Aly,, M. K., Ninomiya,, K., Adachi,, S., Natsume,, T., & Hirose,, T. (2019). Two distinct nuclear stress bodies containing different sets of RNA‐binding proteins are formed with HSATIII architectural noncoding RNAs upon thermal stress exposure. Biochemical and Biophysical Research Communications, 516(2), 419–423. https://doi.org/10.1016/j.bbrc.2019.06.061
Anderson,, D. M., Anderson,, K. M., Chang,, C.‐L., Makarewich,, C. A., Nelson,, B. R., McAnally,, J. R., … Olson,, E. N. (2015). A micropeptide encoded by a putative long noncoding RNA regulates muscle performance. Cell, 160(4), 595–606. https://doi.org/10.1016/j.cell.2015.01.009
Ash,, P. E. A., Bieniek,, K. F., Gendron,, T. F., Caulfield,, T., Lin,, W.‐L., DeJesus‐Hernandez,, M., … Petrucelli,, L. (2013). Unconventional translation of C9ORF72 GGGGCC expansion generates insoluble polypeptides specific to c9FTD/ALS. Neuron, 77(4), 639–646. https://doi.org/10.1016/j.neuron.2013.02.004
Balendra,, R., & Isaacs,, A. M. (2018). C9orf72‐mediated ALS and FTD: Multiple pathways to disease. Nature Reviews Neurology, 14(9), 544–558. https://doi.org/10.1038/s41582-018-0047-2
Batra,, R., Charizanis,, K., Manchanda,, M., Mohan,, A., Li,, M., Finn,, D. J., … Swanson,, M. S. (2014). Loss of MBNL leads to disruption of developmentally regulated alternative polyadenylation in RNA‐mediated disease. Molecular Cell, 56(2), 311–322. https://doi.org/10.1016/j.molcel.2014.08.027
Beermann,, J., Piccoli,, M.‐T., Viereck,, J., & Thum,, T. (2016). Non‐coding RNAs in development and disease: Background, mechanisms, and therapeutic approaches. Physiological Reviews, 96(4), 1297–1325. https://doi.org/10.1152/physrev.00041.2015
Bierhoff,, H., Dammert,, M. A., Brocks,, D., Dambacher,, S., Schotta,, G., & Grummt,, I. (2014). Quiescence‐induced LncRNAs trigger H4K20 Trimethylation and transcriptional silencing. Molecular Cell, 54(4), 675–682. https://doi.org/10.1016/j.molcel.2014.03.032
Blice‐Baum,, A. C., & Mihailescu,, M.‐R. (2014). Biophysical characterization of G‐quadruplex forming FMR1 mRNA and of its interactions with different fragile X mental retardation protein isoforms. RNA, 20(1), 103–114. https://doi.org/10.1261/rna.041442.113
Blythe,, A. J., Fox,, A. H., & Bond,, C. S. (2016). The ins and outs of lncRNA structure: How, why and what comes next? Biochimica et Biophysica Acta (BBA) ‐ Gene Regulatory Mechanisms, 1859(1), 46–58. https://doi.org/10.1016/j.bbagrm.2015.08.009
Brook,, J. D., McCurrach,, M. E., Harley,, H. G., Buckler,, A. J., Church,, D., Aburatani,, H., … Hudson,, T. (1992). Molecular basis of myotonic dystrophy: Expansion of a trinucleotide (CTG) repeat at the 3′ end of a transcript encoding a protein kinase family member. Cell, 68(4), 799–808. https://doi.org/10.1016/0092-8674(92)90154-5
Burberry,, A., Wells,, M. F., Limone,, F., Couto,, A., Smith,, K. S., Keaney,, J., … Eggan,, K. (2020). C9orf72 suppresses systemic and neural inflammation induced by gut bacteria. Nature, 582(7810), 89–94. https://doi.org/10.1038/s41586-020-2288-7
Cai,, X., & Cullen,, B. R. (2007). The imprinted H19 noncoding RNA is a primary microRNA precursor. RNA, 13(3), 313–316. https://doi.org/10.1261/rna.351707
Cao,, X., & Slavoff,, S. A. (2020). Non‐AUG start codons: Expanding and regulating the small and alternative ORFeome. Experimental Cell Research, 391(1), 111973. https://doi.org/10.1016/j.yexcr.2020.111973
Carrieri,, C., Cimatti,, L., Biagioli,, M., Beugnet,, A., Zucchelli,, S., Fedele,, S., … Gustincich,, S. (2012). Long non‐coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature, 491(7424), 454–457. https://doi.org/10.1038/nature11508
Cerase,, A., Armaos,, A., Neumayer,, C., Avner,, P., Guttman,, M., & Tartaglia,, G. G. (2019). Phase separation drives X‐chromosome inactivation: A hypothesis. Nature Structural %26 Molecular Biology, 26(5), 331–334. https://doi.org/10.1038/s41594-019-0223-0
