The DEAD-box RNA-binding protein DDX6 regulates parental RNA decay for cellular reprogramming to pluripotency

Daisuke Kami; Tomoya Kitani; Akihiro Nakamura; Naoki Wakui; Rena Mizutani; Masahito Ohue; Fuyuki Kametani; Nobuyoshi Akimitsu; Satoshi Gojo

doi:10.1371/journal.pone.0203708

The DEAD-box RNA-binding protein DDX6 regulates parental RNA decay for cellular reprogramming to pluripotency

PLoS One. 2018 Oct 1;13(10):e0203708. doi: 10.1371/journal.pone.0203708. eCollection 2018.

Authors

Daisuke Kami¹, Tomoya Kitani², Akihiro Nakamura³, Naoki Wakui⁴, Rena Mizutani⁵, Masahito Ohue⁴, Fuyuki Kametani⁶, Nobuyoshi Akimitsu⁵, Satoshi Gojo¹

Affiliations

¹ Department of Regenerative Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan.
² Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan.
³ Department of Pediatric Cardiology and Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan.
⁴ Department of Computer Science, School of Computing, Tokyo Institute of Technology, Tokyo, Japan.
⁵ Radioisotope Center, The University of Tokyo, Tokyo, Japan.
⁶ Department of Dementia and Higher Brain Function, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.

Abstract

Cellular transitions and differentiation processes require mRNAs supporting the new phenotype but also the clearance of existing mRNAs for the parental phenotype. Cellular reprogramming from fibroblasts to induced pluripotent stem cells (iPSCs) occurs at the early stage of mesenchymal epithelial transition (MET) and involves drastic morphological changes. We examined the molecular mechanism for MET, focusing on RNA metabolism. DDX6, an RNA helicase, was indispensable for iPSC formation, in addition to RO60 and RNY1, a non-coding RNA, which form complexes involved in intracellular nucleotide sensing. RO60/RNY1/DDX6 complexes formed prior to processing body formation, which is central to RNA metabolism. The abrogation of DDX6 expression inhibited iPSC generation, which was mediated by RNA decay targeting parental mRNAs supporting mesenchymal phenotypes, along with microRNAs, such as miR-302b-3p. These results show that parental mRNA clearance is a prerequisite for cellular reprogramming and that DDX6 plays a central role in this process.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cellular Reprogramming / genetics*
DEAD-box RNA Helicases / genetics*
Epithelial-Mesenchymal Transition / genetics
Fibroblasts / cytology
Gene Expression / genetics
Gene Expression Regulation, Developmental
Humans
Immunoprecipitation
Induced Pluripotent Stem Cells / cytology*
Induced Pluripotent Stem Cells / metabolism
MicroRNAs / genetics*
Proto-Oncogene Proteins / genetics*
RNA Stability / genetics
RNA, Small Interfering / genetics
RNA, Untranslated / genetics
Ribonucleoproteins / genetics

Substances

MIRN302A microRNA, human
MicroRNAs
Proto-Oncogene Proteins
RNA, Small Interfering
RNA, Untranslated
Ribonucleoproteins
SS-A antigen
DDX6 protein, human
DEAD-box RNA Helicases

Grants and funding

This research was supported by a grant, Grant-in-Aid for challenging Exploratory Research 16K15260, from the Ministry of Education, Culture, Sports, Science and Technology of Japan. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.