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Related Concept Videos

Lampbrush Chromosomes01:51

Lampbrush Chromosomes

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.
LBCs are made up of two pairs of conjugating homologous chromatids. Each chromatid consists of alternatively positioned regions of condensed-inactive chromatin and loosely placed-active side loops, which can be contracted and extended. The loops resemble the...
Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

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...
Chromatin Packaging02:21

Chromatin Packaging

Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order structures.
Heterochromatin02:38

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 9th...
Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

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...
Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

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 is an enzyme that can...

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Related Experiment Video

Updated: Jun 13, 2026

CRISPR-Mediated Reorganization of Chromatin Loop Structure
09:20

CRISPR-Mediated Reorganization of Chromatin Loop Structure

Published on: September 14, 2018

TM-Loop: Transformer multi-omics hierarchical detection of chromatin loop.

Haixia Zhai1, Hao Yang1, Zhanwei Hou2

  • 1School of Software, Henan Polytechnic University, Jiaozuo, 454003, China.

Scientific Reports
|June 11, 2026
PubMed
Summary

TM-Loop accurately detects chromatin loops, crucial for 3D genome organization and gene regulation. This deep learning framework improves upon existing methods for analyzing Hi-C data, aiding disease research.

Keywords:
Chromatin loopDeep learningHi-CMultiomics dataThresholdTransformer

More Related Videos

Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for Mapping Chromatin Interactions and Understanding Transcription Regulation
21:55

Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for Mapping Chromatin Interactions and Understanding Transcription Regulation

Published on: April 30, 2012

Related Experiment Videos

Last Updated: Jun 13, 2026

CRISPR-Mediated Reorganization of Chromatin Loop Structure
09:20

CRISPR-Mediated Reorganization of Chromatin Loop Structure

Published on: September 14, 2018

Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for Mapping Chromatin Interactions and Understanding Transcription Regulation
21:55

Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for Mapping Chromatin Interactions and Understanding Transcription Regulation

Published on: April 30, 2012

Area of Science:

  • Genomics
  • Computational Biology
  • Molecular Biology

Background:

  • Chromatin loops are fundamental to 3D genome architecture, regulating gene transcription.
  • Disruption of these spatial interactions is implicated in diseases like cancer.
  • Accurate chromatin loop identification from Hi-C data is challenging due to data sparsity and noise.

Purpose of the Study:

  • To develop an advanced computational framework, TM-Loop, for high-precision chromatin loop detection.
  • To integrate multi-omics data and deep learning for improved loop identification accuracy.
  • To provide a robust tool for genome-wide chromatin loop analysis.

Main Methods:

  • TM-Loop utilizes 10 kb Hi-C matrices combined with ATAC-seq and CTCF ChIP-seq signals.
  • A Transformer deep learning model with multi-head attention captures feature dependencies.
  • Hierarchical multi-scale clustering and dual-threshold filtering enhance signal specificity.

Main Results:

  • TM-Loop demonstrates superior performance compared to existing methods.
  • The framework shows improved accuracy in assessing active promoter-anchored loops (APA) and protein enrichment.
  • Results indicate enhanced 3D structural consistency in detected loops.

Conclusions:

  • TM-Loop offers a novel and effective approach for accurate genome-wide chromatin loop detection.
  • The integration of multi-omics data and deep learning advances the field of 3D genomics.
  • This tool has significant potential for research into gene regulation and human diseases.