title: A Systematic Approach to Identify Candidate Transcription Factors that Control Cell Identity.
abstract: Hundreds of transcription factors (TFs) are expressed in each cell type, but cell identity can be induced through the activity of just a small number of core TFs. Systematic identification of these core TFs for a wide variety of cell types is currently lacking and would establish a foundation for understanding the transcriptional control of cell identity in development, disease, and cell-based therapy. Here, we describe a computational approach that generates an atlas of candidate core TFs for a broad spectrum of human cells. The potential impact of the atlas was demonstrated via cellular reprogramming efforts where candidate core TFs proved capable of converting human fibroblasts to retinal pigment epithelial-like cells. These results suggest that candidate core TFs from the atlas will prove a useful starting point for studying transcriptional control of cell identity and reprogramming in many human cell types.
authors.affiliation: Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA.
authors.forename: Ana C
authors.initials: AC
authors.lastname: D'Alessio
authors.affiliation: Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA; Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Zi Peng
authors.initials: ZP
authors.lastname: Fan
authors.affiliation: Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA.
authors.forename: Katherine J
authors.initials: KJ
authors.lastname: Wert
authors.affiliation: Schepens Eye Research Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA.
authors.forename: Petr
authors.initials: P
authors.lastname: Baranov
authors.affiliation: Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA.
authors.forename: Malkiel A
authors.initials: MA
authors.lastname: Cohen
authors.affiliation: Neural Stem Cell Institute, Rensselaer, NY 12144, USA; Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12201, USA.
authors.forename: Janmeet S
authors.initials: JS
authors.lastname: Saini
authors.affiliation: Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA.
authors.forename: Evan
authors.initials: E
authors.lastname: Cohick
authors.affiliation: Neural Stem Cell Institute, Rensselaer, NY 12144, USA.
authors.forename: Carol
authors.initials: C
authors.lastname: Charniga
authors.affiliation: Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Dadon
authors.affiliation: Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA.
authors.forename: Nancy M
authors.initials: NM
authors.lastname: Hannett
authors.affiliation: Schepens Eye Research Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Young
authors.affiliation: Neural Stem Cell Institute, Rensselaer, NY 12144, USA.
authors.forename: Sally
authors.initials: S
authors.lastname: Temple
authors.affiliation: Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Rudolf
authors.initials: R
authors.lastname: Jaenisch
authors.affiliation: Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA. Electronic address: tlee@wi.mit.edu.
authors.forename: Tong Ihn
authors.initials: TI
authors.lastname: Lee
authors.affiliation: Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: young@wi.mit.edu.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Young
mesh_terms: D002460:Cell Line; D065150:Cellular Reprogramming; D003198:Computer Simulation; D004847:Epithelial Cells / Q000166:cytology* / Q000378:metabolism; D005347:Fibroblasts / Q000166:cytology* / Q000378:metabolism; D006801:Humans; D055213:Retinal Pigment Epithelium / Q000166:cytology* / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D014157:Transcription Factors