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Related Experiment Videos

GC/AT-content spikes as genomic punctuation marks.

Lingang Zhang1, Simon Kasif, Charles R Cantor

  • 1Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA. zlg@bu.edu

Proceedings of the National Academy of Sciences of the United States of America
|November 19, 2004
PubMed
Summary

GC content distribution in genes shows distinct patterns between vertebrates and invertebrates. These GC-content spikes at transcription boundaries may serve as genomic punctuation, aiding in gene identification.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • GC-content distribution varies across species genomes.
  • Gene transcription boundaries exhibit sharp GC-content changes in diverse species.
  • Genomic sequences present commonalities and differences in GC-content profiles.

Purpose of the Study:

  • To analyze GC-content distribution at the gene level across different species.
  • To identify distinct GC-content profiles between vertebrates and invertebrates.
  • To investigate the functional implications of GC-content spikes at transcription boundaries.

Main Methods:

  • Large-scale genomic analysis.
  • Comparative genomics of human, mouse, rat, chicken, fruit fly, and worm.
  • Cross-correlation analysis of GC-content spikes.

Related Experiment Videos

  • Analysis of GC-content changes at transcription start and stop sites.

    • Main Results:

    • Two distinct GC-content profile groups identified: warm-blooded vertebrates and invertebrates.
    • Vertebrates show positive/negative GC spikes at start/stop sites, with 5' to 3' decrease.
    • Invertebrates exhibit preceding opposite spikes and highest GC content in coding regions.
    • GC-content spikes are conserved in orthologous genes and clustered on chromosomes.

    Conclusions:

    • GC-content spikes at transcription boundaries represent a conserved genomic feature.
    • These spikes may function as genomic punctuation, potentially influencing gene regulation.
    • The findings provide methods for identifying GC-content spikes in genomic sequences.