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.
journal_name
Genome Resjournal_title
Genome researchauthors
Enuameh MS,Asriyan Y,Richards A,Christensen RG,Hall VL,Kazemian M,Zhu C,Pham H,Cheng Q,Blatti C,Brasefield JA,Basciotta MD,Ou J,McNulty JC,Zhu LJ,Celniker SE,Sinha S,Stormo GD,Brodsky MH,Wolfe SAdoi
10.1101/gr.151472.112subject
Has Abstractpub_date
2013-06-01 00:00:00pages
928-40issue
6eissn
1088-9051issn
1549-5469pii
gr.151472.112journal_volume
23pub_type
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