A coding-independent function of gene and pseudogene mRNAs regulates tumour biology (original) (raw)
Salmena, L., Carracedo, A. & Pandolfi, P. P. Tenets of PTEN tumor suppression. Cell133, 403–414 (2008) ArticleCAS Google Scholar
Di Cristofano, A. et al. Impaired Fas response and autoimmunity in Pten+/− mice. Science285, 2122–2125 (1999) ArticleCAS Google Scholar
Trotman, L. C. et al. Pten dose dictates cancer progression in the prostate. PLoS Biol.1, e59 (2003) Article Google Scholar
Alimonti, A. et al. Subtle variations in Pten dose determine cancer susceptibility. Nature Genet. (2010)
Xiao, C. et al. Lymphoproliferative disease and autoimmunity in mice with increased miR-17–92 expression in lymphocytes. Nature Immunol.9, 405–414 (2008) ArticleCAS Google Scholar
Takakura, S. et al. Oncogenic role of miR-17–92 cluster in anaplastic thyroid cancer cells. Cancer Sci.99, 1147–1154 (2008) ArticleCAS Google Scholar
Lewis, B. P., Shih, I. H., Jones-Rhoades, M. W., Bartel, D. P. & Burge, C. B. Prediction of mammalian microRNA targets. Cell115, 787–798 (2003) ArticleCAS Google Scholar
Meng, F. et al. Involvement of human micro-RNA in growth and response to chemotherapy in human cholangiocarcinoma cell lines. Gastroenterology130, 2113–2129 (2006) ArticleCAS Google Scholar
Huse, J. T. et al. The PTEN-regulating microRNA miR-26a is amplified in high-grade glioma and facilitates gliomagenesis in vivo. Genes Dev.23, 1327–1337 (2009) ArticleCAS Google Scholar
Kato, M. et al. TGF-β activates Akt kinase through a microRNA-dependent amplifying circuit targeting PTEN. Nature Cell Biol.11, 881–889 (2009) ArticleCAS Google Scholar
Yang, H. et al. MicroRNA expression profiling in human ovarian cancer: miR-214 induces cell survival and cisplatin resistance by targeting PTEN. Cancer Res.68, 425–433 (2008) ArticleCAS Google Scholar
Fujii, G. H., Morimoto, A. M., Berson, A. E. & Bolen, J. B. Transcriptional analysis of the PTEN/MMAC1 pseudogene, ΨPTEN. Oncogene18, 1765–1769 (1999) ArticleCAS Google Scholar
D’Errico, I., Gadaleta, G. & Saccone, C. Pseudogenes in metazoa: origin and features. Brief. Funct. Genomics Proteomics3, 157–167 (2004) Article Google Scholar
Harrison, P. M., Zheng, D., Zhang, Z., Carriero, N. & Gerstein, M. Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. Nucleic Acids Res.33, 2374–2383 (2005) ArticleCAS Google Scholar
Birney, E. et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature447, 799–816 (2007) ArticleADSCAS Google Scholar
Bristow, J., Gitelman, S. E., Tee, M. K., Staels, B. & Miller, W. L. Abundant adrenal-specific transcription of the human P450c21A pseudogene. J. Biol. Chem.268, 12919–12924 (1993) CASPubMed Google Scholar
Suo, G. et al. Oct4 pseudogenes are transcribed in cancers. Biochem. Biophys. Res. Commun.337, 1047–1051 (2005) ArticleCAS Google Scholar
Bartel, D. P. MicroRNAs: target recognition and regulatory functions. Cell136, 215–233 (2009) ArticleCAS Google Scholar
Tay, Y., Zhang, J., Thomson, A. M., Lim, B. & Rigoutsos, I. MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature455, 1124–1128 (2008) ArticleADSCAS Google Scholar
Lal, A. et al. miR-24 inhibits cell proliferation by targeting E2F2, MYC, and other cell-cycle genes via binding to “seedless” 3′UTR microRNA recognition elements. Mol. Cell35, 610–625 (2009) ArticleCAS Google Scholar
Ventura, A. & Jacks, T. MicroRNAs and cancer: short RNAs go a long way. Cell136, 586–591 (2009) ArticleCAS Google Scholar
Cummins, J. M. et al. The colorectal microRNAome. Proc. Natl Acad. Sci. USA103, 3687–3692 (2006) ArticleADSCAS Google Scholar
Petrocca, F. et al. E2F1-regulated microRNAs impair TGFβ-dependent cell-cycle arrest and apoptosis in gastric cancer. Cancer Cell13, 272–286 (2008) ArticleCAS Google Scholar
Lu, Z. et al. MicroRNA-21 promotes cell transformation by targeting the programmed cell death 4 gene. Oncogene27, 4373–4379 (2008) ArticleCAS Google Scholar
Pain, D., Chirn, G. W., Strassel, C. & Kemp, D. M. Multiple retropseudogenes from pluripotent cell-specific gene expression indicates a potential signature for novel gene identification. J. Biol. Chem.280, 6265–6268 (2005) ArticleCAS Google Scholar
