New and Prospective Roles for lncRNAs in Organelle Formation and Function

Trends in Genetics - Tập 34 - Trang 736-745 - 2018
Henry M. Krause1
1Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada

Tài liệu tham khảo

Miao, 2017, Trends of long noncoding RNA research from 2007 to 2016: a bibliometric analysis, Oncotarget, 8, 83114, 10.18632/oncotarget.20851 Jandura, 2017, The new RNA world: growing evidence for long noncoding RNA functionality, Trends Genet., 33, 665, 10.1016/j.tig.2017.08.002 Kato, 2012, Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels, Cell, 149, 753, 10.1016/j.cell.2012.04.017 Mao, 2011, Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs, Nat. Cell Biol., 13, 95, 10.1038/ncb2140 Prasanth, 2000, Omega speckles – a novel class of nuclear speckles containing hnRNPs associated with noncoding hsr-omega RNA in Drosophila, J. Cell Sci., 113, 3485, 10.1242/jcs.113.19.3485 Biamonti, 2010, Nuclear stress bodies, Cold Spring Harb. Perspect. Biol., 2, 10.1101/cshperspect.a000695 Watanabe, 1994, S. pombe mei2+ encodes an RNA-binding protein essential for premeiotic DNA synthesis and meiosis I, which cooperates with a novel RNA species meiRNA, Cell, 78, 487, 10.1016/0092-8674(94)90426-X Audas, 2012, The nucleolar detention pathway: a cellular strategy for regulating molecular networks, Cell Cycle, 11, 2059, 10.4161/cc.20140 Mannen, 2016, The Sam68 nuclear body is composed of two RNase-sensitive substructures joined by the adaptor HNRNPL, J. Cell Biol., 214, 45, 10.1083/jcb.201601024 Shelkovnikova, 2014, Compromised paraspeckle formation as a pathogenic factor in FUSopathies, Hum. Mol. Genet., 23, 2298, 10.1093/hmg/ddt622 Jolly, 2006, Human sat III and Drosophila hsr omega transcripts: a common paradigm for regulation of nuclear RNA processing in stressed cells, Nucleic Acids Res., 34, 5508, 10.1093/nar/gkl711 Emmott, 2009, Nucleolar targeting: the hub of the matter, EMBO Rep., 10, 231, 10.1038/embor.2009.14 Audas, 2012, Immobilization of proteins in the nucleolus by ribosomal intergenic spacer noncoding RNA, Mol. Cell, 45, 147, 10.1016/j.molcel.2011.12.012 Chujo, 2016, Architectural RNAs (arcRNAs): a class of long noncoding RNAs that function as the scaffold of nuclear bodies, Biochim. Biophys. Acta, 1859, 139, 10.1016/j.bbagrm.2015.05.007 Wilusz, 2012, A triple helix stabilizes the 3′ ends of long noncoding RNAs that lack poly(A) tails, Genes Dev., 26, 2392, 10.1101/gad.204438.112 Souquere, 2010, Highly ordered spatial organization of the structural long noncoding NEAT1 RNAs within paraspeckle nuclear bodies, Mol. Biol. Cell, 21, 4020, 10.1091/mbc.e10-08-0690 West, 2016, Structural, super-resolution microscopy analysis of paraspeckle nuclear body organization, J. Cell Biol., 214, 817, 10.1083/jcb.201601071 Yamazaki, 2018, Functional domains of NEAT1 architectural lncRNA induce paraspeckle assembly through phase separation, Mol. Cell, 70, 1038, 10.1016/j.molcel.2018.05.019 Kanai, 2004, Kinesin transports RNA: isolation and characterization of an RNA-transporting granule, Neuron, 43, 513, 10.1016/j.neuron.2004.07.022 Andersen, 2002, Directed proteomic analysis of the human nucleolus, Curr. Biol., 12, 1, 10.1016/S0960-9822(01)00650-9 