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Related Concept Videos

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...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

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Related Experiment Video

Updated: May 20, 2026

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis
12:29

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis

Published on: April 16, 2018

Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite.

Xi Wang1, Xuegong Zhang

  • 1MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST / Department of Automation, Tsinghua University, Beijing 100084, China.

BMC Systems Biology
|July 13, 2012
PubMed
Summary
This summary is machine-generated.

SeqSite accurately pinpoints transcription factor binding sites (TFBSs) from ChIP-seq data. This novel method improves resolution for both closely spaced and isolated TFBSs, advancing genomic analysis.

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PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

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Last Updated: May 20, 2026

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis
12:29

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis

Published on: April 16, 2018

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

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
12:24

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

Area of Science:

  • Genomics
  • Computational Biology
  • Molecular Biology

Background:

  • Chromatin immunoprecipitation sequencing (ChIP-seq) is crucial for identifying protein binding sites genome-wide.
  • Existing ChIP-seq analysis tools often detect binding regions but struggle to pinpoint precise transcription factor binding sites (TFBSs), especially in complex genomic areas.
  • Accurate TFBS localization is essential for understanding gene regulation.

Purpose of the Study:

  • To develop a high-resolution method for pinpointing transcription factor binding sites (TFBSs) directly from ChIP-seq data.
  • To address the limitations of current tools in accurately locating TFBSs, particularly when binding events are closely spaced.

Main Methods:

  • Introduced SeqSite, a novel computational method employing a two-step strategy.
  • Step 1: Detects tag-enriched regions within ChIP-seq data.
  • Step 2: Models tag density profiles to pinpoint TFBSs on each DNA strand using least-squares fitting and merges strand-specific detections.

Main Results:

  • SeqSite successfully locates most binding sites separated by as little as 40 base pairs in simulation data.
  • Application to human ChIP-seq datasets demonstrated SeqSite's superior resolution in identifying TFBSs compared to existing methods.
  • The method effectively distinguishes between closely spaced and isolated binding events.

Conclusions:

  • SeqSite is a computational tool that enhances the resolution of TFBS detection from ChIP-seq data.
  • The tool accurately pinpoints both closely spaced and isolated binding sites, offering a significant advancement in ChIP-seq analysis.