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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...

General Transcription Factors

General Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...

Cell Specific Gene Expression

Cell Specific Gene Expression

Position-effect Variegation

Position-effect Variegation

In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.

Regulation of Expression Occurs at Multiple Steps

Regulation of Expression Occurs at Multiple Steps

Chromatin Modification in iPS Cells

Chromatin Modification in iPS Cells

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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Related Experiment Video

Updated: Jul 26, 2025

Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

Published on: April 21, 2023

Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell

David B Morse¹, Aleksandra M Michalowski², Michele Ceribelli³

¹Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge, UK; Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA; John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.

|June 22, 2023

Summary

This study introduces segmentation by exogenous perfusion (SEEP), a new method linking cell location to gene activity in 3D disease models. SEEP helps understand how spatial environments impact cell identity in cancers.

Keywords:

RNA sequencing genomics oncology ovarian cancer scRNA-seq single-cell transcriptomics spatial transcriptomics spatially resolved transcriptomics

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Author Spotlight: Integrating Single-Cell Transcriptomics with Organoid Cultures for Advanced Research and Therapeutic Insights

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Last Updated: Jul 26, 2025

Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

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Published on: April 21, 2023

An Approach to Study Shape-Dependent Transcriptomics at a Single Cell Level

An Approach to Study Shape-Dependent Transcriptomics at a Single Cell Level

Published on: November 2, 2020

Author Spotlight: Integrating Single-Cell Transcriptomics with Organoid Cultures for Advanced Research and Therapeutic Insights

Author Spotlight: Integrating Single-Cell Transcriptomics with Organoid Cultures for Advanced Research and Therapeutic Insights

Published on: June 28, 2024

Area of Science:

Biotechnology
Genomics
Cancer Research

Background:

Single-cell RNA sequencing (scRNA-seq) is vital for cell state analysis.
Mapping cell states spatially in tissues is a significant challenge.
Existing spatial transcriptomics methods often require specialized expertise.

Purpose of the Study:

To develop a rapid, integrated method linking spatial proximity and environmental accessibility to transcriptional identity.
To analyze high-grade serous ovarian cancer (HGSOC) models using the new technique.
To explore how microenvironments influence cell identity within tumors.

Main Methods:

Segmentation by Exogenous Perfusion (SEEP) utilizes fluorescent dye diffusion gradients.
Dye accessibility classifies cells by radial position in 3D models.
Transcriptomic analysis of dissociated and sorted cells reveals regional identities.

Main Results:

SEEP successfully linked cell transcriptional identity with spatial location in 3D models.
Analysis of spheroid, organoid, and in vivo HGSOC models was performed.
Validated known cell state-position relationships and uncovered novel microenvironmental influences.

Conclusions:

SEEP provides a powerful tool for spatial transcriptomics in complex 3D models.
The method enhances understanding of tumor heterogeneity and microenvironment interactions.
SEEP offers new insights into the spatial regulation of cell identity in cancer.