RNAi Reveals Phase-Specific Global Regulators of Human Somatic Cell Reprogramming

Cheng Xu Delon Toh, Jun Wei Chan, Zheng Shan Chong, Hao Fei Wang, Hong Chao Guo, Sandeep Satapathy, Dongrui Ma, Germaine Yen Lin Goh, Ekta Khattar, Lin Yang, Vinay Tergaonkar, Young Tae Chang, James J. Collins, George Q. Daley, Keng Boon Wee, Chadi A.E.L. Farran, Hu Li, Yoon Pin Lim, Frederic A. Bard, Yuin Han Loh

Research output: Contribution to journalArticle

19 Scopus citations

Abstract

Incomplete knowledge of the mechanisms at work continues to hamper efforts to maximize reprogramming efficiency. Here, we present a systematic genome-wide RNAi screen to determine the global regulators during the early stages of human reprogramming. Our screen identifies functional repressors and effectors that act to impede or promote the reprogramming process. Repressors and effectors form close interacting networks in pathways, including RNA processing, G protein signaling, protein ubiquitination, and chromatin modification. Combinatorial knockdown of five repressors (SMAD3, ZMYM2, SFRS11, SAE1, and ESET) synergistically resulted in ~85% TRA-1-60-positive cells. Removal of the novel splicing factor SFRS11 during reprogramming is accompanied by rapid acquisition of pluripotency-specific spliced forms. Mechanistically, SFRS11 regulates exon skipping and mutually exclusive splicing of transcripts in genes involved in cell differentiation, mRNA splicing, and chromatin modification. Our study provides insights into the reprogramming process, which comprises comprehensive and multi-layered transcriptional, splicing, and epigenetic machineries.

Original languageEnglish (US)
Pages (from-to)2597-2607
Number of pages11
JournalCell reports
Volume15
Issue number12
DOIs
StatePublished - Jun 21 2016

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Keywords

  • Genome-wide siRNA screen
  • Human somatic cell reprogramming
  • Reprogramming specific alternative splicing
  • SFRS11
  • ZNF207

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Toh, C. X. D., Chan, J. W., Chong, Z. S., Wang, H. F., Guo, H. C., Satapathy, S., Ma, D., Goh, G. Y. L., Khattar, E., Yang, L., Tergaonkar, V., Chang, Y. T., Collins, J. J., Daley, G. Q., Wee, K. B., Farran, C. A. E. L., Li, H., Lim, Y. P., Bard, F. A., & Loh, Y. H. (2016). RNAi Reveals Phase-Specific Global Regulators of Human Somatic Cell Reprogramming. Cell reports, 15(12), 2597-2607. https://doi.org/10.1016/j.celrep.2016.05.049