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Related Concept Videos

Cell Specific Gene Expression01:58

Cell Specific Gene Expression

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Cell Specific Gene Expression01:58

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Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
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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.
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The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
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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. 
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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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TChIP-Seq: Cell-Type-Specific Epigenome Profiling
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Identifying and mapping cell-type-specific chromatin programming of gene expression.

Troels T Marstrand1, John D Storey

  • 1Lewis-Sigler Institute for Integrative Genomics, and Department of Molecular Biology, Princeton University, Princeton, NJ 08544.

Proceedings of the National Academy of Sciences of the United States of America
|January 29, 2014
PubMed
Summary
This summary is machine-generated.

Researchers mapped chromatin structure variations to gene expression in 20 human cell types. Approximately 25% of genes showed cell-type-specific expression linked to chromatin changes, particularly in distal regions.

Keywords:
associationcomputational biologyencodeepigeneticsgene regulation

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Area of Science:

  • Genomics
  • Molecular Biology
  • Epigenetics

Background:

  • Understanding gene expression regulation is crucial for cell differentiation and function.
  • Chromatin structure plays a key role in controlling gene accessibility and activity.
  • Systematically mapping chromatin structure variations to gene expression across diverse cell types remains a challenge.

Purpose of the Study:

  • To develop and apply a quantitative framework to link high-resolution chromatin structure (DNaseI hypersensitivity) with genome-wide gene expression.
  • To investigate the relationship between chromatin structure and cell-type-specific gene expression in 20 diverse human cell types.

Main Methods:

  • Quantitative framework development for analyzing chromatin structure and gene expression data.
  • High-resolution mapping of DNaseI hypersensitive sites across 20 diverse human cell types.
  • Genome-wide gene expression profiling using RNA sequencing.

Main Results:

  • Approximately 25% of genes exhibited cell-type-specific expression patterns that could be explained by alterations in chromatin structure.
  • Distal chromatin regions (±200 kb) were associated with a larger number of genes showing this relationship compared to local regions (±2.5 kb).
  • Local chromatin regions demonstrated a more pronounced effect on gene expression despite capturing fewer associated genes.

Conclusions:

  • The developed quantitative framework effectively links chromatin structure variations to cell-type-specific gene expression.
  • Chromatin structure, particularly at distal regulatory elements, significantly influences cell-type-specific gene expression.
  • The framework is adaptable for relating other continuous genomic measurements to gene expression variation in various biological contexts.