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Related Concept Videos

Heterochromatin02:38

Heterochromatin

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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...
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Histone Modification02:32

Histone Modification

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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...
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Euchromatin01:01

Euchromatin

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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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Chromatin Modification in iPS Cells01:32

Chromatin Modification in iPS Cells

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Chromatin modification alters gene expression; therefore, scientists can add histone-modifying enzymes, histone variants, and chromatin remodeling complexes to somatic cells to aid reprogramming into pluripotent stem (iPS) cells.
Compact chromatin makes reprogramming difficult. Enzymes, such as histone demethylases and acetyltransferases, are often added during reprogramming to loosen the chromatin, making the DNA more accessible to transcription factors. Molecules that inhibit histone...
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Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

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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...
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Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

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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...
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Updated: Jun 28, 2025

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
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Predicting A/B compartments from histone modifications using deep learning.

Suchen Zheng1, Nitya Thakkar1, Hannah L Harris2

  • 1Department of Computer Science, Brown University, Providence, RI, USA.

Iscience
|April 22, 2024
PubMed
Summary
This summary is machine-generated.

Researchers developed CoRNN, a novel tool predicting genome compartmentalization using histone modifications. This method overcomes the high cost of Hi-C data, enabling cell-type-specific 3D genome organization studies.

Keywords:
Chromosome organizationGenomicsMachine learning

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Area of Science:

  • Genomics
  • Computational Biology
  • Epigenetics

Background:

  • The three-dimensional genome organization, particularly chromatin compartmentalization into active (A) and inactive (B) compartments, is vital for cellular function.
  • Studying cell-type-specific genome organization is hindered by the high cost and complexity of generating Hi-C data.

Purpose of the Study:

  • To develop a cost-effective computational tool for predicting genome compartmentalization.
  • To enable large-scale analysis of cell-type-specific 3D genome organization.

Main Methods:

  • Development of a recurrent neural network (RNN) model named CoRNN.
  • Utilizing histone modification enrichment data as input for CoRNN.
  • Validation of CoRNN's predictive performance using cross-cell-type analysis and independent datasets.

Main Results:

  • CoRNN accurately predicts A/B compartments across different cell types with an average AuROC of 90.9%.
  • Histone marks like H3K27ac and H3K36me3 were identified as strong predictors of compartmental status.
  • Mispredictions were found in regions with ambiguous compartmentalization, indicating areas for further investigation.
  • The model demonstrated generalizability by successfully predicting compartments in independent tissue samples.

Conclusions:

  • CoRNN offers a powerful and accessible method for predicting 3D genome organization.
  • The tool facilitates the study of cell-type-specific genomic activity without expensive experimental data.
  • CoRNN's validation on independent samples highlights its broad applicability in genomic research.