Jain, 2016, ATPase-modulated stress granules contain a diverse proteome and substructure, Cell, 164, 487, 10.1016/j.cell.2015.12.038 Trinkle-Mulcahy, 2017, The Cajal body and the nucleolus: ‘in a relationship’ or ‘it's complicated’?, RNA Biol., 14, 739, 10.1080/15476286.2016.1236169 Panas, 2016, Mechanistic insights into mammalian stress granule dynamics, J. Cell Biol., 215, 313, 10.1083/jcb.201609081 Van Treeck, 2018, RNA self-assembly contributes to stress granule formation and defining the stress granule transcriptome, Proc. Natl. Acad. Sci. U. S. A., 115, 2734, 10.1073/pnas.1800038115 Protter, 2016, Principles and properties of stress granules, Trends Cell Biol., 26, 668, 10.1016/j.tcb.2016.05.004 Khong, 2017, The stress granule transcriptome reveals principles of mRNA accumulation in stress granules, Mol. Cell, 68, 808, 10.1016/j.molcel.2017.10.015 Lee, 2016, Noncoding RNA NORAD regulates genomic stability by sequestering PUMILIO Proteins, Cell, 164, 69, 10.1016/j.cell.2015.12.017 Chujo, 2017, Unusual semi-extractability as a hallmark of nuclear body-associated architectural noncoding RNAs, EMBO J., 36, 1447, 10.15252/embj.201695848 Wilk, 2016, Diverse and pervasive subcellular distributions for both coding and long noncoding RNAs, Genes Dev., 30, 594, 10.1101/gad.276931.115 Cheng, 2005, Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution, Science, 308, 1149, 10.1126/science.1108625 Meijer, 2007, A novel method for poly(A) fractionation reveals a large population of mRNAs with a short poly(A) tail in mammalian cells, Nucleic Acids Res., 35, 10.1093/nar/gkm830 Yang, 2011, Genomewide characterization of non-polyadenylated RNAs, Genome Biol., 12, 14, 10.1186/gb-2011-12-2-r16 van Heesch, 2014, Extensive localization of long noncoding RNAs to the cytosol and mono- and polyribosomal complexes, Genome Biol., 15, R6, 10.1186/gb-2014-15-1-r6 Mercer, 2008, Specific expression of long noncoding RNAs in the mouse brain, Proc. Natl. Acad. Sci. U. S. A., 105, 716, 10.1073/pnas.0706729105 Khvorova, 1999, RNAs that bind and change the permeability of phospholipid membranes, Proc. Natl. Acad. Sci. U. S. A., 96, 10649, 10.1073/pnas.96.19.10649 Michanek, 2010, RNA and DNA interactions with zwitterionic and charged lipid membranes – a DSC and QCM-D study, Biochim. Biophys. Acta, 1798, 829, 10.1016/j.bbamem.2009.12.009 Janas, 2003, Visualization of membrane RNAs, RNA, 9, 1353, 10.1261/rna.5129803 Lin, 2017, The LINK-A lncRNA interacts with PtdIns(3,4,5)P3 to hyperactivate AKT and confer resistance to AKT inhibitors, Nat. Cell Biol., 19, 238, 10.1038/ncb3473 Lin, 2016, The LINK-A lncRNA activates normoxic HIF1alpha signalling in triple-negative breast cancer, Nat. Cell Biol., 18, 213, 10.1038/ncb3295 Kim, 2017, RNA in extracellular vesicles, Wiley Interdiscip. Rev. RNA, 8, 10.1002/wrna.1413 Raposo, 2013, Extracellular vesicles: exosomes, microvesicles, and friends, J. Cell Biol., 200, 373, 10.1083/jcb.201211138 Christianson, 2014, Exosome and microvesicle mediated phene transfer in mammalian cells, Semin. Cancer Biol., 28, 31, 10.1016/j.semcancer.2014.04.007 Zhang, 2014, The emerging role of exosomes in Wnt secretion and transport, Curr. Opin. Genet. Dev., 