An improved predictive recognition model for Cys2-His2 zinc finger proteins
Authors
Gupta, AnkitChristensen, Ryan G.
Bell, Heather A.
Goodwin, Mathew
Patel, Ronak Y.
Pandey, Manishi
Enuameh, Metewo Selase
Rayla, Amy L.
Zhu, Cong
Thibodeau-Beganny, Stacey
Brodsky, Michael H.
Joung, J. Keith
Wolfe, Scot A.
Stormo, Gary D.
UMass Chan Affiliations
Department of Biochemistry and Molecular PharmacologyProgram in Gene Function and Expression
Document Type
Journal ArticlePublication Date
2014-04-01
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Cys2-His2 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.Source
Gupta A, Christensen RG, Bell HA, Goodwin M, Patel RY, Pandey M, Enuameh MS, Rayla AL, Zhu C, Thibodeau-Beganny S, Brodsky MH, Joung JK, Wolfe SA, Stormo GD. An improved predictive recognition model for Cys2-His2 zinc finger proteins. Nucleic Acids Res. 2014 Apr;42(8):4800-12. doi: 10.1093/nar/gku132. Link to article on publisher's siteDOI
10.1093/nar/gku132Permanent Link to this Item
http://hdl.handle.net/20.500.14038/44022PubMed ID
24523353Related Resources
Link to Article in PubMedRights
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
ae974a485f413a2113503eed53cd6c53
10.1093/nar/gku132