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Related Concept Videos

Yeast Signaling01:28

Yeast Signaling

Yeasts are single-celled organisms, but unlike bacteria, they are eukaryotes (cells with a nucleus). Cell signaling in yeast is similar to signaling in other eukaryotic cells. A ligand, such as a protein or a small molecule released from a yeast cell, attaches to a receptor on the cell surface. The binding stimulates second-messenger kinases to activate or inactivate transcription factors that further regulate gene expression. Many of the yeast intracellular signaling cascades have similar...
Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
Writers
The writer is an enzyme that can...
Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
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ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
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...
Euchromatin01:01

Euchromatin

The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions take up more dye, appearing darker, while the less-compact areas take up less dye and appear lighter. Based on the compaction level, chromatins are classified into two primary forms – euchromatin and heterochromatin.
Euchromatin is the less dense region of the chromatin and stains lighter. Euchromatin contains histone H3 extensively...
Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

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 DNA...

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Chromatin Immunoprecipitation (ChIP) of Histone Modifications from Saccharomyces cerevisiae
11:06

Chromatin Immunoprecipitation (ChIP) of Histone Modifications from Saccharomyces cerevisiae

Published on: December 29, 2017

Defining the budding yeast chromatin-associated interactome.

Jean-Philippe Lambert1, Jeffrey Fillingham, Mojgan Siahbazi

  • 1Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada.

Molecular Systems Biology
|December 24, 2010
PubMed
Summary
This summary is machine-generated.

Modified chromatin immunopurification (mChIP) effectively mapped protein networks for 102 yeast chromatin proteins. This advanced method identified thousands of protein associations, improving upon traditional techniques for protein interaction studies.

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Area of Science:

  • Molecular Biology
  • Proteomics
  • Yeast Genetics

Background:

  • Affinity purification (AP) is crucial for studying protein interactions.
  • Traditional AP methods have limitations in identifying comprehensive protein networks, especially for low-abundance proteins.

Purpose of the Study:

  • To apply modified chromatin immunopurification (mChIP) for large-scale analysis of protein networks in budding yeast.
  • To evaluate the efficiency of mChIP compared to classical AP methods.
  • To investigate specific protein interactions, such as those involving Asf1.

Main Methods:

  • Modified chromatin immunopurification (mChIP) coupled with mass spectrometry.
  • Analysis of 102 chromatin-related proteins in budding yeast.
  • Targeted studies of Asf1 and its associated histone chaperones (Rtt106, HIR complex).

Main Results:

  • Detection of 2966 high-confidence protein associations involving 724 distinct prey proteins.
  • mChIP demonstrated significantly improved interaction coverage (∼75%) over classical AP.
  • Identification of novel binding partners for low-abundance transcription factors.
  • Elucidation of the physical interplay between Asf1, Rtt106, and the HIR complex.

Conclusions:

  • mChIP is a powerful and efficient method for large-scale protein network analysis.
  • mChIP enhances the discovery of protein interactions, particularly for challenging targets.
  • The study provides valuable insights into chromatin-related protein interactions in yeast.