imaging and quantification of lanthanide chelate-labeled micro- and nanoplastics in plants.

Nature protocols·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jun 14, 2025

DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments

DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments

Published on: January 27, 2016

Mapping protein-DNA interactions with DiMeLo-seq.

Annie Maslan^1,2,3, Nicolas Altemose^4,5, Jeremy Marcus³

¹Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.

Nature Protocols

|September 5, 2024

Summary

This summary is machine-generated.

Directed methylation with long-read sequencing (DiMeLo-seq) offers a novel method for genome-wide protein-DNA interaction mapping. This technique accurately profiles interactions, even in challenging genomic regions.

More Related Videos

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae

Published on: June 3, 2017

CD Spectroscopy to Study DNA-Protein Interactions

CD Spectroscopy to Study DNA-Protein Interactions

Published on: February 10, 2022

Related Experiment Videos

Last Updated: Jun 14, 2025

DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments

DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments

Published on: January 27, 2016

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae

Published on: June 3, 2017

CD Spectroscopy to Study DNA-Protein Interactions

CD Spectroscopy to Study DNA-Protein Interactions

Published on: February 10, 2022

Area of Science:

Genomics
Molecular Biology
Epigenetics

Background:

Mapping protein-DNA interactions is crucial for understanding genome regulation.
Existing short-read methods face limitations in repetitive regions and haplotype resolution.
Need for a method to profile protein binding in the context of endogenous DNA methylation.

Purpose of the Study:

To present a detailed protocol for directed methylation with long-read sequencing (DiMeLo-seq).
To provide practical guidance for performing DiMeLo-seq on various cell preparations.
To enable genome-wide mapping of protein-DNA interactions with enhanced resolution.

Main Methods:

In situ methylation of adenine bases near target proteins using tethered Hia5 methyltransferase.
Detection of methylated adenine via long-read, single-molecule sequencing (e.g., Nanopore).
Utilizes protein A to link antibodies to the Hia5 methyltransferase.

Main Results:

DiMeLo-seq enables mapping of multiple interaction sites on single DNA molecules.
Profiles protein binding within the context of endogenous DNA methylation.
Identifies haplotype-specific protein-DNA interactions and maps interactions in repetitive genomic regions.

Conclusions:

DiMeLo-seq is a versatile method for comprehensive protein-DNA interaction mapping.
The protocol is adaptable to fresh, lightly fixed, or frozen cells.
A Python package (dimelo) is available for data analysis.