Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

DNA Microarrays02:34

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...
Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...

You might also read

Related Articles

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

Sort by
Same author

Host oxidative stress primes mycobacteria for rapid antibiotic resistance evolution.

Nature communications·2026
Same author

Dormancy regulon reduction was pivotal to the evolution of Mycobacterium tuberculosis.

Nature communications·2026
Same author

Comparative physiological and genomic characterization of a novel <i>Nitrobacter vulgaris</i> strain from a nitrate-contaminated subsurface.

Applied and environmental microbiology·2026
Same author

Host oxidative stress primes mycobacteria for rapid antibiotic resistance evolution.

bioRxiv : the preprint server for biology·2025
Same author

Personalized Clostridioides difficile colonization risk prediction and probiotic therapy assessment in the human gut.

Cell systems·2025
Same author

Emergence and disruption of cooperativity in a denitrifying microbial community.

The ISME journal·2025

Related Experiment Video

Updated: Jul 9, 2026

Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique
06:32

Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique

Published on: March 9, 2022

Model-based deconvolution of genome-wide DNA binding.

David J Reiss1, Marc T Facciotti, Nitin S Baliga

  • 1Institute for Systems Biology, 1441 N. 34th St. Seattle, WA 98103-8904, USA. dreiss@systemsbiology.org

Bioinformatics (Oxford, England)
|December 7, 2007
PubMed
Summary
This summary is machine-generated.

We developed MeDiChI, a new method to improve DNA-binding protein target localization using chromatin immunoprecipitation followed by hybridization to a genomic tiling microarray (ChIP-chip). MeDiChI enhances resolution, surpassing probe spacing limitations for more accurate binding site identification.

More Related Videos

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae
10:43

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

Published on: June 3, 2017

Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin)
10:05

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

Published on: January 20, 2016

Related Experiment Videos

Last Updated: Jul 9, 2026

Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique
06:32

Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique

Published on: March 9, 2022

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae
10:43

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

Published on: June 3, 2017

Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin)
10:05

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

Published on: January 20, 2016

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Chromatin immunoprecipitation followed by hybridization to a genomic tiling microarray (ChIP-chip) is a standard method for identifying DNA-binding protein targets.
  • Current limitations in ChIP-chip resolution stem from microarray probe spacing and the size of immunoprecipitated DNA fragments.

Purpose of the Study:

  • To develop a novel computational approach, MeDiChI, to enhance the resolution and accuracy of DNA-binding site localization in ChIP-chip data.
  • To provide a robust and efficient method for analyzing diverse ChIP-chip datasets.

Main Methods:

  • Developed a generative model for binding sites in ChIP-chip data.
  • Created an approach, MeDiChI, for efficiently learning this model from various datasets.
  • Evaluated MeDiChI using simulated data and experimental ChIP-chip datasets from Saccharomyces cerevisiae and Halobacterium salinarium NRC-1.

Main Results:

  • MeDiChI accurately predicts binding locations beyond the resolution of probe spacing, even for overlapping peaks.
  • The method can improve the effective resolution of tiling array data by 5-fold or more.
  • Analysis of simulated data provided insights for optimizing experimental design to increase binding site localization accuracy.

Conclusions:

  • MeDiChI significantly enhances the resolution and accuracy of ChIP-chip assays.
  • The developed method offers a valuable tool for genomic studies of DNA-binding proteins.
  • MeDiChI is available as an open-source R package, facilitating its widespread adoption and use.