Pharmacological systems analysis defines EIF4A3 functions in cell-cycle and RNA stress granule formation

Communications Biology - Tập 2 Số 1
Alborz Mazloomian1, Shinsuke Araki2, Momoko Ohori2, Amal M. El-Naggar1, Damian Yap3, Ali Bashashati3, Shigetomi Nakao2, Poul H. Sorensen1, Atsushi Nakanishi2, Sohrab P. Shah3, Samuel Aparício3
1Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
2Research Department, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
3Department of Pathology and Laboratory Medicine, G227-2211 Wesbrook Mall, University of British Columbia, Vancouver, BC, V6T 2B5, Canada

Tóm tắt

AbstractThe RNA helicase EIF4A3 regulates the exon junction complex and nonsense-mediated mRNA decay functions in RNA transcript processing. However, a transcriptome-wide network definition of these functions has been lacking, in part due to the lack of suitable pharmacological inhibitors. Here we employ short-duration graded EIF4A3 inhibition using small molecule allosteric inhibitors to define the transcriptome-wide dependencies of EIF4A3. We thus define conserved cellular functions, such as cell cycle control, that are EIF4A3 dependent. We show that EIF4A3-dependent splicing reactions have a distinct genome-wide pattern of associated RNA-binding protein motifs. We also uncover an unanticipated role of EIF4A3 in the biology of RNA stress granules, which sequester and silence the translation of most mRNAs under stress conditions and are implicated in cell survival and tumour progression. We show that stress granule induction and maintenance is suppressed on the inhibition of EIF4A3, in part through EIF4A3-associated regulation of G3BP1 and TIA1 scaffold protein expression.

Từ khóa


Tài liệu tham khảo

Linder, P. & Jankowsky, E. From unwinding to clamping - the DEAD box RNA helicase family. Nat. Rev. Mol. Cell Biol. 12, 505–516 (2011).

Li, Q. et al. Eukaryotic translation initiation factor 4AIII (eIF4AIII) is functionally distinct from eIF4AI and eIF4AII. Mol. Cell. Biol. 19, 7336–7346 (1999).

Chan, C. C. et al. eIF4A3 is a novel component of the exon junction complex. RNA 10, 200–209 (2004).

Favaro, F. P. et al. A Noncoding expansion in EIF4A3 causes richieri-costa-pereira syndrome, a craniofacial disorder associated with limb defects. Am. J. Hum. Genet. 94, 120–128 (2014).

Buchwald, G. et al. Insights into the recruitment of the NMD machinery from the crystal structure of a core EJC-UPF3b complex. Proc. Natl Acad. Sci. USA 107, 10050–10055 (2010).

Noble, C. G. & Song, H. MLN51 stimulates the RNA-helicase activity of eIF4AIII. PLoS ONE 2, e303 (2007).

Le Hir, H., Izaurralde, E., Maquat, L. E. & Moore, M. J. The spliceosome deposits multiple proteins 20–24 nucleotides upstream of mRNA exon-exon junctions. EMBO J. 19, 6860–6869 (2000).

Le Hir, H. & Andersen, G. R. Structural insights into the exon junction complex. Curr. Opin. Struct. Biol. 18, 112–119 (2008).

Nielsen, K. H. et al. Mechanism of ATP turnover inhibition in the EJC. RNA 15, 67–75 (2009).

Ballut, L. et al. The exon junction core complex is locked onto RNA by inhibition of eIF4AIII ATPase activity. Nat. Struct. Mol. Biol. 12, 861–869 (2005).

Hentze, M. W. & Kulozik, A. E. A perfect message: RNA surveillance and nonsense-mediated decay. Cell 96, 307–310 (1999).

Wang, Z., Murigneux, V. & Le Hir, H. Transcriptome-wide modulation of splicing by the exon junction complex. Genome. Biol. 15, 551 (2014).

Lykke-Andersen, J., Shu, M. D. & Steitz, J. A. Communication of the position of exon-exon junctions to the mRNA surveillance machinery by the protein RNPS1. Science 293, 1836–1839 (2001).

Lykke-Andersen, J., Shu, M. D. & Steitz, J. A. Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon. Cell 103, 1121–1131 (2000).

Gehring, N. H., Neu-Yilik, G., Schell, T., Hentze, M. W. & Kulozik, A. E. Y14 and hUpf3b form an NMD-activating complex. Mol. Cell 11, 939–949 (2003).

Patel, A. P. et al. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science 344, 1396–1401 (2014).

Anderson, P., Kedersha, N. & Ivanov, P. Stress granules, p-bodies and cancer. Biochim. Biophys. Acta 1849, 861–870 (2015).

Anderson, P. & Kedersha, N. Stress granules. Curr. Biol. 19, R397–R398 (2009).

Ito, M. et al. Discovery of novel 1,4-diacylpiperazines as selective and cell-active eif4a3 inhibitors. J. Med. Chem. 60, 3335–3351 (2017).

Ito, M. et al. Discovery of selective atp-competitive eif4a3 inhibitors. Bioorg. Med. Chem. 25, 2200–2209 (2017).

Funnell, T. et al. Clk-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor. Nat. Commun. 8, 7 (2017).

Iwatani-Yoshihara, M. et al. Discovery and characterization of a eukaryotic initiation factor 4a-3-selective inhibitor that suppresses nonsense-mediated mrna decay. ACS Chem Biol 12, 1760–1768 (2017).

Katz, Y., Wang, E. T., Airoldi, E. M. & Burge, C. B. Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat. Methods 7, 1009–1015 (2010).

