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| Status |
Public on Dec 06, 2012 |
| Title |
Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. |
| Organism |
synthetic construct |
| Experiment type |
Other
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| Summary |
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 130 Zinc finger sets from Drosophila melanogaster using a bacterial one-hybrid system. This data set contains the DNA-binding specificities for at least one encoded ZFP from 71 unique genes and 22 alternate splice isoforms. This represents the largest block of characterized ZFPs from any organism described to date. These recognition motifs can be used to predict genomic binding sites and potential regulatory targets for these factors within the fruit fly genome. We have characterized subsets of fingers from these ZFPs to define the correct orientation and register of the zinc fingers on their defined binding sites. By correlating individual fingers with motif subsites, we can assign finger specificity throughout each ZFP. This reveals the diversity of recognition potential within the naturally-occurring zinc fingers of a single organism, where the characterized fingers can specify 47 of the 64 possible DNA triplets. To confirm the utility of our finger recognition models, we have employed subsets of Drosophila fingers in combination with an existing archive of zinc finger modules to create ZFPs with novel DNA-binding specificity. These finger combinations can be used to create novel functional Zinc Finger Nucleases for editing vertebrate genomes.
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| Overall design |
Illumina sequencing of Barcoded Binding sites obtained after B1H selection of Cys2-His2 zinc finger proteins cloned as a C-terminal fusions to the omega subunit of E. coli RNA polymerase in the B1H system.
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| Contributor(s) |
Enuameh MS, Asriyan Y, Richards A, Christensen RG, Hall V, 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 SA |
| Citation(s) |
23471540 |
| Submission date |
Dec 04, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Scot Wolfe |
| E-mail(s) |
scot.wolfe@umassmed.edu
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| Organization name |
UMass Medical School
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| Department |
MCCB
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| Street address |
364 Plantation Street, LRB 619
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| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
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| Platforms (2) |
| GPL11631 |
Illumina Genome Analyzer IIx (synthetic construct) |
| GPL15228 |
Illumina HiSeq 2000 (synthetic construct) |
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| Samples (125)
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| Relations |
| BioProject |
PRJNA182907 |
| SRA |
SRP017408 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE42709_RAW.tar |
1.3 Mb |
(http)(custom) |
TAR (of FA) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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