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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
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...
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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.
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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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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Lampbrush Chromosomes01:51

Lampbrush Chromosomes

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In 1882, Flemming observed lampbrush chromosomes (LBC) in salamander eggs. Later in 1892, Rückert observed LBCs in shark egg cells and coined the term "lampbrush chromosomes" because they looked like brushes used to clean kerosene lamps.
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Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

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The process of chromosome duplication during cell division requires genome-wide disruption and re-assembly of chromatin. The chromatin structure must be accurately inherited, reassembled, and maintained in the daughter cells to ensure lineage propagation.
The basic unit of the chromatin is the nucleosome, consisting of DNA wrapped around octameric histone proteins and short stretches of linker DNA separating individual nucleosomes. The histone proteins within the nucleosome have their...
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Polytene Chromosomes02:04

Polytene Chromosomes

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Polytene chromosomes are giant interphase chromosomes with several DNA strands placed side by side. They were discovered in the year 1881 by Balbiani in salivary glands, intestine, muscles, malpighian tubules, and hypoderm of larvae Chironomus plumosus. Hence, these are also called "Salivary gland chromosomes." These are found in insects of the order Diptera and Collembola; in certain organs of mammals; and synergids, antipodes of flowering plants. Polytene chromosomes are also...
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Publisher Correction: Interplay between cohesin and RNA polymerase II in regulating chromatin interactions and gene transcription.

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Related Experiment Video

Updated: Jan 17, 2026

The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin
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The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin

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MIA-Jet: Multi-scale Identification Algorithm of Chromatin Jets.

Sion Kim1,2, Minji Kim1,2

  • 1Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.

Biorxiv : the Preprint Server for Biology
|September 15, 2025
PubMed
Summary
This summary is machine-generated.

Researchers developed MIA-Jet, a new algorithm to detect chromatin jets in 3D genome data. This tool reveals jets are cohesin-dependent and linked to DNA replication and gene regulation, offering new insights into genome organization.

Keywords:
3D genome mappingDNA replicationchromatin jetschromatin loop formationridge detectionscale-space

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Area of Science:

  • Genomics and Molecular Biology
  • Computational Biology
  • 3D Genome Organization

Background:

  • The mammalian genome exhibits hierarchical organization, including chromosome territories, compartments, domains, chromatin loops, and stripes.
  • Chromatin jets, a recently identified feature in Hi-C maps, appear as diffused lines perpendicular to the main diagonal.
  • Previous studies suggest chromatin jets may relate to cohesin loop extrusion and DNA replication, but their biological significance remains unclear due to computational limitations.

Purpose of the Study:

  • To develop an advanced computational method for accurate detection of chromatin jets with varying characteristics.
  • To investigate the biological implications and molecular dependencies of chromatin jets using 3D genome mapping data.
  • To provide a broadly applicable tool for analyzing chromatin jets across different genomic datasets and species.

Main Methods:

  • Development of MIA-Jet, a multi-scale ridge detection algorithm designed for identifying chromatin jets.
  • Application and validation of MIA-Jet on diverse 3D genome mapping datasets, including Hi-C, Repli-HiC, ChIA-PET, ChIA-Drop, and Micro-C.
  • Testing MIA-Jet across multiple species (mouse, human, roundworm, zebrafish) and experimental conditions (protein degradation).

Main Results:

  • MIA-Jet demonstrated superior performance compared to existing methods in detecting chromatin jets across various data types and species.
  • In human cells, detected chromatin jets were found to be enriched at cohesin loading sites and early DNA replication initiation zones.
  • Experiments involving protein degradation revealed that chromatin jets are dependent on cohesin but not YY1, and their signals intensify upon WAPL depletion.

Conclusions:

  • MIA-Jet is an effective and versatile tool for the accurate detection and analysis of chromatin jets in 3D genome mapping data.
  • Chromatin jets are structurally dependent on cohesin and play a role in processes such as DNA replication and genome organization.
  • The findings provide novel insights into the functional roles of chromatin jets and their contribution to the higher-order structure of the genome.