Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants

Enuameh, Metewo S.; Asriyan, Y.; Richards, A.; Christensen, R. G.; Hall, V. L.; Kazemian, M.; Zhu, C.; Pham, H.; Cheng, Q.; Blatti, C.; Brasefield, J. A.; Basciotta, M. D.; Ou, J.; McNulty, J. C.; Zhu, L. J.; Celniker, S. E.; Sinha, S.; Stormo, G. D.; Brodsky, M. H.; Wolfe, S. A.

doi:10.1101/gr.151472.112

Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants

Journal Article · Wed Mar 06 23:00:00 EST 2013 · Genome Research

DOI:https://doi.org/10.1101/gr.151472.112· OSTI ID:1625622

Enuameh, Metewo S. ^[1]; Asriyan, Y. ^[2]; Richards, A. ^[2]; Christensen, R. G. ^[3]; Hall, V. L. ^[2]; Kazemian, M. ^[4]; Zhu, C. ^[2]; Pham, H. ^[2]; Cheng, Q. ^[4]; Blatti, C. ^[4]; Brasefield, J. A. ^[2]; Basciotta, M. D. ^[2]; Ou, J. ^[2]; McNulty, J. C. ^[2]; Zhu, L. J. ^[5]; Celniker, S. E. ^[6]; Sinha, S. ^[7]; Stormo, G. D. ^[3]; Brodsky, M. H. ^[2]; Wolfe, S. A. ^[8]

Univ. of Massachusetts, Worcester, MA (United States). Medical School. Program in Gene Function and Expression; DOE/OSTI
Univ. of Massachusetts, Worcester, MA (United States). Medical School. Program in Gene Function and Expression
Washington Univ., St. Louis, MO (United States). School of Medicine. Dept. of Genetics
Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Computer Science
Univ. of Massachusetts, Worcester, MA (United States). Medical School. Program in Gene Function and Expression; Univ. of Massachusetts, Worcester, MA (United States). Medical School. Dept. of Molecular Medicine; Univ. of Massachusetts, Worcester, MA (United States). Medical School. Program in Bioinformatics and Integrative Biology
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Dept. of Genome Dynamics
Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Computer Science; Univ. of Illinois at Urbana-Champaign, IL (United States). Inst. for Genomic Biology
Univ. of Massachusetts, Worcester, MA (United States). Medical School. Program in Gene Function and Expression; Univ. of Massachusetts, Worcester, MA (United States). Dept. of Biochemistry and Molecular Pharmacology

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.

View Accepted Manuscript (DOE)

Research Organization:: Univ. of California, Oakland, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625622

Journal Information:: Genome Research, Journal Name: Genome Research Journal Issue: 6 Vol. 23; ISSN 1088-9051

Publisher:: Cold Spring Harbor Laboratory PressCopyright Statement

Country of Publication:: United States

Language:: English

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Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants

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