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Related Concept Videos

Chromatin Modification in iPS Cells01:32

Chromatin Modification in iPS Cells

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...
Methods of Nuclear Reprogramming01:24

Methods of Nuclear Reprogramming

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 injury repair.
Somatic to iPS Cell Reprogramming01:29

Somatic to iPS Cell Reprogramming

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 for this...
Combinatorial Gene Control02:33

Combinatorial Gene Control

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...
RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences  access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area. 
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the timing and level of...

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Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers
10:28

Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers

Published on: September 20, 2018

Reprogramming factor expression initiates widespread targeted chromatin remodeling.

Richard P Koche1, Zachary D Smith, Mazhar Adli

  • 1Broad Institute, Cambridge, MA 02142, USA.

Cell Stem Cell
|January 8, 2011
PubMed
Summary
This summary is machine-generated.

Early epigenetic changes, including H3K4me2 modifications at thousands of gene loci, precede transcriptional shifts during induced pluripotent stem cell (iPSC) reprogramming. This reveals an organized response that resets somatic cell identity.

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CRISPR-Mediated Reorganization of Chromatin Loop Structure

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Last Updated: Jun 5, 2026

Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers
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Published on: September 20, 2018

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CRISPR-Mediated Reorganization of Chromatin Loop Structure
09:20

CRISPR-Mediated Reorganization of Chromatin Loop Structure

Published on: September 14, 2018

Area of Science:

  • Epigenetics
  • Stem Cell Biology
  • Molecular Biology

Background:

  • Transcription factor-driven reprogramming generates induced pluripotent stem cells (iPSCs).
  • Mechanisms underlying early reprogramming events remain incompletely understood.

Purpose of the Study:

  • To systematically analyze early transcriptional and epigenetic changes during somatic cell reprogramming.
  • To elucidate the temporal order of events in induced pluripotent stem cell (iPSC) generation.

Main Methods:

  • Analysis of transcriptional and epigenetic modifications after discrete cell divisions during reprogramming.
  • Genome-wide assessment of histone modifications H3K4me2 and H3K27me3.

Main Results:

  • Rapid, genome-wide H3K4me2 changes occurred at over a thousand loci, including pluripotency-related gene promoters and enhancers.
  • H3K27me3 patterns remained stable, with depletion only where H3K4me2 increased.
  • These chromatin changes preceded transcriptional alterations at the affected loci.

Conclusions:

  • Ectopic reprogramming factors induce an early, organized, and population-wide epigenetic response.
  • Epigenetic modifications play a crucial role in resetting somatic cell identity during reprogramming.
  • The findings clarify the temporal sequence of events in induced pluripotent stem cell (iPSC) reprogramming.