Irimia, M. et al. A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell 159, 1511–1523 (2014).

Ray, D. et al. A compendium of rna-binding motifs for decoding gene regulation. Nature 499, 172–177 (2013).

Lai, M.-C., Kuo, H.-W., Chang, W.-C. & Tarn, W.-Y. A novel splicing regulator shares a nuclear import pathway with sr proteins. EMBO J. 22, 1359–1369 (2003).

Patton, J. G., Porro, E., Galceran, J., Tempst, P. & Nadal-Ginard, B. Cloning and characterization of psf, a novel pre-mrna splicing factor. Genes Development 7, 393–406 (1993).

Kalsotra, A. et al. A postnatal switch of celf and mbnl proteins reprograms alternative splicing in the developing heart. Proc. Natl Acad. Sci. USA 105, 20333–20338 (2008).

Merico, D., Isserlin, R., Stueker, O., Emili, A. & Bader, G. D. Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS ONE 5, e13984 (2010).

Mao, H., McMahon, J. J., Tsai, Y. H., Wang, Z. & Silver, D. L. Haploinsufficiency for core exon junction complex components disrupts embryonic neurogenesis and causes p53-mediated microcephaly. PLoS Genet. 12, e1006282 (2016).

Fukumura, K. et al. The exon junction complex controls the efficient and faithful splicing of a subset of transcripts involved in mitotic cell-cycle progression. Int. J. Mol. Sci. 17, 1153 (2016).

Michelle, L. et al. Proteins associated with the exon junction complex also control the alternative splicing of apoptotic regulators. Mol. Cell. Biol. 32, 954–967 (2012).

Buchan, J. R. & Parker, R. Eukaryotic stress granules: the ins and outs of translation. Mol. Cell 36, 932–941 (2009).

Ohn, T., Kedersha, N., Hickman, T., Tisdale, S. & Anderson, P. A functional RNAi screen links O-GlcNAc modification of ribosomal proteins to stress granule and processing body assembly. Nat. Cell Biol. 10, 1224–1231 (2008).

Tourrière, H. et al. The RasGAP-associated endoribonuclease G3BP assembles stress granules. J. Cell Biol. 160, 823–831 (2003).

Tian, Q., Streuli, M., Saito, H., Schlossman, S. F. & Anderson, P. A polyadenylate binding protein localized to the granules of cytolytic lymphocytes induces DNA fragmentation in target cells. Cell 67, 629–639 (1991).

Gilks, N. Stress granule assembly is mediated by prion-like aggregation of TIA-1. Mol. Biol. Cell 15, 5383–5398 (2004).

El-Naggar, A. et al. Translational activation of HIF1α by YB-1 promotes sarcoma metastasis. Cancer Cell 27, 682–697 (2015).

Gehring, N. H., Lamprinaki, S., Hentze, M. W., Kulozik, A. E. & Bindereif, A. The hierarchy of exon-junction complex assembly by the spliceosome explains key features of mammalian nonsense-mediated mRNA decay. PLoS Biol. 7, e1000120 (2009).

Mendell, J. T., Sharifi, N. A., Meyers, J. L., Martinez-Murillo, F. & Dietz, H. C. Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat. Genet. 36, 1073–1078 (2004).

Kim, V. N. et al. The Y14 protein communicates to the cytoplasm the position of exon-exon junctions. EMBO J. 20, 2062–2068 (2001).

Kittler, R. et al. An endoribonuclease-prepared siRNA screen in human cells identifies genes essential for cell division. Nature 432, 1036–1040 (2004).

Somasekharan, S. P. et al. YB-1 regulates stress granule formation and tumor progression by translationally activating G3BP1. J. Cell Biol. 208, 913–929 (2015).

Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).

Meyer, L. R. et al. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res. 41, 64–69 (2013).

Li, H. et al. The sequence alignment/map format and samtools. Bioinformatics 25, 2078–2079 (2009).

Li, H. A statistical framework for snp calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987–2993 (2011).

Trapnell, C. et al. Differential gene and transcript expression analysis of rna-seq experiments with tophat and cufflinks. Nat. Protoc. 7, 562–578 (2012).

Cunningham, F. et al. Ensembl 2015. Nucleic Acids Res. 43, D662–D669 (2015).

Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edger: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).

Robinson, M. D. & Oshlack, A. A scaling normalization method for differential expression analysis of rna-seq data. Genome Biol. 11, R25 (2010).

Braunschweig, U. et al. Widespread intron retention in mammals functionally tunes transcriptomes. Genome Res. 24, 1774–1786 (2014).

Langfelder, P. & Horvath, S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinf. 9, 559 (2008).

Liberzon, A. et al. Molecular signatures database (msigdb) 3.0. Bioinformatics 27, 1739–1740 (2011).

Team, R. C. R: A Language and Environment for Statistical Computing. (R Foundation for Statistical Computing, Vienna, Austria, 2014).

Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003).

Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P.-L. & Ideker, T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27, 431–432 (2011).

Sorokin, A. V. et al. Proteasome-mediated cleavage of the Y-box-binding protein 1 is linked to DNA-damage stress response. EMBO J. 24, 3602–3612 (2005).

Lyons, S. M., Achorn, C., Kedersha, N. L., Anderson, P. J. & Ivanov, P. YB-1 regulates tiRNA-induced stress granule formation but not translational repression. Nucleic Acids Res. 44, 6949–6960 (2016).

Thông tin
Thông tin xuất bản

Communications Biology

Tập 2 Số 1

Thông tin tác giả