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Related Concept Videos

Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.
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...
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...
Abnormal Proliferation02:23

Abnormal Proliferation

Under normal conditions, most adult cells remain in a non-proliferative state unless stimulated by internal or external factors to replace lost cells. Abnormal cell proliferation is a condition in which the cell's growth exceeds and is uncoordinated with normal cells. In such situations, cell division persists in the same excessive manner even after cessation of the stimuli, leading to persistent tumors. The tumor arises from the damaged cells that replicate to pass the damage to the daughter...
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...
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,...

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Related Experiment Video

Updated: May 12, 2026

Yeast As a Chassis for Developing Functional Assays to Study Human P53
14:57

Yeast As a Chassis for Developing Functional Assays to Study Human P53

Published on: August 4, 2019

Models incorporating chromatin modification data identify functionally important p53 binding sites.

Ji-Hyun Lim1, Richard D Iggo, Daniel Barker

  • 1Sir Harold Mitchell Building, School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK.

Nucleic Acids Research
|April 20, 2013
PubMed
Summary
This summary is machine-generated.

Predicting transcription factor binding sites is challenging. A new logistic regression model incorporating sequence and chromatin data improved biological relevance over sequence-only models for p53 binding site prediction.

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High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

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Sequential Salt Extractions for the Analysis of Bulk Chromatin Binding Properties of Chromatin Modifying Complexes
07:41

Sequential Salt Extractions for the Analysis of Bulk Chromatin Binding Properties of Chromatin Modifying Complexes

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Related Experiment Videos

Last Updated: May 12, 2026

Yeast As a Chassis for Developing Functional Assays to Study Human P53
14:57

Yeast As a Chassis for Developing Functional Assays to Study Human P53

Published on: August 4, 2019

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
06:38

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

Published on: February 7, 2019

Sequential Salt Extractions for the Analysis of Bulk Chromatin Binding Properties of Chromatin Modifying Complexes
07:41

Sequential Salt Extractions for the Analysis of Bulk Chromatin Binding Properties of Chromatin Modifying Complexes

Published on: October 2, 2017

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Predicting transcription factor binding sites (TFBS) genome-wide is crucial for understanding gene regulation but remains a significant challenge.
  • Existing methods often rely solely on sequence information, potentially missing broader biological context.

Purpose of the Study:

  • To develop and evaluate a novel logistic regression model for predicting p53 transcription factor binding sites.
  • To assess the added value of incorporating chromatin modification data alongside sequence information.

Main Methods:

  • A logistic regression model was developed integrating sequence position weight matrix (PWM) data with chromatin modification data.
  • Predictions were validated against known p53 binding sites identified by chromatin immunoprecipitation (ChIP).
  • Analyses included site location relative to genes, function of nearby genes, and gene expression changes upon p53 activation.

Main Results:

  • While both sequence-only and integrated models identified a similar fraction of known p53 binding sites in whole-genome assays, significant biological differences emerged.
  • The integrated model showed superior performance in predicting binding site locations relative to genes.
  • Genes near predicted sites by the integrated model exhibited more relevant functions and greater responsiveness to p53 activation.

Conclusions:

  • Chromatin modification data, while not improving direct identification of binding sites, provides critical biologically relevant functional information.
  • The novel model offers a more comprehensive approach to TFBS prediction by integrating diverse data types.
  • This suggests that sequence data captures biophysical interactions, while chromatin data reflects functional regulatory roles.