Chen,, J., Brunner,, A.‐D., Cogan,, J. Z., Nuñez,, J. K., Fields,, A. P., Adamson,, B., … Weissman,, J. S. (2020). Pervasive functional translation of noncanonical human open reading frames. Science, 367(6482), 1140–1146. https://doi.org/10.1126/science.aay0262
Childs‐Disney,, J. L., Yildirim,, I., Park,, H., Lohman,, J. R., Guan,, L., Tran,, T., … Disney,, M. D. (2013). Structure of the myotonic dystrophy type 2 RNA and designed small molecules that reduce toxicity. ACS Chemical Biology, 9(2), 538–550. https://doi.org/10.1021/cb4007387
Cid‐Samper,, F., Gelabert‐Baldrich,, M., Lang,, B., Lorenzo‐Gotor,, N., Ponti,, R. D., Severijnen,, L.‐A. W. F. M., … Tartaglia,, G. G. (2018). An integrative study of protein‐RNA condensates identifies scaffolding RNAs and reveals players in fragile X‐associated tremor/Ataxia syndrome. Cell Reports, 25(12), 3422–3434.e7. https://doi.org/10.1016/j.celrep.2018.11.076
Cooper‐Knock,, J., Walsh,, M. J., Higginbottom,, A., Highley,, J. R., Dickman,, M. J., Edbauer,, D., … Shaw,, P. J. (2014). Sequestration of multiple RNA recognition motif‐containing proteins by C9orf72 repeat expansions. Brain, 137(7), 2040–2051. https://doi.org/10.1093/brain/awu120
Dai,, B., Qiao,, L., Zhang,, M., Cheng,, L., Zhang,, L., Geng,, L., … Yang,, J. (2019). lncRNA AK054386 functions as a ceRNA to sequester miR‐199 and induce sustained endoplasmic reticulum stress in hepatic reperfusion injury. Oxidative Medicine and Cellular Longevity, 2019, 1–15. https://doi.org/10.1155/2019/8189079
DeJesus‐Hernandez,, M., Mackenzie,, I. R., Boeve,, B. F., Boxer,, A. L., Baker,, M., Rutherford,, N. J., … Rademakers,, R. (2011). Expanded GGGGCC Hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p‐linked FTD and ALS. Neuron, 72(2), 245–256. https://doi.org/10.1016/j.neuron.2011.09.011
Dere,, R., Napierala,, M., Ranum,, L. P. W., & Wells,, R. D. (2004). Hairpin structure‐forming propensity of the (CCTG·CAGG) Tetranucleotide repeats contributes to the genetic instability associated with myotonic dystrophy type 2. Journal of Biological Chemistry, 279(40), 41715–41726. https://doi.org/10.1074/jbc.m406415200
Diederichs,, S. (2014). The four dimensions of noncoding RNA conservation. Trends in Genetics, 30(4), 121–123. https://doi.org/10.1016/j.tig.2014.01.004
Dunham,, I., Kundaje,, A., Aldred,, S. F., Collins,, P. J., Davis,, C. A., Doyle,, F., … Birney,, E. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414), 57–74. https://doi.org/10.1038/nature11247
Emmrich,, S., Streltsov,, A., Schmidt,, F., Thangapandi,, V., Reinhardt,, D., & Klusmann,, J.‐H. (2014). LincRNAs MONC and MIR100HG act as oncogenes in acute megakaryoblastic leukemia. Molecular Cancer, 13(1), 171. https://doi.org/10.1186/1476-4598-13-171
Erdel,, F., & Rippe,, K. (2018). Formation of chromatin subcompartments by phase separation. Biophysical Journal, 114(10), 2262–2270. https://doi.org/10.1016/j.bpj.2018.03.011
Fay,, M. M., Anderson,, P. J., & Ivanov,, P. (2017). ALS/FTD‐associated C9ORF72 repeat RNA promotes phase transitions in vitro and in cells. Cell Reports, 21(12), 3573–3584. https://doi.org/10.1016/j.celrep.2017.11.093
Fickett,, J. W. (1982). Recognition of protein coding regions in DNA sequences. Nucleic Acids Research, 10(17), 5303–5318. https://doi.org/10.1093/nar/10.17.5303
Fratta,, P., Mizielinska,, S., Nicoll,, A. J., Zloh,, M., Fisher,, E. M. C., Parkinson,, G., & Isaacs,, A. M. (2012). C9orf72 hexanucleotide repeat associated with amyotrophic lateral sclerosis and frontotemporal dementia forms RNA G‐quadruplexes. Scientific Reports, 2(1), 1016. https://doi.org/10.1038/srep01016
Gloss,, B. S., & Dinger,, M. E. (2016). The specificity of long noncoding RNA expression. Biochimica et Biophysica Acta (BBA) ‐ Gene Regulatory Mechanisms, 1859(1), 16–22. https://doi.org/10.1016/j.bbagrm.2015.08.005
Green,, K. M., Glineburg,, M. R., Kearse,, M. G., Flores,, B. N., Linsalata,, A. E., Fedak,, S. J., … Todd,, P. K. (2017). RAN translation at C9orf72‐associated repeat expansions is selectively enhanced by the integrated stress response. Nature Communications, 8(1), 2005. https://doi.org/10.1038/s41467-017-02200-0
