Genome-wide functional analysis reveals factors needed at the transition steps of induced reprogramming

Chao-Shun Yang; Kung-Yen Chang; Tariq M Rana

doi:10.1016/j.celrep.2014.07.002

Genome-wide functional analysis reveals factors needed at the transition steps of induced reprogramming

Cell Rep. 2014 Jul 24;8(2):327-37. doi: 10.1016/j.celrep.2014.07.002. Epub 2014 Jul 17.

Authors

Chao-Shun Yang¹, Kung-Yen Chang², Tariq M Rana³

Affiliations

¹ 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.
² 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.
³ 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.

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.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Animals
Cells, Cultured
Cellular Reprogramming / genetics*
Chromosomal Proteins, Non-Histone / genetics
Chromosomal Proteins, Non-Histone / metabolism
Cyclin-Dependent Kinase Inhibitor p16 / genetics
Cyclin-Dependent Kinase Inhibitor p16 / metabolism
Embryonic Stem Cells / cytology
Embryonic Stem Cells / metabolism*
Epidermal Growth Factor / genetics
Epidermal Growth Factor / metabolism
Genome*
Hepatocyte Nuclear Factor 4 / genetics
Hepatocyte Nuclear Factor 4 / metabolism
Homeodomain Proteins / genetics
Homeodomain Proteins / metabolism
Induced Pluripotent Stem Cells / cytology
Induced Pluripotent Stem Cells / metabolism*
Inositol 1,4,5-Trisphosphate Receptors / genetics
Inositol 1,4,5-Trisphosphate Receptors / metabolism
Membrane Glycoproteins / genetics
Membrane Glycoproteins / metabolism
Mice
NF-E2 Transcription Factor, p45 Subunit / genetics
NF-E2 Transcription Factor, p45 Subunit / metabolism
Neoplasm Proteins / genetics
Neoplasm Proteins / metabolism
Nerve Tissue Proteins / genetics
Nerve Tissue Proteins / metabolism
Otx Transcription Factors / genetics
Otx Transcription Factors / metabolism
Protein Disulfide-Isomerases / genetics
Protein Disulfide-Isomerases / metabolism
Signal Transduction
Suppressor of Cytokine Signaling Proteins / genetics
Suppressor of Cytokine Signaling Proteins / metabolism
Trans-Activators / genetics
Trans-Activators / metabolism
Transcription Factors / genetics
Transcription Factors / metabolism
Transcription Factors, TFII / genetics
Transcription Factors, TFII / metabolism
Transcriptome
Tumor Suppressor Proteins / genetics
Tumor Suppressor Proteins / metabolism

Substances

Asb4 protein, mouse
Cdkn2a protein, mouse
Chromosomal Proteins, Non-Histone
Cyclin-Dependent Kinase Inhibitor p16
Dbx1 protein, mouse
Gtf2i protein, mouse
Hepatocyte Nuclear Factor 4
Hnf4g protein, mouse
Homeodomain Proteins
Inositol 1,4,5-Trisphosphate Receptors
Itpr1 protein, mouse
Lzts1 protein, mouse
Membrane Glycoproteins
Msx3 protein, mouse
NF-E2 Transcription Factor, p45 Subunit
Neoplasm Proteins
Nerve Tissue Proteins
Nfe2 protein, mouse
Og2x protein, mouse
Otx Transcription Factors
Otx3 protein, mouse
Suppressor of Cytokine Signaling Proteins
Tdgf1 protein, mouse
Trans-Activators
Transcription Factors
Transcription Factors, TFII
Tumor Suppressor Proteins
Utf1 protein, mouse
Epidermal Growth Factor
Pdia3 protein, mouse
Protein Disulfide-Isomerases

Abstract

Publication types

MeSH terms

Substances

Grants and funding