title: Genome-wide functional analysis reveals factors needed at the transition steps of induced reprogramming.
abstract: Although transcriptome analysis can uncover the molecular changes that occur during induced reprogramming, the functional requirements for a given factor during stepwise cell-fate transitions are left unclear. Here, we used a genome-wide RNAi screen and performed integrated transcriptome analysis to identify key genes and cellular events required at the transition steps in reprogramming. Genes associated with cell signaling pathways (e.g., Itpr1, Itpr2, and Pdia3) constitute the major regulatory networks before cells acquire pluripotency. Activation of a specific gene set (e.g., Utf1 or Tdgf1) is important for mature induced pluripotent stem cell formation. Strikingly, a major proportion of RNAi targets (∼ 53% to 70%) includes genes whose expression levels are unchanged during reprogramming. Among these non-differentially expressed genes, Dmbx1, Hnf4g, Nobox, and Asb4 are important, whereas Nfe2, Cdkn2aip, Msx3, Dbx1, Lzts1, Gtf2i, and Ankrd22 are roadblocks to reprogramming. Together, our results provide a wealth of information about gene functions required at transition steps during reprogramming.
authors.affiliation: Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Pediatrics, University of California San Diego School of Medicine, 9500 Gilman Drive, Mail Code 0762, La Jolla, CA 92093, USA.
authors.forename: Chao-Shun
authors.initials: CS
authors.lastname: Yang
authors.affiliation: Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Pediatrics, University of California San Diego School of Medicine, 9500 Gilman Drive, Mail Code 0762, La Jolla, CA 92093, USA.
authors.forename: Kung-Yen
authors.initials: KY
authors.lastname: Chang
authors.affiliation: Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Pediatrics, University of California San Diego School of Medicine, 9500 Gilman Drive, Mail Code 0762, La Jolla, CA 92093, USA. Electronic address: trana@ucsd.edu.
authors.forename: Tariq M
authors.initials: TM
authors.lastname: Rana
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D065150:Cellular Reprogramming / Q000235:genetics*; D002868:Chromosomal Proteins, Non-Histone / Q000235:genetics / Q000378:metabolism; D019941:Cyclin-Dependent Kinase Inhibitor p16 / Q000235:genetics / Q000378:metabolism; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism*; D004815:Epidermal Growth Factor / Q000235:genetics / Q000378:metabolism; D016678:Genome; D051557:Hepatocyte Nuclear Factor 4 / Q000235:genetics / Q000378:metabolism; D018398:Homeodomain Proteins / Q000235:genetics / Q000378:metabolism; D057026:Induced Pluripotent Stem Cells / Q000166:cytology / Q000378:metabolism*; D053496:Inositol 1,4,5-Trisphosphate Receptors / Q000235:genetics / Q000378:metabolism; D008562:Membrane Glycoproteins / Q000235:genetics / Q000378:metabolism; D051379:Mice; D050984:NF-E2 Transcription Factor, p45 Subunit / Q000235:genetics / Q000378:metabolism; D009363:Neoplasm Proteins / Q000235:genetics / Q000378:metabolism; D009419:Nerve Tissue Proteins / Q000235:genetics / Q000378:metabolism; D051857:Otx Transcription Factors / Q000235:genetics / Q000378:metabolism; D019704:Protein Disulfide-Isomerases / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction; D050826:Suppressor of Cytokine Signaling Proteins / Q000235:genetics / Q000378:metabolism; D015534:Trans-Activators / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D019473:Transcription Factors, TFII / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome; D025521:Tumor Suppressor Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: C530435:Asb4 protein, mouse; C417743:Cdkn2a protein, mouse; D002868:Chromosomal Proteins, Non-Histone; D019941:Cyclin-Dependent Kinase Inhibitor p16; C103403:Dbx1 protein, mouse; C486330:Gtf2i protein, mouse; D051557:Hepatocyte Nuclear Factor 4; C496598:Hnf4g protein, mouse; D018398:Homeodomain Proteins; D053496:Inositol 1,4,5-Trisphosphate Receptors; C025389:Itpr1 protein, mouse; C574993:Lzts1 protein, mouse; D008562:Membrane Glycoproteins; C104294:Msx3 protein, mouse; D050984:NF-E2 Transcription Factor, p45 Subunit; D009363:Neoplasm Proteins; D009419:Nerve Tissue Proteins; C494693:Nfe2 protein, mouse; C456265:Og2x protein, mouse; D051857:Otx Transcription Factors; C470836:Otx3 protein, mouse; D050826:Suppressor of Cytokine Signaling Proteins; C489450:Tdgf1 protein, mouse; D015534:Trans-Activators; D014157:Transcription Factors; D019473:Transcription Factors, TFII; D025521:Tumor Suppressor Proteins; C112198:Utf1 protein, mouse; D004815:Epidermal Growth Factor; C513195:Pdia3 protein, mouse; D019704:Protein Disulfide-Isomerases