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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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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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Chromatin Position Affects Gene Expression02:35

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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)
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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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Lampbrush Chromosomes01:51

Lampbrush Chromosomes

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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.
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Position-effect Variegation02:32

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In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.
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Related Experiment Video

Updated: Dec 15, 2025

CRISPR-Mediated Reorganization of Chromatin Loop Structure
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Genome-wide R-loop Landscapes during Cell Differentiation and Reprogramming.

Pengze Yan1, Zunpeng Liu2, Moshi Song3

  • 1State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.

Cell Reports
|July 9, 2020
PubMed
Summary

DNA:RNA hybrids, or R-loops, are crucial for cell identity. This study reveals how R-loops influence cell fate determination and memory during differentiation and reprogramming, impacting cell plasticity.

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Area of Science:

  • Molecular Biology
  • Epigenetics
  • Stem Cell Biology

Background:

  • DNA:RNA hybrids (R-loops) are nucleic acid structures involved in gene regulation, chromatin organization, and genome stability.
  • Maintaining R-loop homeostasis is critical for cellular processes like differentiation and plasticity, but remains poorly understood.

Purpose of the Study:

  • To systematically investigate the role and dynamics of R-loops during human stem cell differentiation and reprogramming.
  • To characterize the interplay between R-loops, DNA methylation, histone modifications, and chromatin accessibility across different cell states.

Main Methods:

  • Utilized an isogenic human stem cell platform for comprehensive analysis.
  • Assessed R-loops, DNA methylation, histone modifications, and chromatin accessibility in pluripotent and differentiated cells.
  • Examined R-loop dynamics during cellular reprogramming and serial passaging.

Main Results:

  • R-loops form co-transcriptionally at pluripotency genes in stem cells and lineage-specific genes in differentiated cells.
  • Persistent R-loops after differentiation associate with repressive chromatin marks on silenced genes.
  • Cell-of-origin-specific R-loops are transiently present during reprogramming and resolve with passaging.

Conclusions:

  • R-loops play a multifaceted role in cell fate determination, acting as a regulatory layer for cell fate memory.
  • R-loop dynamics are integral to understanding and potentially manipulating cell plasticity and lineage commitment.