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Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
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Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)
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Detection of DNA structural motifs in functional genomic elements.

Jason A Greenbaum1, Stephen C J Parker, Thomas D Tullius

  • 1Program in Bioinformatics, Boston University, Boston, Massachusetts 02215, USA.

Genome Research
|June 15, 2007
PubMed
Summary

Researchers developed a new computational method to identify DNA structural motifs in regulatory elements. This approach reveals common structural patterns in DNase I hypersensitive sites (DHSs) that are independent of DNA sequence, offering new insights into gene regulation.

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Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • The human genome project has spurred research into identifying regulatory elements.
  • Current methods often focus on DNA sequence and chromatin structure.
  • Detecting sequence motifs within DNase I hypersensitive sites (DHSs) has been challenging.

Purpose of the Study:

  • To introduce a novel computational method for detecting DNA structural motifs in DHSs.
  • To investigate whether DNA structure, beyond sequence and chromatin, plays a role in regulatory element recognition.
  • To explore the association of DNA structural motifs with functional regulatory elements.

Main Methods:

  • Development of a new computational approach to analyze DNA structural motifs.
  • Application of the method to a collection of DHSs within ENCODE regions of the human genome.
  • Comparison of structural motifs in DHSs located in CpG islands near transcription start sites (TSSs) versus those farther away.

Main Results:

  • Identified common DNA structural motifs within DHSs that lack apparent sequence consensus.
  • Discovered a specific structural motif significantly enriched in DHSs within CpG islands and near TSSs.
  • Demonstrated that DNA structural motifs can be associated with functional regulatory elements.

Conclusions:

  • DNA structural motifs represent a critical, previously underappreciated feature of regulatory elements.
  • The developed computational method can uncover regulatory patterns independent of DNA sequence.
  • Studying DNA structure conservation offers a new avenue to link DNA sequence to function and understand gene regulation.