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Inheritance of Chromatin Structures

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...

Chromatin Position Affects Gene Expression

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...

Heterochromatin

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...

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Updated: Jul 4, 2025

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

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

Published on: April 5, 2018

Decoding the universal human chromatin landscape through teratoma-based profiling.

Benjamin L Kidder^1,2

¹Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.

Nucleic Acids Research

|January 28, 2024

Summary

This summary is machine-generated.

Human pluripotent stem cell teratomas reveal insights into epigenome and transcriptome dynamics. This study maps cell types and epigenetic signatures, advancing stem cell differentiation research.

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Area of Science:

Developmental Biology
Stem Cell Biology
Epigenetics

Background:

Teratoma formation is crucial for assessing human pluripotent stem cell differentiation into embryonic germ layers.
Teratomas serve as a model for understanding stem cell differentiation and developmental biology.
Epigenome and transcriptome profiling of teratomas offers significant insights.

Purpose of the Study:

To integrate epigenome and transcriptome analysis of human embryonic stem cell (hESC)-generated teratomas.
To compare transcriptomes between hESCs and teratomas.
To identify cell types and epigenetic features within teratomas.

Main Methods:

Deconvolution of RNA-Seq data using cell type-specific expression patterns from single-cell data.
Analysis of activating and repressive histone modifications and chromatin states.
Construction of an epigenetic signature matrix for quantifying cell populations.
Generation of a single-cell multiome atlas (scRNA-Seq and scATAC-Seq) of human teratomas.
Application of a histology-based digital staining tool for cell type annotation.

Main Results:

A catalog of activating and repressive histone modifications was generated.
Distinctive features of chromatin states in teratomas were elucidated.
An epigenetic signature matrix enabled quantification of diverse cell populations.
The complexity of human teratoma tissues was revealed through multiome atlas.
Enhanced annotation of teratoma cell types was achieved.

Conclusions:

This study provides a comprehensive epigenomic and transcriptomic landscape of hESC-derived teratomas.
The findings enhance the understanding of epigenetic regulation in heterogeneous tissue contexts.
This research serves as a valuable resource and model for epigenetic data comparison in stem cell studies.