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Related Concept Videos

Maintenance of the ES Cell State01:14

Maintenance of the ES Cell State

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The cells of the blastocyst inner cell mass only remain pluripotent for a short time. This state of pluripotency and self-renewal can be maintained in embryonic stem (ES) cell culture by adding specific chemicals or growth factors to ensure the cells can continue dividing and later differentiate into different cell types. In some cases, the cells are grown on a feeder layer of differentiated cells, which provides the growth factors and extracellular matrix components necessary for stem cell...
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Chromatin Modification in iPS Cells01:32

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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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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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Inheritance of Chromatin Structures03:17

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Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying...
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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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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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Related Experiment Video

Updated: Jun 10, 2025

CRISPR-Mediated Reorganization of Chromatin Loop Structure
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SRF promotes long-range chromatin loop formation and stem cell pluripotency.

Pavel Tsaytler1, Gaby Blaess1, Manuela Scholze-Wittler1

  • 1Department Developmental Genetics, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany.

Cell Reports
|October 11, 2024
PubMed
Summary

Serum response factor (SRF) is crucial for embryonic development and cell functions. This study reveals SRF

Keywords:
CP: Molecular biologyCP: Stem cell researchCTCFNANOGOSN enhancersSOX2SRFTAD insulationchromatin loopschromatin organizationlong-range contact regulationpluripotency

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Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions
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Related Experiment Videos

Last Updated: Jun 10, 2025

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The use of SC1 Pluripotin to Support mESC Self-renewal in the Absence of LIF
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Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions
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Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions

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Area of Science:

  • Molecular Biology
  • Developmental Biology
  • Genomics

Background:

  • Serum response factor (SRF) is a key transcription factor regulating cell proliferation, differentiation, and migration.
  • SRF plays a vital role in early embryonic development, including primitive streak and mesoderm formation.
  • The functions of SRF are known to be modulated by various context-dependent cofactors.

Purpose of the Study:

  • To investigate the role of SRF in higher-order chromatin organization.
  • To determine if SRF interacts with architectural proteins like CTCF and cohesin.
  • To elucidate SRF's contribution to 3D genome structure in embryonic stem cells.

Main Methods:

  • Chromatin conformation capture techniques (e.g., Hi-C) to analyze 3D genome structure.
  • Co-immunoprecipitation assays to detect protein-protein interactions between SRF, CTCF, and cohesin.
  • ChIP-seq to map the genomic binding sites of SRF and associated factors.

Main Results:

  • SRF physically interacts with CTCF and cohesin subunits at topologically associating domain (TAD) boundaries and loop anchors.
  • SRF actively promotes the formation of long-range chromatin loops and contributes to TAD insulation.
  • In embryonic stem cells (ESCs), SRF associates with pluripotency factors SOX2 and NANOG, forming 3D pluripotency hubs.

Conclusions:

  • SRF is involved in organizing higher-order chromatin structure beyond its known transcriptional roles.
  • SRF's interaction with CTCF and cohesin influences genome architecture, including TAD formation and insulation.
  • SRF plays a significant role in establishing 3D chromatin organization critical for pluripotency in ESCs.