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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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Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes.

Ariel Afek¹, Hila Cohen¹, Shiran Barber-Zucker¹

¹Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel.

Plos Computational Biology

|August 19, 2015

Summary

Transcription factors (TFs) bind DNA through non-consensus mechanisms, not just specific sites. This non-consensus binding influences TF occupancy and nucleosome-free regions genome-wide.

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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Genome-wide studies reveal transcription factor (TF) binding at sites lacking canonical TF binding sites (TFBSs).
In vitro data show TFs bind DNA sequences without consensus motifs with varying affinities.
These findings challenge traditional models of specific protein-DNA interactions.

Purpose of the Study:

To investigate non-consensus protein-DNA binding mechanisms.
To calculate non-consensus binding free energy across eukaryotic genomes.
To correlate non-consensus binding with experimental TF and nucleosome occupancy.

Main Methods:

Statistical mechanics modeling to calculate non-consensus binding free energy.
Analysis of ChIP-seq data for TF occupancy and nucleosome occupancy.
Large-scale analysis of in vitro TF-DNA binding preferences from protein binding microarrays (PBM).

Main Results:

Low non-consensus binding free energy correlates with higher TF occupancy and lower nucleosome occupancy.
Non-consensus binding is a widespread phenomenon across C. elegans and D. melanogaster genomes.
Non-consensus binding significantly impacts TF-DNA binding preferences, independent of consensus TFBSs.

Conclusions:

Non-consensus protein-DNA binding is a significant mechanism affecting TF genome-wide binding specificity.
This mechanism contributes to the formation of nucleosome-free regions by TFs outcompeting nucleosomes.
Non-consensus binding is a prevalent mode of TF-DNA interaction across diverse eukaryotic TFs.