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Related Concept Videos

Histone Modification02:32

Histone Modification

The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone deacetylase,...
Histone Modification02:32

Histone Modification

The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone deacetylase,...
Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
Writers
The writer is an enzyme that can...
Western Blotting01:15

Western Blotting

Western blotting is an analytical technique for protein identification. It has various applications in immunology and medicine, including detecting diseases like bovine spongiform encephalopathy, mad cow disease, and human and feline immunodeficiency virus from biological samples.
The technique begins with separating proteins from the sample using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), followed by protein transfer, immunoblotting, and finally, protein detection.

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Related Experiment Video

Updated: May 18, 2026

Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis
11:02

Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis

Published on: May 17, 2016

WaveSeq: a novel data-driven method of detecting histone modification enrichments using wavelets.

Apratim Mitra1, Jiuzhou Song

  • 1Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA.

Plos One
|October 3, 2012
PubMed
Summary

WaveSeq is a novel method for analyzing ChIP-Seq data, effectively identifying histone modification regions. This technique accurately detects both narrow and broad enrichment patterns, even with low signal-to-noise ratios.

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Histone Modification Screening using Liquid Chromatography, Trapped Ion Mobility Spectrometry, and Time-Of-Flight Mass Spectrometry
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Last Updated: May 18, 2026

Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis
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Histone Modification Screening using Liquid Chromatography, Trapped Ion Mobility Spectrometry, and Time-Of-Flight Mass Spectrometry

Published on: January 12, 2024

Area of Science:

  • Epigenetics
  • Genomics
  • Computational Biology

Background:

  • Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-Seq) is crucial for genome-wide epigenetic analysis.
  • Identifying transcription factor binding sites and histone modifications can be challenging due to diverse enrichment patterns.
  • Existing methods struggle with distinguishing true enrichment from background noise, especially for diffuse patterns.

Purpose of the Study:

  • To develop a robust and sensitive method for detecting enriched regions in ChIP-Seq data.
  • To address limitations of current methods in handling various data characteristics and enrichment patterns.
  • To provide a data-driven approach for accurate identification of epigenetic marks.

Main Methods:

  • Wavelet transform-based algorithm named WaveSeq.
  • Data-driven approach, free of distributional assumptions.
  • Designed to be robust to low signal-to-noise ratios and broad enrichment patterns.

Main Results:

  • WaveSeq demonstrates high sensitivity and precision in detecting both punctate and diffuse enrichment regions.
  • The method performs favorably compared to existing approaches, even without control data.
  • Successfully applied to complex histone modification data, leading to novel functional discoveries.

Conclusions:

  • WaveSeq is a highly sensitive and accurate method for identifying enriched regions in diverse ChIP-Seq datasets.
  • It effectively detects narrow and broad peaks, even in low signal-to-noise conditions.
  • WaveSeq is valuable for complex experimental scenarios and aids in making biologically relevant discoveries.