Green,, K. M., Linsalata,, A. E., & Todd,, P. K. (2016). RAN translation—What makes it run? Brain Research, 1647, 30–42. https://doi.org/10.1016/j.brainres.2016.04.003
Guo,, G., Kang,, Q., Zhu,, X., Chen,, Q., Wang,, X., Chen,, Y., … Chen,, J.‐L. (2015). A long noncoding RNA critically regulates Bcr‐Abl‐mediated cellular transformation by acting as a competitive endogenous RNA. Oncogene, 34(14), 1768–1779. https://doi.org/10.1038/onc.2014.131
HafezQorani,, S., Houdjedj,, A., Arici,, M., Said,, A., & Kazan,, H. (2019). RBPSponge: Genome‐wide identification of lncRNAs that sponge RBPs. Bioinformatics, 35(22), 4760–4763. https://doi.org/10.1093/bioinformatics/btz448
Handa,, V., Saha,, T., & Usdin,, K. (2003). The fragile X syndrome repeats form RNA hairpins that do not activate the interferon‐inducible protein kinase, PKR, but are cut by Dicer. Nucleic Acids Research, 31(21), 6243–6248. https://doi.org/10.1093/nar/gkg818
Hautbergue,, G. M., Castelli,, L. M., Ferraiuolo,, L., Sanchez‐Martinez,, A., Cooper‐Knock,, J., Higginbottom,, A., … Shaw,, P. J. (2017). SRSF1‐dependent nuclear export inhibition of C9ORF72 repeat transcripts prevents neurodegeneration and associated motor deficits. Nature Communications, 8(1), 16063. https://doi.org/10.1038/ncomms16063
HGNC Database, 2020. HUGO Gene Nomenclature Committee (HGNC), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL‐EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom. www.genenames.org. Retrieval from https://www.genenames.org/data/genegroup/#!/group/1688
Ho,, T. H., Bundman,, D., Armstrong,, D. L., & Cooper,, T. A. (2005). Transgenic mice expressing CUG‐BP1 reproduce splicing mis‐regulation observed in myotonic dystrophy. Human Molecular Genetics, 14(11), 1539–1547. https://doi.org/10.1093/hmg/ddi162
Holt,, I., Mittal,, S., Furling,, D., Butler‐Browne,, G. S., Brook,, J. D., & Morris,, G. E. (2007). Defective mRNA in myotonic dystrophy accumulates at the periphery of nuclear splicing speckles. Genes to Cells, 12(9), 1035–1048. https://doi.org/10.1111/j.1365-2443.2007.01112.x
Huang,, Y.‐S., Chang,, C.‐C., Lee,, S.‐S., Jou,, Y.‐S., & Shih,, H.‐M. (2016). Xist reduction in breast cancer upregulates AKT phosphorylation via HDAC3‐mediated repression of PHLPP1 expression. Oncotarget, 7(28), 43256–43266. https://doi.org/10.18632/oncotarget.9673
Ingolia,, N. T., Lareau,, L. F., & Weissman,, J. S. (2011). Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell, 147(4), 789–802. https://doi.org/10.1016/j.cell.2011.10.002
Jackson,, R., Kroehling,, L., Khitun,, A., Bailis,, W., Jarret,, A., York,, A. G., … Flavell,, R. A. (2018). The translation of non‐canonical open reading frames controls mucosal immunity. Nature, 564(7736), 434–438. https://doi.org/10.1038/s41586-018-0794-7
Jain,, A., & Vale,, R. D. (2017). RNA phase transitions in repeat expansion disorders. Nature, 546(7657), 243–247. https://doi.org/10.1038/nature22386
Ji,, Z., Song,, R., Regev,, A., & Struhl,, K. (2015). Many lncRNAs, 5′UTRs, and pseudogenes are translated and some are likely to express functional proteins. eLife, 4, e08890. https://doi.org/10.7554/elife.08890
Jiang,, H., Mankodi,, A., Swanson,, M. S., Moxley,, R. T., & Thornton,, C. A. (2004). Myotonic dystrophy type 1 is associated with nuclear foci of mutant RNA, sequestration of muscleblind proteins and deregulated alternative splicing in neurons. Human Molecular Genetics, 13(24), 3079–3088. https://doi.org/10.1093/hmg/ddh327
Jones,, K., Wei,, C., Iakova,, P., Bugiardini,, E., Schneider‐Gold,, C., Meola,, G., … Timchenko,, L. T. (2012). GSK3β mediates muscle pathology in myotonic dystrophy. Journal of Clinical Investigation, 122(12), 4461–4472. https://doi.org/10.1172/jci64081