van der Wal, J. E. et al. Comparative genomic hybridisation divides retinoblastomas into a high and a low level chromosomal instability group. J. Clin. Pathol.56, 26–30 (2003) ArticleCAS Google Scholar
Zimonjic, D. B., Keck, C. L., Thorgeirsson, S. S. & Popescu, N. C. Novel recurrent genetic imbalances in human hepatocellular carcinoma cell lines identified by comparative genomic hybridization. Hepatology29, 1208–1214 (1999) ArticleCAS Google Scholar
Plantaz, D. et al. Gain of chromosome 17 is the most frequent abnormality detected in neuroblastoma by comparative genomic hybridization. Am. J. Pathol.150, 81–89 (1997) CASPubMedPubMed Central Google Scholar
Tam, O. H. et al. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature453, 534–538 (2008) ArticleADSCAS Google Scholar
Okamura, K., Chung, W. J. & Lai, E. C. The long and short of inverted repeat genes in animals: microRNAs, mirtrons and hairpin RNAs. Cell Cycle7, 2840–2845 (2008) ArticleCAS Google Scholar
Robine, N. et al. A broadly conserved pathway generates 3′UTR-directed primary piRNAs. Curr. Biol.19, 2066–2076 (2009) ArticleCAS Google Scholar
Franco-Zorrilla, J. M. et al. Target mimicry provides a new mechanism for regulation of microRNA activity. Nature Genet.39, 1033–1037 (2007) ArticleCAS Google Scholar
Ebert, M. S., Neilson, J. R. & Sharp, P. A. MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nature Methods4, 721–726 (2007) ArticleCAS Google Scholar
Lee, D. Y. et al. A 3′-untranslated region (3′UTR) induces organ adhesion by regulating miR-199a* functions. PLoS ONE4, e4527 (2009) ArticleADS Google Scholar
Gu, S., Jin, L., Zhang, F., Sarnow, P. & Kay, M. A. Biological basis for restriction of microRNA targets to the 3′ untranslated region in mammalian mRNAs. Nature Struct. Mol. Biol.16, 144–150 (2009) ArticleCAS Google Scholar
Balasubramanian, S. et al. Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes. Genome Biol.10, R2 (2009) Article Google Scholar
Winter, J., Jung, S., Keller, S., Gregory, R. I. & Diederichs, S. Many roads to maturity: microRNA biogenesis pathways and their regulation. Nature Cell Biol.11, 228–234 (2009) ArticleCAS Google Scholar
Kawahara, Y. et al. Redirection of silencing targets by adenosine-to-inosine editing of miRNAs. Science315, 1137–1140 (2007) ArticleADSCAS Google Scholar
Mayr, C. & Bartel, D. P. Widespread shortening of 3′UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell138, 673–684 (2009) ArticleCAS Google Scholar
Kim, J. & Bartel, D. P. Allelic imbalance sequencing reveals that single-nucleotide polymorphisms frequently alter microRNA-directed repression. Nature Biotechnol.27, 472–477 (2009) ArticleCAS Google Scholar
Guttman, M. et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature458, 223–227 (2009) ArticleADSCAS Google Scholar
Frith, M. C. et al. Pseudo-messenger RNA: phantoms of the transcriptome. PLoS Genet.2, e23 (2006) Article Google Scholar
Jiang, S. L., Lozanski, G., Samols, D. & Kushner, I. Induction of human serum amyloid A in Hep 3B cells by IL-6 and IL-1 beta involves both transcriptional and post-transcriptional mechanisms. J. Immunol.154, 825–831 (1995) CASPubMed Google Scholar
Scaglioni, P. P. & Pandolfi, P. P. The theory of APL revisited. Curr. Top. Microbiol. Immunol.313, 85–100 (2007) CASPubMed Google Scholar
Berger, M. F. et al. Integrative analysis of the melanoma transcriptome. Genome Res.20, 413–427 (2010) ArticleCAS Google Scholar
Stephens, P. J. et al. Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature462, 1005–1010 (2009) ArticleADSCAS Google Scholar
Maeda, T. et al. Role of the proto-oncogene Pokemon in cellular transformation and ARF repression. Nature433, 278–285 (2005) ArticleADSCAS Google Scholar
Myers, M. P. et al. P-TEN, the tumour suppressor from human chromosome 10q23, is a dual-specificity phosphatase. Proc. Natl Acad. Sci. USA94, 9052–9057 (1997) ArticleADSCAS Google Scholar
Drabkin, H. A. et al. Quantitative HOX expression in chromosomally defined subsets of acute myelogenous leukemia. Leukemia16, 186–195 (2002) ArticleCAS Google Scholar
Chen, C. et al. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res.33, e179 (2005) Article Google Scholar