Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants
- Metewo Selase Enuameh1,
- Yuna Asriyan1,
- Adam Richards1,
- Ryan G Christensen2,
- Victoria L. Hall1,
- Majid Kazemian3,
- Cong Zhu1,
- Hannah Pham1,
- Qiong Cheng3,
- Charles Blatti3,
- Jessie A Brasefield1,
- Matthew D Basciotta1,
- Jianhong Ou1,
- Joseph C McNulty1,
- Lihua J Zhu1,
- Susan E Celniker4,
- Saurabh Sinha3,
- Gary D Stormo2,
- Michael H Brodsky1 and
- Scot A Wolfe1,5
- 1 University of Massachusetts Medical School;
- 2 Washington University School of Medicine;
- 3 University of Illinois at Urbana-Champaign;
- 4 Lawrence Berkeley National Laboratory
- ↵* Corresponding author; email: scot.wolfe{at}umassmed.edu
Abstract
Cys2-His2 zinc finger proteins (ZFPs) are the largest group of transcription factors in higher metazoans. A complete characterization of these ZFPs and their associated target sequences is pivotal to fully annotate transcriptional regulatory networks in metazoan genomes. As a first step in this process, we have characterized the DNA-binding specificities of 129 Zinc finger sets from Drosophila using a bacterial one-hybrid system. This data set contains the DNA-binding specificities for at least one encoded ZFP from 70 unique genes and 23 alternate splice isoforms representing the largest set of characterized ZFPs from any organism described to date. These recognition motifs can be used to predict genomic binding sites for these factors within the fruit fly genome. Subsets of fingers from these ZFPs were characterized to define their orientation and register on their recognition sequences, thereby allowing us to define the recognition diversity within this finger set. We find that the characterized fingers can specify 47 of the 64 possible DNA triplets. To confirm the utility of our finger recognition models, we employed subsets of Drosophila fingers in combination with an existing archive of artificial zinc finger modules to create ZFPs with novel DNA-binding specificity. These hybrids of natural and artificial fingers can be used to create functional Zinc Finger Nucleases for editing vertebrate genomes.
- Received October 30, 2012.
- Accepted February 28, 2013.
- © 2013, Published by Cold Spring Harbor Laboratory Press
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