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 artificialmore »
- Authors:
-
- 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
- Publication Date:
- Research Org.:
- Univ. of California, Oakland, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
- OSTI Identifier:
- 1625622
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Genome Research
- Additional Journal Information:
- Journal Volume: 23; Journal Issue: 6; Journal ID: ISSN 1088-9051
- Publisher:
- Cold Spring Harbor Laboratory Press
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Genetics & Heredity
Citation Formats
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., and Wolfe, S. A. Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. United States: N. p., 2013.
Web. doi:10.1101/gr.151472.112.
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. Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. United States. https://doi.org/10.1101/gr.151472.112
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., and Wolfe, S. A. Thu .
"Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants". United States. https://doi.org/10.1101/gr.151472.112. https://www.osti.gov/servlets/purl/1625622.
@article{osti_1625622,
title = {Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants},
author = {Enuameh, Metewo S. and Asriyan, Y. and Richards, A. and Christensen, R. G. and Hall, V. L. and Kazemian, M. and Zhu, C. and Pham, H. and Cheng, Q. and Blatti, C. and Brasefield, J. A. and Basciotta, M. D. and Ou, J. and McNulty, J. C. and Zhu, L. J. and Celniker, S. E. and Sinha, S. and Stormo, G. D. and Brodsky, M. H. and Wolfe, S. A.},
abstractNote = {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.},
doi = {10.1101/gr.151472.112},
journal = {Genome Research},
number = 6,
volume = 23,
place = {United States},
year = {Thu Mar 07 00:00:00 EST 2013},
month = {Thu Mar 07 00:00:00 EST 2013}
}
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