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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...
Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences  access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area. 
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the timing and level of...
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,...
Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying DNA...
Structure of a Gene01:30

Structure of a Gene

A gene is the fundamental unit of heredity. Every individual has two copies of each gene, one inherited from each parent. Although most people contain the same genes, there is a small fraction that is slightly different amongst people. A gene with a small difference in its sequence of DNA bases forms different alleles, contributing to different phenotypes.
However, only 1% of the DNA is composed of genes that encode proteins; the rest, 99% is non-coding DNA. This non-coding DNA performs...
Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

The process of chromosome duplication during cell division requires genome-wide disruption and re-assembly of chromatin. The chromatin structure must be accurately inherited, reassembled, and maintained in the daughter cells to ensure lineage propagation.
The basic unit of the chromatin is the nucleosome, consisting of DNA wrapped around octameric histone proteins and short stretches of linker DNA separating individual nucleosomes. The histone proteins within the nucleosome have their...

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Related Experiment Video

Updated: Jun 4, 2026

Chromatin Immunoprecipitation of Murine Brown Adipose Tissue
07:50

Chromatin Immunoprecipitation of Murine Brown Adipose Tissue

Published on: November 21, 2018

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets.

Chao Cheng1, Koon-Kiu Yan, Kevin Y Yip

  • 1Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520, USA.

Genome Biology
|February 18, 2011
PubMed
Summary
This summary is machine-generated.

We created a statistical model to predict gene expression using chromatin features in worms. This framework identifies how specific chromatin patterns near genes influence expression levels for protein-coding genes and microRNAs.

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

Published on: October 5, 2018

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
10:05

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Published on: December 12, 2017

Related Experiment Videos

Last Updated: Jun 4, 2026

Chromatin Immunoprecipitation of Murine Brown Adipose Tissue
07:50

Chromatin Immunoprecipitation of Murine Brown Adipose Tissue

Published on: November 21, 2018

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

Published on: October 5, 2018

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
10:05

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Published on: December 12, 2017

Area of Science:

  • Genomics
  • Computational Biology
  • Molecular Biology

Background:

  • Gene expression is regulated by complex interactions between DNA and associated proteins.
  • Chromatin features, such as histone modifications and DNA accessibility, play a crucial role in modulating gene activity.
  • Understanding these relationships is key to deciphering gene regulation.

Purpose of the Study:

  • To develop a statistical framework for analyzing the relationship between chromatin features and gene expression.
  • To enable prediction of gene expression levels for both protein-coding genes and microRNAs.
  • To investigate the impact of chromatin feature positions relative to genes on expression.

Main Methods:

  • Development of a novel statistical framework.
  • Application of the framework to analyze chromatin data and gene expression profiles.
  • Utilizing the modENCODE datasets from Caenorhabditis elegans (worm) for validation.
  • Analysis of positional effects of chromatin features (upstream and downstream of genes).

Main Results:

  • Successfully predicted gene expression levels using chromatin features.
  • Demonstrated the framework's applicability across various biological contexts, particularly in the modENCODE worm datasets.
  • Identified distinct contributions of specific chromatin features located upstream and downstream of genes to expression prediction.
  • Showcased the ability to predict expression for both protein-coding genes and microRNAs.

Conclusions:

  • The developed statistical framework provides a robust method for predicting gene expression from chromatin data.
  • Chromatin features exhibit context-dependent positional effects on gene expression.
  • The framework offers valuable insights into gene regulatory mechanisms and can be applied to diverse genomic datasets.