title: Reprogramming cell fate with a genome-scale library of artificial transcription factors.
abstract: Artificial transcription factors (ATFs) are precision-tailored molecules designed to bind DNA and regulate transcription in a preprogrammed manner. Libraries of ATFs enable the high-throughput screening of gene networks that trigger cell fate decisions or phenotypic changes. We developed a genome-scale library of ATFs that display an engineered interaction domain (ID) to enable cooperative assembly and synergistic gene expression at targeted sites. We used this ATF library to screen for key regulators of the pluripotency network and discovered three combinations of ATFs capable of inducing pluripotency without exogenous expression of Oct4 (POU domain, class 5, TF 1). Cognate site identification, global transcriptional profiling, and identification of ATF binding sites reveal that the ATFs do not directly target Oct4; instead, they target distinct nodes that converge to stimulate the endogenous pluripotency network. This forward genetic approach enables cell type conversions without a priori knowledge of potential key regulators and reveals unanticipated gene network dynamics that drive cell fate choices.
authors.affiliation: Cellular and Molecular Biology Training Program, University of Wisconsin-Madison, Madison, WI 53706.|Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706.
authors.forename: Asuka
authors.initials: A
authors.lastname: Eguchi
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Wleklinski
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706.
authors.forename: Mackenzie C
authors.initials: MC
authors.lastname: Spurgat
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706.
authors.forename: Evan A
authors.initials: EA
authors.lastname: Heiderscheit
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706.|Genetics Training Program, University of Wisconsin-Madison, Madison, WI 53706.
authors.forename: Anna S
authors.initials: AS
authors.lastname: Kropornicka
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706.
authors.forename: Catherine K
authors.initials: CK
authors.lastname: Vu
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706.|Department of Electrical and Computer Engineering, University of Wisconsin-Madison, Madison, WI 53706.
authors.forename: Devesh
authors.initials: D
authors.lastname: Bhimsaria
authors.affiliation: Morgridge Institute for Research, Madison, WI 53715.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Swanson
authors.affiliation: Morgridge Institute for Research, Madison, WI 53715.
authors.forename: Ron
authors.initials: R
authors.lastname: Stewart
authors.affiliation: Department of Electrical and Computer Engineering, University of Wisconsin-Madison, Madison, WI 53706.
authors.forename: Parameswaran
authors.initials: P
authors.lastname: Ramanathan
authors.affiliation: Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792.
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Kamp
authors.affiliation: Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715.|Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53715.
authors.forename: Igor
authors.initials: I
authors.lastname: Slukvin
authors.affiliation: Morgridge Institute for Research, Madison, WI 53715.|Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706.|The Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706.
authors.forename: James A
authors.initials: JA
authors.lastname: Thomson
authors.affiliation: Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455.
authors.forename: James R
authors.initials: JR
authors.lastname: Dutton
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706; azansari@wisc.edu.|The Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706.
authors.forename: Aseem Z
authors.initials: AZ
authors.lastname: Ansari
mesh_terms: D000818:Animals; D001665:Binding Sites / Q000235:genetics; D019070:Cell Lineage; D065150:Cellular Reprogramming; D056404:Chaperonin Containing TCP-1 / Q000378:metabolism; D044127:Epigenesis, Genetic; D005347:Fibroblasts / Q000378:metabolism; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D015698:Genomic Library; D057809:HEK293 Cells; D006801:Humans; D051379:Mice; D000072417:Protein Domains; D015202:Protein Engineering; D017423:Sequence Analysis, RNA; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic; D016335:Zinc Fingers / Q000235:genetics
chemical_list: C533300:CCT4 protein, human; D014157:Transcription Factors; D056404:Chaperonin Containing TCP-1
keywords: artificial transcription factor; cell fate; gene regulatory networks; genome-scale library; reprogramming