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Related Concept Videos

RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
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...
Chromatin Immunoprecipitation- ChIP02:36

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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Related Experiment Video

Updated: May 22, 2026

The ChIP-exo Method: Identifying Protein-DNA Interactions with Near Base Pair Precision
09:27

The ChIP-exo Method: Identifying Protein-DNA Interactions with Near Base Pair Precision

Published on: December 23, 2016

Inferring direct DNA binding from ChIP-seq.

Timothy L Bailey1, Philip Machanick

  • 1Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia. t.bailey@imb.uq.edu.au

Nucleic Acids Research
|May 22, 2012
PubMed
Summary
This summary is machine-generated.

Central motif enrichment analysis (CMEA) improves transcription factor binding motif identification from ChIP-seq data. The CentriMo tool precisely centers motifs within peak regions, revealing accurate in vivo binding affinities.

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Generation of High Quality Chromatin Immunoprecipitation DNA Template for High-throughput Sequencing (ChIP-seq)
09:52

Generation of High Quality Chromatin Immunoprecipitation DNA Template for High-throughput Sequencing (ChIP-seq)

Published on: April 19, 2013

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • ChIP-seq experiments provide genome-wide transcription factor binding data.
  • Standard motif analysis can misidentify binding motifs for ChIP-ed factors.
  • Accurate motif identification is crucial for understanding in vivo DNA-binding affinity.

Purpose of the Study:

  • To develop a novel method for accurate transcription factor binding motif identification from ChIP-seq data.
  • To introduce CentriMo, a tool for central motif enrichment analysis (CMEA).
  • To validate CMEA and CentriMo using various transcription factor datasets.

Main Methods:

  • Central motif enrichment analysis (CMEA) based on unimodal positional distribution of binding sites.
  • Development and application of the CentriMo tool for identifying maximal central enrichment.
  • Analysis of ChIP-seq datasets for transcription factors Nanog, E2f1, NFIC, and Smad1.

Main Results:

  • CentriMo accurately identifies binding motifs by centering them within ChIP-seq peak regions.
  • Demonstrated differential in vivo vs. in vitro binding affinity for Nanog.
  • Provided evidence for cooperative DNA binding by E2f1 and confirmed NFIC binding.
  • Showed no evidence of direct DNA binding for Smad1 in a challenging dataset.

Conclusions:

  • CMEA and CentriMo enhance the accuracy of motif discovery from ChIP-seq data.
  • CentriMo reveals insights into transcription factor binding affinities and interactions.
  • The CentriMo tool is a valuable addition to the MEME Suite for genomic analysis.