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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...
Chromatin Structure Regulates pre-mRNA Processing02:41

Chromatin Structure Regulates pre-mRNA Processing

In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...
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...
Heterochromatin02:38

Heterochromatin

The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at 9th...

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Related Experiment Video

Updated: May 9, 2026

The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin
24:02

The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin

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Human Transcriptome and Chromatin Modifications: An ENCODE Perspective.

Li Shen1, Inchan Choi, Eric J Nestler

  • 1Department of Neuroscience, Mount Sinai School of Medicine, New York, NY 10029, USA.

Genomics & Informatics
|July 12, 2013
PubMed
Summary

The Encyclopedia of DNA Elements (ENCODE) project offers vast human biological data. This review details ENCODE

Keywords:
ENCODEGENCODEchromatin modificationtranscriptome

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Last Updated: May 9, 2026

The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin
24:02

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An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • The Encyclopedia of DNA Elements (ENCODE) project has generated a comprehensive dataset.
  • ENCODE data encompasses transcriptome, cistrome, epigenome, and interactome information from over 1,600 human experiments.

Purpose of the Study:

  • To elucidate the ENCODE project's data types and experimental methodologies.
  • To summarize key findings from ENCODE data analysis.
  • To review computational methods for predicting gene expression from ENCODE data, focusing on the human transcriptome and chromatin modifications.

Main Methods:

  • Data generation across multiple experimental platforms.
  • Computational analysis of large-scale genomic datasets.
  • Review of gene expression prediction models.

Main Results:

  • ENCODE provides an unprecedented resource for understanding human genome function.
  • Analysis reveals associations between chromatin modifications and gene expression.
  • Computational approaches can effectively predict gene expression patterns.

Conclusions:

  • Understanding ENCODE data and methods is crucial for its effective utilization.
  • The ENCODE dataset significantly advances knowledge of the human transcriptome and epigenome.
  • Chromatin modifications are key determinants of gene expression variability.