mRNA circularization by METTL3-eIF3h enhances translation and promotes oncogenesis

N6-methyladenosine (m6A) modification of mRNA is emerging as an important regulator of gene expression that affects different developmental and biological processes, and altered m6A homeostasis is linked to cancer1–5. m6A modification is catalysed by METTL3 and enriched in the 3′ untranslated region of a large subset of mRNAs at sites close to the stop codon5. METTL3 can promote translation but the mechanism and relevance of this process remain unknown1. Here we show that METTL3 enhances translation only when tethered to reporter mRNA at sites close to the stop codon, supporting a mechanism of mRNA looping for ribosome recycling and translational control. Electron microscopy reveals the topology of individual polyribosomes with single METTL3 foci in close proximity to 5′ cap-binding proteins. We identify a direct physical and functional interaction between METTL3 and the eukaryotic translation initiation factor 3 subunit h (eIF3h). METTL3 promotes translation of a large subset of oncogenic mRNAs—including bromodomain-containing protein 4—that is also m6A-modified in human primary lung tumours. The METTL3–eIF3h interaction is required for enhanced translation, formation of densely packed polyribosomes and oncogenic transformation. METTL3 depletion inhibits tumorigenicity and sensitizes lung cancer cells to BRD4 inhibition. These findings uncover a mechanism of translation control that is based on mRNA looping and identify METTL3–eIF3h as a potential therapeutic target for patients with cancer.METTL3, the enzyme responsible for m6A modification, influences translation by interacting with eIF3h to mediate looping between the regions near the stop codon and 5′ cap of mRNA.

[1]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[2]  J. Hershey,et al.  Individual Overexpression of Five Subunits of Human Translation Initiation Factor eIF3 Promotes Malignant Transformation of Immortal Fibroblast Cells* , 2007, Journal of Biological Chemistry.

[3]  R. Vale,et al.  Circularization of mRNA by eukaryotic translation initiation factors. , 1998, Molecular cell.

[4]  Samie R. Jaffrey,et al.  The dynamic epitranscriptome: N6-methyladenosine and gene expression control , 2014, Nature Reviews Molecular Cell Biology.

[5]  Lan Lin,et al.  rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data , 2014, Proceedings of the National Academy of Sciences.

[6]  Gianluca Bontempi,et al.  TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data , 2015, Nucleic acids research.

[7]  N. Sonenberg,et al.  A newly identified N‐terminal amino acid sequence of human eIF4G binds poly(A)‐binding protein and functions in poly(A)‐dependent translation , 1998, The EMBO journal.

[8]  Joachim Frank,et al.  Structure of mammalian eIF3 in the context of the 43S preinitiation complex , 2015, Nature.

[9]  Itay Mayrose,et al.  ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules , 2016, Nucleic Acids Res..

[10]  Michael J E Sternberg,et al.  The Phyre2 web portal for protein modeling, prediction and analysis , 2015, Nature Protocols.

[11]  J. Cate,et al.  eIF3 targets cell proliferation mRNAs for translational activation or repression , 2015, Nature.

[12]  R. Gregory,et al.  The m(6)A Methyltransferase METTL3 Promotes Translation in Human Cancer Cells. , 2016, Molecular cell.

[13]  Ke Liu,et al.  Structural basis for selective binding of m6A RNA by the YTHDC1 YTH domain. , 2014, Nature chemical biology.

[14]  Andrzej Kloczkowski,et al.  The GOR Method of Protein Secondary Structure Prediction and Its Application as a Protein Aggregation Prediction Tool. , 2017, Methods in molecular biology.

[15]  J. Hershey,et al.  An Oncogenic Role for the Phosphorylated h-Subunit of Human Translation Initiation Factor eIF3* , 2008, Journal of Biological Chemistry.

[16]  Junwei Shi,et al.  Promoter-bound METTL3 maintains myeloid leukaemia by m6A-dependent translation control , 2017, Nature.

[17]  Lai Wei,et al.  RNA N6‐methyladenosine methyltransferase‐like 3 promotes liver cancer progression through YTHDF2‐dependent posttranscriptional silencing of SOCS2 , 2018, Hepatology.

[18]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[19]  J. Hershey The role of eIF3 and its individual subunits in cancer. , 2015, Biochimica et biophysica acta.

[20]  Miao Yu,et al.  A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation , 2013, Nature chemical biology.

[21]  T. Jones,et al.  A siRNA screen identifies RAD21, EIF3H, CHRAC1 and TANC2 as driver genes within the 8q23, 8q24.3 and 17q23 amplicons in breast cancer with effects on cell growth, survival and transformation. , 2014, Carcinogenesis.

[22]  Francine E. Garrett-Bakelman,et al.  The N6-methyladenosine (m6A)-forming enzyme METTL3 controls myeloid differentiation of normal and leukemia cells , 2017, Nature Medicine.

[23]  Cécile E. Malnou,et al.  Free Poly(A) Stimulates Capped mRNA Translation in Vitro through the eIF4G-Poly(A)-binding Protein Interaction* , 2002, The Journal of Biological Chemistry.

[24]  Chuan He,et al.  N 6 -methyladenosine Modulates Messenger RNA Translation Efficiency , 2015, Cell.

[25]  Bronwen L. Aken,et al.  GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.

[26]  Zhike Lu,et al.  m6A-dependent regulation of messenger RNA stability , 2013, Nature.

[27]  J. Doudna,et al.  eIF3d is an mRNA cap-binding protein required for specialized translation initiation , 2016, Nature.

[28]  A. Sachs,et al.  Association of the yeast poly(A) tail binding protein with translation initiation factor eIF‐4G. , 1996, The EMBO journal.