Jones,, K., Wei,, C., Schoser,, B., Meola,, G., Timchenko,, N., & Timchenko,, L. (2015). Reduction of toxic RNAs in myotonic dystrophies type 1 and type 2 by the RNA helicase p68/DDX5. Proceedings of the National Academy of Sciences, 112(26), 8041–8045. https://doi.org/10.1073/pnas.1422273112
Karreth,, F. A., Tay,, Y., Perna,, D., Ala,, U., Tan,, S. M., Rust,, A. G., … Pandolfi,, P. P. (2011). In vivo identification of tumor‐ suppressive PTEN ceRNAs in an oncogenic BRAF‐induced mouse model of melanoma. Cell, 147(2), 382–395. https://doi.org/10.1016/j.cell.2011.09.032
Kearse,, M. G., Green,, K. M., Krans,, A., Rodriguez,, C. M., Linsalata,, A. E., Goldstrohm,, A. C., & Todd,, P. K. (2016). CGG repeat‐associated non‐AUG translation utilizes a cap‐dependent scanning mechanism of initiation to produce toxic proteins. Molecular Cell, 62(2), 314–322. https://doi.org/10.1016/j.molcel.2016.02.034
Kim,, D.‐H., Langlois,, M.‐A., Lee,, K.‐B., Riggs,, A. D., Puymirat,, J., & Rossi,, J. J. (2005). HnRNP H inhibits nuclear export of mRNA containing expanded CUG repeats and a distal branch point sequence. Nucleic Acids Research, 33(12), 3866–3874. https://doi.org/10.1093/nar/gki698
Kim,, D. H., Marinov,, G. K., Pepke,, S., Singer,, Z. S., He,, P., Williams,, B., … Wold,, B. J. (2015). Single‐cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming. Cell Stem Cell, 16(1), 88–101. https://doi.org/10.1016/j.stem.2014.11.005
Kim,, Y.‐K., Kim,, B., & Kim,, V. N. (2016). Re‐evaluation of the roles of DROSHA, Exportin 5, and DICER in microRNA biogenesis. Proceedings of the National Academy of Sciences, 113(13), E1881–E1889. https://doi.org/10.1073/pnas.1602532113
Kong,, X., Duan,, Y., Sang,, Y., Li,, Y., Zhang,, H., Liang,, Y., … Yang,, Q. (2019). LncRNA–CDC6 promotes breast cancer progression and function as ceRNA to target CDC6 by sponging microRNA‐215. Journal of Cellular Physiology, 234(6), 9105–9117. https://doi.org/10.1002/jcp.27587
Koscianska,, E., Witkos,, T. M., Kozlowska,, E., Wojciechowska,, M., & Krzyzosiak,, W. J. (2015). Cooperation meets competition in microRNA‐mediated DMPK transcript regulation. Nucleic Acids Research, 43(19), 9500–9518. https://doi.org/10.1093/nar/gkv849
Kraan,, C. M., Godler,, D. E., & Amor,, D. J. (2019). Epigenetics of fragile X syndrome and fragile X‐related disorders. Developmental Medicine %26 Child Neurology, 61(2), 121–127. https://doi.org/10.1111/dmcn.13985
Krause,, H. M. (2018). New and prospective roles for lncRNAs in organelle formation and function. Trends in Genetics, 34(10), 736–745. https://doi.org/10.1016/j.tig.2018.06.005
Kremer,, E., Pritchard,, M., Lynch,, M., Yu,, S., Holman,, K., Baker,, E., … Richards,, R. (1991). Mapping of DNA instability at the fragile X to a trinucleotide repeat sequence p(CCG)n. Science, 252(5013), 1711–1714. https://doi.org/10.1126/science.1675488
Krol,, J., Fiszer,, A., Mykowska,, A., Sobczak,, K., de Mezer,, M., & Krzyzosiak,, W. J. (2007). Ribonuclease Dicer cleaves triplet repeat hairpins into shorter repeats that silence specific targets. Molecular Cell, 25(4), 575–586. https://doi.org/10.1016/j.molcel.2007.01.031
Kumar,, A., Park,, H., Fang,, P., Parkesh,, R., Guo,, M., Nettles,, K. W., & Disney,, M. D. (2011). Myotonic dystrophy type 1 RNA crystal structures reveal heterogeneous 1 × 1 nucleotide UU internal loop conformations. Biochemistry, 50(45), 9928–9935. https://doi.org/10.1021/bi2013068
Kuyumcu‐Martinez,, N. M., Wang,, G.‐S., & Cooper,, T. A. (2007). Increased steady‐state levels of CUGBP1 in myotonic dystrophy 1 are due to PKC‐mediated hyperphosphorylation. Molecular Cell, 28(1), 68–78. https://doi.org/10.1016/j.molcel.2007.07.027
Laurent,, F.‐X., Sureau,, A., Klein,, A. F., Trouslard,, F., Gasnier,, E., Furling,, D., & Marie,, J. (2012). New function for the RNA helicase p68/DDX5 as a modifier of MBNL1 activity on expanded CUG repeats. Nucleic Acids Research, 40(7), 3159–3171. https://doi.org/10.1093/nar/gkr1228
