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Related Concept Videos

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...
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...
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...
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...
Euchromatin01:01

Euchromatin

The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions take up more dye, appearing darker, while the less-compact areas take up less dye and appear lighter. Based on the compaction level, chromatins are classified into two primary forms – euchromatin and heterochromatin.
Euchromatin is the less dense region of the chromatin and stains lighter. Euchromatin contains histone H3 extensively...

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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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Published on: April 5, 2018

Discovering and mapping chromatin states using a tree hidden Markov model.

Jacob Biesinger1, Yuanfeng Wang, Xiaohui Xie

  • 1Department of Computer Science, University of California-Irvine, CA, USA.

BMC Bioinformatics
|June 6, 2013
PubMed
Summary

This study introduces a novel Bayesian network to model chromatin states and their transitions during cell differentiation and disease. The method accurately infers chromatin states and handles missing data, advancing epigenetic research.

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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
  • Epigenetics
  • Computational Biology

Background:

  • High-throughput sequencing enables comprehensive genome annotation, revealing cell-type and disease-specific differences.
  • Epigenetic modifications display cell-type diversity, correlate with gene expression, and are implicated in diseases.
  • Previous chromatin state studies often overlooked cell lineage in multi-cell type analyses.

Purpose of the Study:

  • To develop a Bayesian network for modeling chromatin states and their transitions.
  • To simultaneously model chromatin mark combinations and state transitions through differentiation or disease progression.
  • To address limitations of previous methods by incorporating cell lineage information.

Main Methods:

  • Developed a Bayesian network incorporating epigenetic modifications.
  • Applied the model to a dataset of histone modifications across nine human cell types.
  • Implemented variational approximations for intractable exact inference in large datasets.

Main Results:

  • Achieved improved accuracy in inferring chromatin states.
  • Demonstrated enhanced handling of missing data in epigenetic datasets.
  • Showcased linear scaling of the method with increasing dataset size.

Conclusions:

  • The developed Bayesian network provides a robust framework for analyzing chromatin states and their dynamics.
  • The method offers advancements in accuracy, data handling, and scalability for epigenetic studies.
  • Source code is available, facilitating further research and application in genomics and disease studies.