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Related Concept Videos

Euchromatin01:01

Euchromatin

6.7K
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...
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Euchromatin01:01

Euchromatin

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Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

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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...
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Heterochromatin02:38

Heterochromatin

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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.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at...
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Heterochromatin02:38

Heterochromatin

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3.7K
Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

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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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Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo
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Open chromatin in plant genomes.

Wenli Zhang1, Tao Zhang, Yufeng Wu

  • 1Department of Horticulture, University of Wisconsin-Madison, Madison, Wis., USA.

Cytogenetic and Genome Research
|June 14, 2014
PubMed
Summary

DNase I hypersensitive sites (DHSs) reveal open chromatin, crucial for gene regulation in plants and animals. DNase-seq technology enables genome-wide mapping of these regulatory elements, advancing plant genomics.

Area of Science:

  • Genomics
  • Molecular Biology
  • Epigenetics

Background:

  • Chromatin accessibility and configuration are critical for eukaryotic genome function.
  • DNase I digestion sensitivity serves as a key indicator of open chromatin regions.
  • DNase I hypersensitive sites (DHSs) are frequently linked to cis-regulatory DNA elements.

Purpose of the Study:

  • To provide a historical overview of DNase I hypersensitive site (DHS) research in eukaryotes.
  • To summarize key findings from DHS research in model animal species.
  • To review recent advancements in DHS research specifically within plant genomics.

Main Methods:

  • DNase I treatment followed by high-throughput sequencing (DNase-seq) for genome-wide DHS identification.
  • Comparative analysis of DHS data across different eukaryotic species, with a focus on plants.

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  • Literature review synthesizing historical and recent developments in DHS research.

    • Main Results:

    • DHSs are consistently associated with regulatory elements like promoters, enhancers, and silencers in both animals and plants.
    • Genome-wide DHS mapping offers an effective strategy for identifying and annotating regulatory DNA sequences.
    • Significant progress has been made in understanding DHSs in plants, highlighting their utility in plant genomics.

    Conclusions:

    • DNase I hypersensitive sites are valuable genomic markers for regulatory element discovery.
    • DNase-seq is a powerful tool for functional genomics, particularly in interpreting un-annotated regulatory regions.
    • Future research directions involve leveraging DHSs for advanced applications in plant genomics.