Lee,, Y.‐B., Chen,, H.‐J., Peres,, J. N., Gomez‐Deza,, J., Attig,, J., Štalekar,, M., … Shaw,, C. E. (2013). Hexanucleotide repeats in ALS/FTD form length‐dependent RNA foci, sequester RNA binding proteins, and are neurotoxic. Cell Reports, 5(5), 1178–1186. https://doi.org/10.1016/j.celrep.2013.10.049
Li,, Q., Dong,, C., Cui,, J., Wang,, Y., & Hong,, X. (2018). Over‐expressed lncRNA HOTAIRM1 promotes tumor growth and invasion through up‐regulating HOXA1 and sequestering G9a/EZH2/Dnmts away from the HOXA1 gene in glioblastoma multiforme. Journal of Experimental %26 Clinical Cancer Research, 37(1), 265. https://doi.org/10.1186/s13046-018-0941-x
Lin,, X., Miller,, J. W., Mankodi,, A., Kanadia,, R. N., Yuan,, Y., Moxley,, R. T., … Thornton,, C. A. (2006). Failure of MBNL1‐dependent post‐natal splicing transitions in myotonic dystrophy. Human Molecular Genetics, 15(13), 2087–2097. https://doi.org/10.1093/hmg/ddl132
Liquori,, C. L., Ricker,, K., Moseley,, M. L., Jacobsen,, J. F., Kress,, W., Naylor,, S. L., … Ranum,, L. P. W. (2001). Myotonic dystrophy type 2 caused by a CCTG expansion in intron 1 of ZNF9. Science, 293(5531), 864–867. https://doi.org/10.1126/science.1062125
Liu,, C., Peng,, Z., Li,, P., Fu,, H., Feng,, J., Zhang,, Y., … Wu,, M. (2020). LncRNA RMST suppressed GBM cells mitophagy through enhancing FUS SUMOylation. Molecular Therapy ‐ Nucleic Acids, 19, 1198–1208. https://doi.org/10.1016/j.omtn.2020.01.008
Liu,, S. J., Nowakowski,, T. J., Pollen,, A. A., Lui,, J. H., Horlbeck,, M. A., Attenello,, F. J., … Lim,, D. A. (2016). Single‐cell analysis of long non‐coding RNAs in the developing human neocortex. Genome Biology, 17(1), 67. https://doi.org/10.1186/s13059-016-0932-1
Liu,, X., Xiao,, Z.‐D., Han,, L., Zhang,, J., Lee,, S.‐W., Wang,, W., … Gan,, B. (2016). LncRNA NBR2 engages a metabolic checkpoint by regulating AMPK under energy stress. Nature Cell Biology, 18(4), 431–442. https://doi.org/10.1038/ncb3328
Liu,, X., Zhu,, Q., Guo,, Y., Xiao,, Z., Hu,, L., & Xu,, Q. (2019). LncRNA LINC00689 promotes the growth, metastasis and glycolysis of glioma cells by targeting miR‐338‐3p/PKM2 axis. Biomedicine %26 Pharmacotherapy, 117, 109069. https://doi.org/10.1016/j.biopha.2019.109069
Lu,, S., Zhang,, J., Lian,, X., Sun,, L., Meng,, K., Chen,, Y., … He,, Q.‐Y. (2019). A hidden human proteome encoded by ‘non‐coding’ genes. Nucleic Acids Research, 47(15), 8111–8125. https://doi.org/10.1093/nar/gkz646
Lu,, Z., Zhang,, Q. C., Lee,, B., Flynn,, R. A., Smith,, M. A., Robinson,, J. T., … Chang,, H. Y. (2016). RNA duplex map in living cells reveals higher‐order transcriptome structure. Cell, 165(5), 1267–1279. https://doi.org/10.1016/j.cell.2016.04.028
Luo,, S., Lu,, J. Y., Liu,, L., Yin,, Y., Chen,, C., Han,, X., … Shen,, X. (2016). Divergent lncRNAs regulate gene expression and lineage differentiation in pluripotent cells. Cell Stem Cell, 18(5), 637–652. https://doi.org/10.1016/j.stem.2016.01.024
Ma,, L., Sun,, X., Kuai,, W., Hu,, J., Yuan,, Y., Feng,, W., & Lu,, X. (2019). LncRNA SOX2 overlapping transcript acts as a miRNA sponge to promote the proliferation and invasion of Ewing`s sarcoma. American Journal of Translational Research, 11(6), 3841–3849 Retrieved from https://pubmed.ncbi.nlm.nih.gov/31312393
Ma,, L., Cao,, J., Liu,, L., Du,, Q., Li,, Z., Zou,, D., … Zhang,, Z. (2018). LncBook: A curated knowledgebase of human long non‐coding RNAs. Nucleic Acids Research, 47(D1), gky960. https://doi.org/10.1093/nar/gky960
Maida,, Y., Yasukawa,, M., Furuuchi,, M., Lassmann,, T., Possemato,, R., Okamoto,, N., … Masutomi,, K. (2009). An RNA‐dependent RNA polymerase formed by TERT and the RMRP RNA. Nature, 461(7261), 230–235. https://doi.org/10.1038/nature08283
Mao,, C., Wang,, X., Liu,, Y., Wang,, M., Yan,, B., Jiang,, Y., … Tao,, Y. (2018). A G3BP1‐interacting lncRNA promotes ferroptosis and apoptosis in cancer via nuclear sequestration of p53. Cancer Research, 78(13), 3484–3496. https://doi.org/10.1158/0008-5472.can-17-3454.
