title: Construction of combinatorial libraries that encode zinc finger-based transcription factors.
abstract: Combinatorial retroviral libraries of zinc finger transcription factors (ZF-TFs) can be constructed that encode tens of thousands of different, multi-finger zinc finger proteins (ZFPs) with distinct DNA-binding specificities, each of which is fused to a transcriptional activation or repression domain. Individual zinc fingers (ZFs) recognize their target DNA subsites and retain their binding specificities in the context of artificially constructed multi-finger ZFPs. Because of this modular nature, expression libraries that specify diverse multi-finger ZF-TFs can be created by the combinatorial stitching together of individual modules in a pool of single-ZF-encoding DNA segments. When these libraries are introduced into cells, the encoded ZF-TFs are expressed and can then activate or repress the transcription of endogenous target genes. Ideally, the ZF-TF-encoding retroviral vectors in the library enter cells randomly at a ratio of approximately 1 per cell. As a result, individual cells express different ZF-TFs and thus display distinct phenotypical changes. Using an appropriate screening or selection method, one can isolate clonal cells that display phenotypes of interest. One can then identify the ZF-TFs responsible for the phenotypes and, ultimately, the genes that are targeted by the selected ZF-TFs. Here, we provide protocols for the preparation of retroviral libraries that encode ZF-TFs for use in mammalian cells.
authors.affiliation: Department of Chemistry, Seoul National University, Seoul, South Korea.
authors.forename: Seokjoong
authors.initials: S
authors.lastname: Kim
authors.forename: Eun Ji
authors.initials: EJ
authors.lastname: Kim
authors.forename: Jin-Soo
authors.initials: JS
authors.lastname: Kim
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D002460:Cell Line; D006801:Humans; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D019151:Peptide Library; D015202:Protein Engineering / Q000379:methods*; D014157:Transcription Factors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D016335:Zinc Fingers / Q000235:genetics*
chemical_list: D019151:Peptide Library; D014157:Transcription Factors