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Related Concept Videos

Chromatin Modification in iPS Cells01:32

Chromatin Modification in iPS Cells

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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.
Compact chromatin makes reprogramming difficult. Enzymes, such as histone demethylases and acetyltransferases, are often added during reprogramming to loosen the chromatin, making the DNA more accessible to transcription factors. Molecules that inhibit histone...
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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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Introduction to Nuclear Reprogramming01:14

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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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Related Experiment Video

Updated: Dec 9, 2025

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
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Diversification of reprogramming trajectories revealed by parallel single-cell transcriptome and chromatin

Q R Xing1,2, Chadi A El Farran1,3, Pradeep Gautam1,3

  • 1Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.

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|September 12, 2020
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Summary

This study reveals diverse cellular reprogramming routes using single-cell sequencing. Identifying specific markers and regulatory networks enhances understanding of efficient human cell reprogramming.

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Area of Science:

  • Biotechnology
  • Genomics
  • Cell Biology

Background:

  • Cellular reprogramming efficiency is a significant challenge, particularly in human cells.
  • Understanding the heterogeneity and mechanisms driving successful reprogramming is crucial.

Purpose of the Study:

  • To deconstruct cellular heterogeneity during reprogramming.
  • To identify mechanisms underlying successful human cell reprogramming.
  • To develop strategies for enriching early reprogrammed cells.

Main Methods:

  • Single-cell RNA sequencing (scRNA-Seq) to profile gene expression.
  • Single-cell assay for transposase-accessible chromatin (scATAC-Seq) to analyze chromatin accessibility.
  • Identification and combinatory usage of surface markers for cell enrichment.

Main Results:

  • Reprogramming cells exhibit asynchronous trajectories and heterogeneous subpopulations.
  • Fluorescent probes and surface markers were identified to enrich early reprogrammed human cells.
  • scATAC-Seq revealed genomic elements and transcription factors (FOSL1, TEAD4) governing reprogramming phases.
  • A binary choice between FOSL1 and TEAD4 regulatory networks dictates reprogramming success.

Conclusions:

  • Cellular reprogramming involves diverse asynchronous routes.
  • Integrative single-cell analyses provide a roadmap for understanding reprogramming machinery.
  • Targeting identified markers and regulatory networks can improve reprogramming efficiency.