McCauley,, M. E., O`Rourke,, J. G., Yáñez,, A., Markman,, J. L., Ho,, R., Wang,, X., … Baloh,, R. H. (2020). C9orf72 in myeloid cells suppresses STING‐induced inflammation. Nature, 585(7823), 96–101. https://doi.org/10.1038/s41586-020-2625-x
Miller,, J. W., Urbinati,, C. R., Teng‐umnuay,, P., Stenberg,, M. G., Byrne,, B. J., Thornton,, C. A., & Swanson,, M. S. (2000). Recruitment of human muscleblind proteins to (CUG)n expansions associated with myotonic dystrophy. The EMBO Journal, 19(17), 4439–4448. https://doi.org/10.1093/emboj/19.17.4439
Min,, K.‐W., Davila,, S., Zealy,, R. W., Lloyd,, L. T., Lee,, I. Y., Lee,, R., … Yoon,, J.‐H. (2017). eIF4E phosphorylation by MST1 reduces translation of a subset of mRNAs, but increases lncRNA translation. Biochimica et Biophysica Acta (BBA) ‐ Gene Regulatory Mechanisms, 1860(7), 761–772. https://doi.org/10.1016/j.bbagrm.2017.05.002
Mitrea,, D. M., & Kriwacki,, R. W. (2016). Phase separation in biology; functional organization of a higher order. Cell Communication and Signaling, 14(1), 1. https://doi.org/10.1186/s12964-015-0125-7
Mooers,, B. H., Logue,, J. S., & Berglund,, J. A. (2005). The structural basis of myotonic dystrophy from the crystal structure of CUG repeats. Proceedings of the National Academy of Sciences of the United States of America, 102(46), 16626–16631. https://doi.org/10.1073/pnas.0505873102
Morriss,, G. R., & Cooper,, T. A. (2017). Protein sequestration as a normal function of long noncoding RNAs and a pathogenic mechanism of RNAs containing nucleotide repeat expansions. Human Genetics, 136(9), 1247–1263. https://doi.org/10.1007/s00439-017-1807-6
Niu,, L., Lou,, F., Sun,, Y., Sun,, L., Cai,, X., Liu,, Z., … Wang,, H. (2020). A micropeptide encoded by lncRNA MIR155HG suppresses autoimmune inflammation via modulating antigen presentation. Science Advances, 6(21), eaaz2059. https://doi.org/10.1126/sciadv.aaz2059
Palazzo,, A. F., & Lee,, E. S. (2015). Non‐coding RNA: What is functional and what is junk? Frontiers in Genetics, 6, 2. https://doi.org/10.3389/fgene.2015.00002
Paul,, S., Dansithong,, W., Kim,, D., Rossi,, J., Webster,, N. J., Comai,, L., & Reddy,, S. (2006). Interaction of musleblind, CUG‐BP1 and hnRNP H proteins in DM1‐associated aberrant IR splicing. The EMBO Journal, 25(18), 4271–4283. https://doi.org/10.1038/sj.emboj.7601296
Pearson,, C. E. (2011). Repeat associated non‐ATG translation initiation: One DNA, two transcripts, seven Reading frames, potentially nine toxic entities! PLoS Genetics, 7(3), e1002018. https://doi.org/10.1371/journal.pgen.1002018
Peng,, W.‐X., Koirala,, P., & Mo,, Y.‐Y. (2017). LncRNA‐mediated regulation of cell signaling in cancer. Oncogene, 36(41), 5661–5667. https://doi.org/10.1038/onc.2017.184
Ponting,, C. P., Oliver,, P. L., & Reik,, W. (2009). Evolution and functions of long noncoding RNAs. Cell, 136(4), 629–641. https://doi.org/10.1016/j.cell.2009.02.006
Prasanth,, K. V., Rajendra,, T. K., Lal,, A. K., & Lakhotia,, S. C. (2000). Omega speckles ‐ a novel class of nuclear speckles containing hnRNPs associated with noncoding hsr‐omega RNA in Drosophila. Journal of Cell Science, 113(19), 3485. Retrieved from. http://jcs.biologists.org/content/113/19/3485.abstract
Qu,, L., Ding,, J., Chen,, C., Wu,, Z.‐J., Liu,, B., Gao,, Y., … Wang,, L.‐H. (2016). Exosome‐transmitted lncARSR promotes Sunitinib resistance in renal Cancer by acting as a competing endogenous RNA. Cancer Cell, 29(5), 653–668. https://doi.org/10.1016/j.ccell.2016.03.004
