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Related Concept Videos

Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

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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
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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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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.
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Chromatin Position Affects Gene Expression02:35

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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. 
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Chromatin Modification in iPS Cells01:32

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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.
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Euchromatin01:01

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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.
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Related Experiment Video

Updated: Nov 16, 2025

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq
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Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

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Spatially mapped single-cell chromatin accessibility.

Casey A Thornton1, Ryan M Mulqueen1, Kristof A Torkenczy1

  • 1Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA.

Nature Communications
|February 25, 2021
PubMed
Summary
This summary is machine-generated.

We developed sciMAP-ATAC, a new method for spatially resolved single-cell epigenomic profiling. This technique maps cell chromatin states with their precise locations, aiding brain tissue analysis.

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Single-Cell Factor Localization on Chromatin using Ultra-Low Input Cleavage Under Targets and Release using Nuclease
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Area of Science:

  • Molecular Biology
  • Neuroscience
  • Genomics

Background:

  • High-throughput single-cell epigenomic assays identify cell heterogeneity but lose spatial information.
  • Understanding cell positions is crucial for studying complex tissue organization and function.

Purpose of the Study:

  • To introduce sciMAP-ATAC (single-cell combinatorial indexing on Microbiopsies Assigned to Positions for the Assay for Transposase Accessible Chromatin).
  • To enable scalable, spatially resolved single-cell profiling of chromatin accessibility.
  • To analyze spatial organization in brain tissues and disease models.

Main Methods:

  • Developed sciMAP-ATAC, integrating combinatorial indexing with spatial micro-biopsies for ATAC-seq.
  • Retained positional information of individual cells within a defined spatial region (214 micron cubic).
  • Applied the method to mouse and human brain tissues, integrating with other single-cell datasets.

Main Results:

  • sciMAP-ATAC generated data quality comparable to non-spatial methods.
  • Successfully mapped spatial chromatin states in adult mouse and human cortical tissues.
  • Characterized the spatial progression of cerebral ischemic infarction in a mouse model.

Conclusions:

  • sciMAP-ATAC is a powerful tool for high-resolution spatial epigenomic mapping.
  • The method facilitates the study of cellular organization and spatial dynamics in complex biological systems.
  • Enables integration of spatial epigenomic data with other single-cell modalities for comprehensive analysis.