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Related Concept Videos

Euchromatin01:01

Euchromatin

6.8K
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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Position-effect Variegation02:32

Position-effect Variegation

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In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.
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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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Chromatin Modification in iPS Cells01:32

Chromatin Modification in iPS Cells

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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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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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The chromatin accessibility landscape during early maize seed development.

Guang Ming Zheng1, Jia Wen Wu1, Jun Li1

  • 1State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China.

The Plant Journal : for Cell and Molecular Biology
|March 24, 2025
PubMed
Summary

Chromatin accessibility changes in maize seeds are crucial for development. Open chromatin regions influence gene expression and trait-associated genetic variations, aiding maize breeding advancements.

Keywords:
Zea maysaccessible chromatin region (ACR)maize seed developmentstage‐specific ACRstranscription factor footprintstranscription regulatory network

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Area of Science:

  • Plant biology
  • Genomics
  • Developmental biology

Background:

  • Cis-regulatory elements (CREs) are found in accessible chromatin regions (ACRs).
  • Genome-wide ACRs in plant tissues are well-studied, but their impact on maize seed development is unclear.

Purpose of the Study:

  • To investigate chromatin accessibility during early maize seed development.
  • To correlate ACRs with gene expression and identify regulatory transcription factors (TFs).
  • To explore the role of ACRs in trait-associated genetic variations and their potential for maize breeding.

Main Methods:

  • Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) was used to map ACRs.
  • Gene expression analysis was performed to correlate with ACRs.
  • TF binding footprints within ACRs were identified to predict regulatory networks.
  • Editing of an ACR containing a trait-associated SNP in the NKD1 gene was conducted.

Main Results:

  • 37,952 to 59,887 high-quality ACRs were identified in maize seeds (0-8 DAP).
  • A positive correlation was observed between promoter-ACRs and gene expression.
  • Key TF families and regulatory networks were identified.
  • Reduced DNA sequence diversity and enrichment of trait-associated SNPs were found in ACRs.
  • Editing of an NKD1 ACR with a trait-associated SNP resulted in observable phenotypes.

Conclusions:

  • Chromatin accessibility significantly impacts maize seed development.
  • Open chromatin regions are important for gene regulation and harbor trait-associated variations.
  • Understanding ACRs offers potential for improving maize breeding strategies.