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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, 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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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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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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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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Certain biochemical processes, such as embryonic development and cell growth regulation, depend on the repression of specific genes. DNA binding proteins known as eukaryotic transcription inhibitors regulate the repression of gene expression in eukaryotes. The presence of these inhibitors at the required location and time in the cell is triggered by the presence of hormones and additional signals from other cells.
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TFIIIC-based chromatin insulators through eukaryotic evolution.

Rebecca E Sizer1, Nisreen Chahid1, Sienna P Butterfield1

  • 1Department of Biology, The University of York, York YO10 5DD, UK.

Gene
|May 27, 2022
PubMed
Summary

Transfer RNA (tRNA) genes function as crucial insulators in yeast, blocking gene silencing. This conserved mechanism involves transcription factor TFIIIC and has evolved in higher organisms with additional factors like USF1 and CTCF.

Keywords:
BarrierInsulatorPichia pastorisRNA polymerase IIITFIIICUSFtRNA gene

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Area of Science:

  • Molecular Biology
  • Genetics
  • Epigenetics

Background:

  • Eukaryotic chromosomes are organized into distinct domains, including heterochromatin (compact, inactive) and euchromatin (open, active).
  • Insulators are essential DNA elements that maintain these domain boundaries, preventing the spread of transcriptional silencing or activation.
  • Transfer RNA (tRNA) genes are found in many known insulators and can block the spread of silencing activities.

Purpose of the Study:

  • To investigate the insulator function of tRNA genes from Pichia pastoris in budding yeast.
  • To explore the role of transcription factor TFIIIC in tRNA gene-mediated insulation.
  • To examine the evolution of TFIIIC-based insulation mechanisms from yeast to metazoa.

Main Methods:

  • Functional assays in budding yeast to test the insulating capacity of Pichia pastoris tRNA genes.
  • Analysis of TFIIIC binding sites genome-wide.
  • Bioinformatic analysis of publicly available ChIP-seq data for human tDNAs and associated transcription factors (USF1, CTCF).

Main Results:

  • Pichia pastoris tRNA genes function as effective insulators in budding yeast, demonstrating conserved function across species.
  • TFIIIC is essential for tRNA gene insulator activity, binding to both tRNA genes and other insulator loci.
  • Human tDNAs are enriched for binding sites of vertebrate-specific factors like USF1 and CTCF, suggesting evolutionary adaptations for enhanced insulation.

Conclusions:

  • tRNA genes, with the help of TFIIIC, act as conserved insulators in yeast.
  • Metazoan insulators have likely evolved by incorporating additional regulatory modules, such as binding sites for USF1 and CTCF, to enhance function and enable cell-type-specific regulation.
  • Understanding these evolutionary adaptations is crucial for comprehending insulation in complex metazoan chromatin environments.