27, 14, 10.1016/j.gde.2014.03.006 Thery, 2009, Membrane vesicles as conveyors of immune responses, Nat. Rev. Immunol., 9, 581, 10.1038/nri2567 Robbins, 2014, Regulation of immune responses by extracellular vesicles, Nat. Rev. Immunol., 14, 195, 10.1038/nri3622 Azmi, 2013, Exosomes in cancer development, metastasis, and drug resistance: a comprehensive review, Cancer Metastasis Rev., 32, 623, 10.1007/s10555-013-9441-9 Huang, 2013, Characterization of human plasma-derived exosomal RNAs by deep sequencing, BMC Genomics, 14, 319, 10.1186/1471-2164-14-319 Li, 2015, Plasma long noncoding RNA protected by exosomes as a potential stable biomarker for gastric cancer, Tumour Biol., 36, 2007, 10.1007/s13277-014-2807-y Sun, 2018, Emerging role of exosome-derived long non-coding RNAs in tumor microenvironment, Mol. Cancer, 17, 82, 10.1186/s12943-018-0831-z Arita, 2013, Circulating long non-coding RNAs in plasma of patients with gastric cancer, Anticancer Res., 33, 3185 Shi, 2016, Long noncoding RNAs as novel biomarkers have a promising future in cancer diagnostics, Dis. Markers, 2016, 10.1155/2016/9085195 Hou, 2017, Long noncoding RNA Braveheart promotes cardiogenic differentiation of mesenchymal stem cells in vitro, Stem Cell Res. Ther., 8, 4, 10.1186/s13287-016-0454-5 Jiang, 2016, Circulating long noncoding RNAs as novel biomarkers of human diseases, Biomark. Med., 10, 757, 10.2217/bmm-2016-0039 Bolha, 2017, Long noncoding RNAs as biomarkers in cancer, Dis. Markers, 2017, 10.1155/2017/7243968 Chen, 2017, Gene regulation in the immune system by long noncoding RNAs, Nat. Immunol., 18, 962, 10.1038/ni.3771 Corrigan, 2014, BMP-regulated exosomes from Drosophila male reproductive glands reprogram female behavior, J. Cell Biol., 206, 671, 10.1083/jcb.201401072 Ronquist, 1985, The prostasome: its secretion and function in man, Biochim. Biophys. Acta, 822, 203, 10.1016/0304-4157(85)90008-5 Asea, 2008, Heat shock protein-containing exosomes in mid-trimester amniotic fluids, J. Reprod. Immunol., 79, 12, 10.1016/j.jri.2008.06.001 Admyre, 2007, Exosomes with immune modulatory features are present in human breast milk, J. Immunol., 179, 1969, 10.4049/jimmunol.179.3.1969 Kim, 2017, Mitochondrial noncoding RNA transport, BMB Rep., 50, 164, 10.5483/BMBRep.2017.50.4.013 Hrdlickova, 2014, Genetic variation in the non-coding genome: involvement of micro-RNAs and long non-coding RNAs in disease, Biochim. Biophys. Acta, 1842, 1910, 10.1016/j.bbadis.2014.03.011 Eisenberg, 2012, The amyloid state of proteins in human diseases, Cell, 148, 1188, 10.1016/j.cell.2012.02.022 Lo Piccolo, 2017, FUS toxicity is rescued by the modulation of lncRNA hsromega expression in Drosophila melanogaster, Sci. Rep., 7, 10.1038/s41598-017-15944-y Sengupta, 2006, Altered expressions of the noncoding hsromega gene enhances poly-Q-induced neurotoxicity in Drosophila, RNA Biol., 3, 28, 10.4161/rna.3.1.2559 Rajendran, 2006, Alzheimer’s disease beta-amyloid peptides are released in association with exosomes, Proc. Natl. Acad. Sci. U. S. A., 103, 11172, 10.1073/pnas.0603838103 Corey, 2017, Nusinersen, an antisense oligonucleotide drug for spinal muscular atrophy, Nat. Neurosci., 20, 497, 10.1038/nn.4508