Multi-omics Approach Reveals Posttranscriptionally Regulated Genes Are Essential for Human Pluripotent Stem Cells

Overview

Journal iScience

Publisher Cell Press

Date 2022 May 16

PMID 35573189

Authors

Mio Iwasaki

Yuka Kawahara

Chikako Okubo

Tatsuya Yamakawa

Michiko Nakamura

Tsuyoshi Tabata

Yohei Nishi

Megumi Narita

Akira Ohta

Hirohide Saito

Takuya Yamamoto

Masato Nakagawa

Shinya Yamanaka

Kazutoshi Takahashi

Affiliations

Soon will be listed here.

Abstract

The effects of transcription factors on the maintenance and differentiation of human-induced or embryonic pluripotent stem cells (iPSCs/ESCs) have been well studied. However, the importance of posttranscriptional regulatory mechanisms, which cause the quantitative dissociation of mRNA and protein expression, has not been explored in detail. Here, by combining transcriptome and proteome profiling, we identified 228 posttranscriptionally regulated genes with strict upregulation of the protein level in iPSCs/ESCs. Among them, we found 84 genes were vital for the survival of iPSCs and HDFs, including 20 genes that were specifically necessary for iPSC survival. These 20 proteins were upregulated only in iPSCs/ESCs and not in differentiated cells derived from the three germ layers. Although there are still unknown mechanisms that downregulate protein levels in HDFs, these results reveal that posttranscriptionally regulated genes have a crucial role in iPSC survival.

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References

Chen Q, Hu G . Post-transcriptional regulation of the pluripotent state. Curr Opin Genet Dev. 2017; 46:15-23. PMC: 6476425. DOI: 10.1016/j.gde.2017.06.010. View

Darnell A, Subramaniam A, OShea E . Translational Control through Differential Ribosome Pausing during Amino Acid Limitation in Mammalian Cells. Mol Cell. 2018; 71(2):229-243.e11. PMC: 6516488. DOI: 10.1016/j.molcel.2018.06.041. View

Tresenrider A, Morse K, Jorgensen V, Chia M, Liao H, van Werven F . Integrated genomic analysis reveals key features of long undecoded transcript isoform-based gene repression. Mol Cell. 2021; 81(10):2231-2245.e11. PMC: 8153250. DOI: 10.1016/j.molcel.2021.03.013. View

Komatsu K, Taya T, Matsumoto S, Miyashita E, Kashida S, Saito H . RNA structure-wide discovery of functional interactions with multiplexed RNA motif library. Nat Commun. 2020; 11(1):6275. PMC: 7723054. DOI: 10.1038/s41467-020-19699-5. View

Howe K, Achuthan P, Allen J, Allen J, Alvarez-Jarreta J, Amode M . Ensembl 2021. Nucleic Acids Res. 2020; 49(D1):D884-D891. PMC: 7778975. DOI: 10.1093/nar/gkaa942. View

Li B, Dewey C . RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011; 12:323. PMC: 3163565. DOI: 10.1186/1471-2105-12-323. View

Dendooven T, Luisi B, Bandyra K . RNA lifetime control, from stereochemistry to gene expression. Curr Opin Struct Biol. 2019; 61:59-70. DOI: 10.1016/j.sbi.2019.10.002. View

Paz I, Kosti I, Ares Jr M, Cline M, Mandel-Gutfreund Y . RBPmap: a web server for mapping binding sites of RNA-binding proteins. Nucleic Acids Res. 2014; 42(Web Server issue):W361-7. PMC: 4086114. DOI: 10.1093/nar/gku406. View

DOrazio K, Green R . Ribosome states signal RNA quality control. Mol Cell. 2021; 81(7):1372-1383. PMC: 8041214. DOI: 10.1016/j.molcel.2021.02.022. View

10.

Buccitelli C, Selbach M . mRNAs, proteins and the emerging principles of gene expression control. Nat Rev Genet. 2020; 21(10):630-644. DOI: 10.1038/s41576-020-0258-4. View

11.

Kainov Y, Makeyev E . A transcriptome-wide antitermination mechanism sustaining identity of embryonic stem cells. Nat Commun. 2020; 11(1):361. PMC: 6969169. DOI: 10.1038/s41467-019-14204-z. View

12.

Ohta S, Nishida E, Yamanaka S, Yamamoto T . Global splicing pattern reversion during somatic cell reprogramming. Cell Rep. 2013; 5(2):357-66. DOI: 10.1016/j.celrep.2013.09.016. View

13.

Roumeliotis T, Williams S, Goncalves E, Alsinet C, Del Castillo Velasco-Herrera M, Aben N . Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells. Cell Rep. 2017; 20(9):2201-2214. PMC: 5583477. DOI: 10.1016/j.celrep.2017.08.010. View

14.

Pohl C, Dikic I . Cellular quality control by the ubiquitin-proteasome system and autophagy. Science. 2019; 366(6467):818-822. DOI: 10.1126/science.aax3769. View

15.

Wang L, Wang S, Li W . RSeQC: quality control of RNA-seq experiments. Bioinformatics. 2012; 28(16):2184-5. DOI: 10.1093/bioinformatics/bts356. View

16.

Iwasaki M, Tabata T, Kawahara Y, Ishihama Y, Nakagawa M . Removal of Interference MS/MS Spectra for Accurate Quantification in Isobaric Tag-Based Proteomics. J Proteome Res. 2019; 18(6):2535-2544. DOI: 10.1021/acs.jproteome.9b00078. View

17.

Salomonis N, Schlieve C, Pereira L, Wahlquist C, Colas A, Zambon A . Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation. Proc Natl Acad Sci U S A. 2010; 107(23):10514-9. PMC: 2890851. DOI: 10.1073/pnas.0912260107. View

18.

Chia N, Chan Y, Feng B, Lu X, Orlov Y, Moreau D . A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Nature. 2010; 468(7321):316-20. DOI: 10.1038/nature09531. View

19.

Warner J, Knopf P . The discovery of polyribosomes. Trends Biochem Sci. 2002; 27(7):376-80. DOI: 10.1016/s0968-0004(02)02126-6. View

20.

Nakagawa M, Taniguchi Y, Senda S, Takizawa N, Ichisaka T, Asano K . A novel efficient feeder-free culture system for the derivation of human induced pluripotent stem cells. Sci Rep. 2014; 4:3594. PMC: 3884228. DOI: 10.1038/srep03594. View