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The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences.  The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...
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Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions
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Published on: June 28, 2018

Exceptional human core promoter nucleotide compositions.

H Darvish1, M Olad Nabi, S Ghasemi Firouzabadi

  • 1Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.

Gene
|February 1, 2011
PubMed
Summary
This summary is machine-generated.

This study reveals unique human gene promoters with unusual nucleotide compositions and multiple short tandem repeats. These exceptional promoters, lacking typical motifs, may explain gene expression variations and complex traits.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Proximal promoter sequences are crucial for gene expression.
  • Understanding core promoter nucleotide composition is essential for deciphering gene regulation.

Purpose of the Study:

  • To perform genome-scale computational analyses of human gene core promoters.
  • To identify and characterize exceptional promoter sequences with unusual nucleotide compositions and short tandem repeats.
  • To investigate the functional significance and evolutionary conservation of these exceptional promoters.

Main Methods:

  • Genome-scale computational analysis of 120-bp sequences upstream of transcription start sites (TSSs) for 10,117 human protein-coding genes.
  • Analysis of purine/pyrimidine ratios and identification of short tandem repeats (STRs) within core promoters.
  • Cross-species sequence bias analysis and gene ontology tracking.

Main Results:

  • Identified exceptional human gene promoters with highly skewed purine/pyrimidine ratios (e.g., VWA3A, Sox5, BRWD3) and islands of purines or pyrimidines.
  • Discovered promoters exceptionally rich in multiple STRs (e.g., UBE2QL1, GRIA2), deviating from the norm in over 95% of genes.
  • Found sequence conservation across species for these exceptional promoters, suggesting functional importance in gene expression.
  • Determined that downstream genes are of significant ontological importance, traceable to lower species.

Conclusions:

  • Exceptional human gene promoters with unique nucleotide compositions and STRs offer novel mechanisms for gene expression.
  • These promoters lack conventional TATA or TATA-less motifs, suggesting alternative regulatory pathways.
  • The findings may provide insights into inter-individual variations in gene expression, complex traits, and associated disorders.