GSBS Student Publications

Student Author(s)

Ankit Gupta

GSBS Program

Biochemistry & Molecular Pharmacology

UMMS Affiliation

Program in Gene Function and Expression; Department of Biochemistry and Molecular Pharmacology; Program in Molecular Medicine

Date

4-1-2014

Document Type

Article

Medical Subject Headings

Artificial Intelligence; Binding Sites; DNA; DNA-Binding Proteins; Models, Biological; Nucleotide Motifs; *Regulatory Elements, Transcriptional; Transcription Factors; *Zinc Fingers

Disciplines

Biochemistry | Computational Biology

Abstract

Cys(2)-His(2) zinc finger proteins (ZFPs) are the largest family of transcription factors in higher metazoans. They also represent the most diverse family with regards to the composition of their recognition sequences. Although there are a number of ZFPs with characterized DNA-binding preferences, the specificity of the vast majority of ZFPs is unknown and cannot be directly inferred by homology due to the diversity of recognition residues present within individual fingers. Given the large number of unique zinc fingers and assemblies present across eukaryotes, a comprehensive predictive recognition model that could accurately estimate the DNA-binding specificity of any ZFP based on its amino acid sequence would have great utility. Toward this goal, we have used the DNA-binding specificities of 678 two-finger modules from both natural and artificial sources to construct a random forest-based predictive model for ZFP recognition. We find that our recognition model outperforms previously described determinant-based recognition models for ZFPs, and can successfully estimate the specificity of naturally occurring ZFPs with previously defined specificities.

Rights and Permissions

Citation: Nucleic Acids Res. 2014 Apr;42(8):4800-12. doi: 10.1093/nar/gku132. Epub 2014 Feb 12. Link to article on publisher's site

DOI of Published Version

10.1093/nar/gku132

Comments

Copyright © The Author(s) 2014. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Related Resources

Link to Article in PubMed

Journal Title

Nucleic acids research

PubMed ID

24523353

Creative Commons License

Creative Commons Attribution-Noncommercial 3.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial 3.0 License

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