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Identifying functional single nucleotide polymorphisms in the human CArGome.

Craig C Benson1, Qian Zhou, Xiaochun Long

  • 1University of Rochester Medical Center, Rochester, NY, USA.

Physiological Genomics
|July 21, 2011
PubMed
Summary
This summary is machine-generated.

Regulatory SNPs (rSNPs) can alter gene expression by affecting transcription factor binding. This study developed a bioinformatics method to identify rSNPs in Serum Response Factor (SRF) binding sites (CArG boxes), revealing their potential role in human diseases.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Regulatory SNPs (rSNPs) are genetic variations in non-coding DNA.
  • rSNPs are hypothesized to influence gene expression by altering transcription factor binding.
  • The functional impact of rSNPs in human disease remains largely unknown.

Purpose of the Study:

  • To develop and apply a bioinformatics approach to identify rSNPs affecting transcription factor binding sites.
  • To investigate the role of rSNPs in the context of Serum Response Factor (SRF) and its CArG box binding sites.
  • To provide a foundation for understanding rSNP function in human genetic diseases.

Main Methods:

  • Developed an in silico bioinformatics screening method to identify conserved CArG boxes around human genes.
  • Utilized phastCons scores to define CArG box conservation and identified 8,252 strand-specific CArGs.
  • Interrogated the CArG dataset for common polymorphisms (SNPs) and validated findings with gel shift and luciferase assays.

Main Results:

  • Identified 8,252 conserved CArG boxes within 8 kb of transcription start sites for 5,213 genes.
  • Found 118 CArG boxes with SNPs within the 10 bp binding sequence and 1,130 with SNPs nearby.
  • Demonstrated that SNPs within or adjacent to CArG boxes can alter SRF binding affinity and transcriptional activity.

Conclusions:

  • The study presents a robust computational method for identifying rSNPs in the human CArGome.
  • rSNPs located within or near CArG boxes can functionally impact SRF binding and gene regulation.
  • This approach can be extended to other transcription factor binding sites, aiding in the study of rSNP function in human diseases.