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Related Concept Videos

General Transcription Factors01:30

General Transcription Factors

5.9K
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...
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Combinatorial Gene Control02:33

Combinatorial Gene Control

8.6K
Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
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Transcription01:17

Transcription

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Transcription is the synthesis of RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene sequence. Additionally, many other proteins and regulatory sequences are involved in correctly synthesizing messenger RNA (mRNA). Transcriptional regulation is responsible for the differentiation of different types of cells and often for the proper cellular response to environmental signals.
Transcription Can Produce Different Kinds of RNA Molecules
In eukaryotes,...
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Transcription01:10

Transcription

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Overview
Transcription is the process of synthesizing RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene sequence. Additionally, many other proteins and regulatory sequences are involved in the proper synthesis of messenger RNA (mRNA). Regulation of transcription is responsible for the differentiation of all the different types of cells and often for the proper cellular response to environmental signals.
Transcription Can Produce Different Kinds...
138.2K
Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

16.3K
Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
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Cancers Originate from Somatic Mutations in a Single Cell02:21

Cancers Originate from Somatic Mutations in a Single Cell

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Cancer arises from mutations in the critical genes that allow healthy cells to escape cell cycle regulation and acquire the ability to proliferate indefinitely. Though originating from a single mutation event in one of the originator cells, cancer progresses when the mutant cell lines continue to gain more and more mutations, and finally, become malignant. For example, chronic myelogenous leukemia (CML) develops initially as a non-lethal increase in white blood cells, which progressively...
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Related Experiment Video

Updated: May 1, 2026

Mapping the Structure-Function Relationships of Disordered Oncogenic Transcription Factors Using Transcriptomic Analysis
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Reconstructing 3D transcriptional organization from spatial transcriptomics reveals consistent oncogenic

Yifei Sheng1,2,3,4, Shiying Li1,2, Zhengyang Xue1,2

  • 1Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, China.

Briefings in Bioinformatics
|April 30, 2026
PubMed
Summary

Cytocraft reconstructs 3D genome organization from 2D data, revealing spatial patterns in cancer and development. This computational framework accurately maps transcription centers, aiding research into gene regulation in disease and biology.

Keywords:
3D transcriptional organizationspatial configurationsubcellular spatial transcriptomicstranscription center

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Area of Science:

  • Genomics
  • Computational Biology
  • Molecular Biology

Background:

  • Reconstructing 3D genome organization from 2D spatial data is a significant challenge.
  • Understanding the spatial arrangement of transcription is crucial for gene regulation insights.

Purpose of the Study:

  • To introduce Cytocraft, a computational framework for inferring 3D transcription center configurations from 2D spatial transcriptomics data.
  • To validate Cytocraft's accuracy and apply it to explore spatial patterns in biological systems.

Main Methods:

  • Cytocraft infers shared, cell-type-specific 3D configurations of transcription centers.
  • The framework was validated using simulations and applied to human cancer and axolotl brain datasets.

Main Results:

  • Cytocraft demonstrated robust accuracy in simulations (median relative error: 0.0346).
  • Analysis of human nonsmall cell lung cancer revealed consistent spatial repositioning of the MALAT1 marker during malignant transformation.
  • In the developing axolotl brain, transcription center reorganization showed conserved developmental dynamics across cell types.

Conclusions:

  • Cytocraft enables the 3D reconstruction of transcription center configurations from 2D data.
  • The framework provides a powerful tool for investigating the spatial organization of transcription in development and disease.
  • Findings suggest directional translocation of MALAT1 in cancer and coordinated dynamics in brain development.