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Related Concept Videos

Introduction to Nuclear Reprogramming01:14

Introduction to Nuclear Reprogramming

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Nuclear reprogramming is the process of switching gene expression of one cell type to that of another cell type, usually from a differentiated cell state to an undifferentiated cell state. Differentiation occurs during processes such as development and morphogenesis, tissue regeneration, and malignancy. Cells can also be artificially induced to reprogram their gene expression by techniques such as nuclear transfer, induced pluripotency, and cell fusion. Such techniques have many applications in...
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Methods of Nuclear Reprogramming01:24

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Nuclear reprogramming is a process of transforming one cell type into an unrelated cell type by epigenetic changes that alter the cell’s original gene expression pattern. Such epigenetic changes force cells to express a different set of genes, which play a significant role in inducing transformation into other cell types. Nuclear reprogramming offers applications in reproductive cloning for livestock propagation and regenerative medicine — developing patient-specific cells for...
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Somatic to iPS Cell Reprogramming01:29

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Reprogramming alters the gene expression in somatic cells, transforming them into induced pluripotent stem (iPS) cells over several generations. Scientists can reprogram cells by introducing genes for four transcription factors—Oct4, Sox2, Klf4, and c-Myc (OSKM) by viral or non-viral methods. These factors are also known as Yamanaka factors after Shinya Yamanaka, who first generated iPS cells using mouse skin cells. Yamanaka was awarded the Nobel Prize in Physiology or Medicine in 2012...
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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.
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Updated: Sep 23, 2025

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TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach.

Ryohei Eguchi1, Momoko Hamano1, Michio Iwata1

  • 1Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka 820-8502, Japan.

Bioinformatics (Oxford, England)
|May 13, 2022
PubMed
Summary

We developed TRANSDIRE, a computational method to predict transcription factors for direct cell reprogramming. This approach uses multi-omics data to identify factors driving cell fate changes, aiding regenerative medicine applications.

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Area of Science:

  • Biotechnology
  • Computational Biology
  • Regenerative Medicine

Background:

  • Direct reprogramming converts mature cells to other types, bypassing pluripotency.
  • Transcription factors (TFs), including pioneer and cooperative types, regulate this process.
  • Experimental identification of these TFs is challenging and expensive.

Purpose of the Study:

  • To develop a novel computational method for predicting transcription factors that induce direct reprogramming.
  • To utilize multi-omics data for accurate TF prediction across various human cell types.

Main Methods:

  • Developed TRANSDIRE (TRANS-omics-based approach for DIrect REprogramming).
  • Predicted pioneer factors (PFs) using low signal chromatin regions.
  • Predicted cooperative TFs via trans-omics analysis (genomic, transcriptome, epigenome, interactome data).

Main Results:

  • Successfully predicted TFs for direct reprogramming from fibroblasts to six cell types (hepatocytes, cartilaginous cells, neurons, cardiomyocytes, pancreatic cells, Paneth cells).
  • Demonstrated high accuracy in predicting TFs for most cell conversions.
  • The method shows promise for practical applications in regenerative medicine.

Conclusions:

  • TRANSDIRE offers an effective computational approach for identifying TFs in direct reprogramming.
  • The method leverages multi-omics data for robust TF prediction.
  • This tool is valuable for advancing regenerative medicine strategies.