Ren,, J., Fu,, J., Ma,, T., Yan,, B., Gao,, R., An,, Z., & Wang,, D. (2018). LncRNA H19‐elevated LIN28B promotes lung cancer progression through sequestering miR‐196b. Cell Cycle, 17(11), 1372–1380. https://doi.org/10.1080/15384101.2018.1482137
Rivas,, E., Clements,, J., & Eddy,, S. R. (2017). A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs. Nature Methods, 14(1), 45–48. https://doi.org/10.1038/nmeth.4066
Rogler,, L. E., Kosmyna,, B., Moskowitz,, D., Bebawee,, R., Rahimzadeh,, J., Kutchko,, K., … Rogler,, C. E. (2014). Small RNAs derived from lncRNA RNase MRP have gene‐silencing activity relevant to human cartilage–Hair hypoplasia. Human Molecular Genetics, 23(2), 368–382. https://doi.org/10.1093/hmg/ddt427
Ruan,, X., Li,, P., Chen,, Y., Shi,, Y., Pirooznia,, M., Seifuddin,, F., … Cao,, H. (2020). In vivo functional analysis of non‐conserved human lncRNAs associated with cardiometabolic traits. Nature Communications, 11(1), 45. https://doi.org/10.1038/s41467-019-13688-z
Rybak‐Wolf,, A., Jens,, M., Murakawa,, Y., Herzog,, M., Landthaler,, M., & Rajewsky,, N. (2014). A variety of Dicer substrates in human and C. elegans. Cell, 159(5), 1153–1167. https://doi.org/10.1016/j.cell.2014.10.040
Salmena,, L., Poliseno,, L., Tay,, Y., Kats,, L., & Pandolfi,, P. P. (2011). A ceRNA hypothesis: The Rosetta Stone of a hidden RNA language? Cell, 146(3), 353–358. https://doi.org/10.1016/j.cell.2011.07.014
Santoro,, M., Fontana,, L., Masciullo,, M., Bianchi,, M. L. E., Rossi,, S., Leoncini,, E., … Silvestri,, G. (2015). Expansion size and presence of CCG/CTC/CGG sequence interruptions in the expanded CTG array are independently associated to hypermethylation at the DMPK locus in myotonic dystrophy type 1 (DM1). Biochimica et Biophysica Acta (BBA) ‐ Molecular Basis of Disease, 1852(12), 2645–2652. https://doi.org/10.1016/j.bbadis.2015.09.007
Sellier,, C., Rau,, F., Liu,, Y., Tassone,, F., Hukema,, R. K., Gattoni,, R., … Charlet‐Berguerand,, N. (2010). Sam68 sequestration and partial loss of function are associated with splicing alterations in FXTAS patients. The EMBO Journal, 29(7), 1248–1261. https://doi.org/10.1038/emboj.2010.21
Smola,, M. J., Christy,, T. W., Inoue,, K., Nicholson,, C. O., Friedersdorf,, M., Keene,, J. D., … Weeks,, K. M. (2016). SHAPE reveals transcript‐wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells. Proceedings of the National Academy of Sciences, 113(37), 10322–10327. https://doi.org/10.1073/pnas.1600008113
Spencer,, H. L., Sanders,, R., Boulberdaa,, M., Meloni,, M., Cochrane,, A., Spiroski,, A.‐M., … Baker,, A. H. (2020). The LINC00961 transcript and its encoded micropeptide SPAAR regulate endothelial cell function. Cardiovascular Research, 116, 1981–1994. https://doi.org/10.1093/cvr/cvaa008
Starck,, S. R., Tsai,, J. C., Chen,, K., Shodiya,, M., Wang,, L., Yahiro,, K., … Walter,, P. (2016). Translation from the 5′ untranslated region shapes the integrated stress response. Science, 351(6272), aad3867. https://doi.org/10.1126/science.aad3867
Su,, Z., Zhang,, Y., Gendron,, T. F., Bauer,, P. O., Chew,, J., Yang,, W. Y., … Disney,, M. D. (2014). Discovery of a biomarker and lead small molecules to target r(GGGGCC)‐associated defects in c9FTD/ALS. Neuron, 83(5), 1043–1050. https://doi.org/10.1016/j.neuron.2014.07.041
