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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.
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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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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 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.
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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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CSCS: a chromatin state interface for Chinese Spring bread wheat.

Xiaojuan Ran1,2, Tengfei Tang1,3, Meiyue Wang1,2

  • 1National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China.

Abiotech
|October 31, 2022
PubMed
Summary
This summary is machine-generated.

A new web platform, Chinese Spring Chromatin State (CSCS), identifies regulatory elements in bread wheat by analyzing epigenomic data. This resource aids in understanding gene regulation and discovering functional elements in wheat genomes.

Keywords:
Bread wheatChinese SpringChromatin stateDatabaseEpigenetics

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Area of Science:

  • Plant genomics and epigenetics
  • Bioinformatics and computational biology

Background:

  • A chromosome-level genome assembly for bread wheat Chinese Spring (CS) is available.
  • Identifying regulatory elements (REs) is crucial for understanding gene activity regulation.
  • Epigenetic activity correlates with RE activity, making chromatin state definition an effective detection method.

Purpose of the Study:

  • To present the Chinese Spring Chromatin State (CSCS) web-based platform.
  • To provide CS chromatin signature information for RE identification.
  • To facilitate data mining for biological insights into wheat gene regulation.

Main Methods:

  • Integrated 15 epigenomic datasets (open chromatin, major chromatin marks) for CS.
  • Defined 15 distinct chromatin states using epigenomic features.
  • Incorporated Self-Organizing Mapping (SOM), JBrowse visualization, motif analysis, and Gene Ontology (GO) analysis within the platform.

Main Results:

  • The CSCS database curates detailed information on 15 chromatin states.
  • The platform enables trained SOM for chromatin state segments and JBrowse visualization.
  • Integrated analyses facilitate the detection of functional elements and regulatory activities.

Conclusions:

  • CSCS provides a comprehensive resource for combinatorial patterns of chromatin signatures in wheat.
  • The platform aids in the detection of functional elements and clarification of regulatory activities.
  • CSCS is a valuable tool for intensive data mining and biological discovery in wheat.