title: Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants.
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.
authors.affiliation: Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
authors.forename: Metewo Selase
authors.initials: MS
authors.lastname: Enuameh
authors.forename: Yuna
authors.initials: Y
authors.lastname: Asriyan
authors.forename: Adam
authors.initials: A
authors.lastname: Richards
authors.forename: Ryan G
authors.initials: RG
authors.lastname: Christensen
authors.forename: Victoria L
authors.initials: VL
authors.lastname: Hall
authors.forename: Majid
authors.initials: M
authors.lastname: Kazemian
authors.forename: Cong
authors.initials: C
authors.lastname: Zhu
authors.forename: Hannah
authors.initials: H
authors.lastname: Pham
authors.forename: Qiong
authors.initials: Q
authors.lastname: Cheng
authors.forename: Charles
authors.initials: C
authors.lastname: Blatti
authors.forename: Jessie A
authors.initials: JA
authors.lastname: Brasefield
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Basciotta
authors.forename: Jianhong
authors.initials: J
authors.lastname: Ou
authors.forename: Joseph C
authors.initials: JC
authors.lastname: McNulty
authors.forename: Lihua J
authors.initials: LJ
authors.lastname: Zhu
authors.forename: Susan E
authors.initials: SE
authors.lastname: Celniker
authors.forename: Saurabh
authors.initials: S
authors.lastname: Sinha
authors.forename: Gary D
authors.initials: GD
authors.lastname: Stormo
authors.forename: Michael H
authors.initials: MH
authors.lastname: Brodsky
authors.forename: Scot A
authors.initials: SA
authors.lastname: Wolfe
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D004330:Drosophila / Q000235:genetics*; D029721:Drosophila Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D008958:Models, Molecular; D059372:Nucleotide Motifs; D010802:Phylogeny; D056510:Position-Specific Scoring Matrices; D011485:Protein Binding; D011487:Protein Conformation; D016335:Zinc Fingers / Q000235:genetics*
chemical_list: D029721:Drosophila Proteins