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Updated: May 24, 2026

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)

Published on: August 21, 2016

Methods to detect selection on noncoding DNA.

Ying Zhen¹, Peter Andolfatto

¹Department of Ecology and Evolutionary Biology, The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.

Methods in Molecular Biology (Clifton, N.J.)

|March 9, 2012

Summary

This summary is machine-generated.

Most noncoding DNA in eukaryotes is functional, challenging previous assumptions. Evolutionary models reveal adaptive evolution in noncoding DNA, particularly in Drosophila and conserved human elements.

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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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Published on: June 15, 2011

Area of Science:

Genomics and Evolutionary Biology
Molecular and Cellular Biology

Background:

Vast noncoding DNA regions in eukaryotes contain gene regulatory elements.
Identifying and understanding the evolution of these regulatory elements is a significant biological challenge.

Purpose of the Study:

To review current computational and evolutionary methods for identifying functional elements in noncoding DNA.
To assess the functional significance and evolutionary pressures on noncoding DNA across species.

Main Methods:

Application of evolutionary models and computational tools to genome-scale DNA sequence data.
Analysis of noncoding DNA across multiple species to identify conserved and divergent elements.
Examination of selection pressures, including recurrent adaptive substitution and positive selection.

Main Results:

A larger fraction of eukaryotic noncoding DNA is likely functional than previously estimated, indicating incomplete functional annotation.
In Drosophila, significant noncoding DNA divergence between species suggests recurrent adaptive substitution.
In humans, signatures of positive selection are predominantly found in conserved noncoding DNA elements.

Conclusions:

Current methods highlight the substantial functionality of noncoding DNA, necessitating improved annotation.
Comparative genomic analyses reveal diverse evolutionary patterns of noncoding DNA, with species-specific adaptive processes.
Further genome-scale polymorphism and divergence data are crucial for a comprehensive understanding of noncoding DNA evolution across diverse organisms.