Tang,, J., Zhong,, G., Zhang,, H., Yu,, B., Wei,, F., Luo,, L., … Bi,, A. (2018). LncRNA DANCR upregulates PI3K/AKT signaling through activating serine phosphorylation of RXRA. Cell Death %26 Disease, 9(12), 1167. https://doi.org/10.1038/s41419-018-1220-7
Tavares,, R. C. A., Pyle,, A. M., & Somarowthu,, S. (2019). Phylogenetic analysis with improved parameters reveals conservation in lncRNA structures. Journal of Molecular Biology, 431(8), 1592–1603. https://doi.org/10.1016/j.jmb.2019.03.012
Thomson,, D. W., & Dinger,, M. E. (2016). Endogenous microRNA sponges: Evidence and controversy. Nature Reviews Genetics, 17(5), 272–283. https://doi.org/10.1038/nrg.2016.20
Tian,, B., White,, R. J., Xia,, T., Welle,, S., Turner,, D. H., Mathews,, M. B., & Thornton,, C. A. (2000). Expanded CUG repeat RNAs form hairpins that activate the double‐stranded RNA‐dependent protein kinase PKR. RNA, 6(1), 79–87. https://doi.org/10.1017/s1355838200991544
Todd,, P. K., Oh,, S. Y., Krans,, A., He,, F., Sellier,, C., Frazer,, M., … Paulson,, H. L. (2013). CGG repeat‐associated translation mediates neurodegeneration in fragile X tremor Ataxia syndrome. Neuron, 78(3), 440–455. https://doi.org/10.1016/j.neuron.2013.03.026
Ulitsky,, I., & Bartel,, D. P. (2013). lincRNAs: Genomics, evolution, and mechanisms. Cell, 154(1), 26–46. https://doi.org/10.1016/j.cell.2013.06.020
Uroda,, T., Anastasakou,, E., Rossi,, A., Teulon,, J.‐M., Pellequer,, J.‐L., Annibale,, P., … Marcia,, M. (2019). Conserved pseudoknots in lncRNA MEG3 are essential for stimulation of the p53 pathway. Molecular Cell, 75(5), 982–995. https://doi.org/10.1016/j.molcel.2019.07.025
van Cruchten,, R. T. P., Wieringa,, B., & Wansink,, D. G. (2019). Expanded CUG repeats in DMPK transcripts adopt diverse hairpin conformations without influencing the structure of the flanking sequences. RNA, 25(4), 481–495. https://doi.org/10.1261/rna.068940.118
Venter,, J. C., Adams,, M. D., Myers,, E. W., Li,, P. W., Mural,, R. J., Sutton,, G. G., … Zhu,, X. (2001). The sequence of the human genome. Science, 291(5507), 1304–1351. https://doi.org/10.1126/science.1058040
Wan,, G., Hu,, X., Liu,, Y., Han,, C., Sood,, A. K., Calin,, G. A., … Lu,, X. (2013). A novel non‐coding RNA lncRNA‐JADE connects DNA damage signalling to histone H4 acetylation. The EMBO Journal, 32(21), 2833–2847. https://doi.org/10.1038/emboj.2013.221
Wang,, C., Ge,, L., Wu,, J., Wang,, X., & Yuan,, L. (2018). MiR‐219 represses expression of dFMR1 in Drosophila melanogaster. Life Sciences, 218, 31–37. https://doi.org/10.1016/j.lfs.2018.12.008
Wang,, E. T., Ward,, A. J., Cherone,, J. M., Giudice,, J., Wang,, T. T., Treacy,, D. J., … Burge,, C. B. (2015). Antagonistic regulation of mRNA expression and splicing by CELF and MBNL proteins. Genome Research, 25(6), 858–871. https://doi.org/10.1101/gr.184390.114
Witkos,, T. M., Krzyzosiak,, W. J., Fiszer,, A., & Koscianska,, E. (2018). A potential role of extended simple sequence repeats in competing endogenous RNA crosstalk. RNA Biology, 15(11), 1399–1409. https://doi.org/10.1080/15476286.2018.1536593
Wu,, H., Yin,, Q.‐F., Luo,, Z., Yao,, R.‐W., Zheng,, C.‐C., Zhang,, J., … Chen,, L.‐L. (2016). Unusual processing generates SPA LncRNAs that sequester multiple RNA binding proteins. Molecular Cell, 64(3), 534–548. https://doi.org/10.1016/j.molcel.2016.10.007
Xing,, W., Xu,, W.‐Y., Chang,, L., Zhang,, K., & Wang,, S.‐R. (2020). SP1‐induced lncRNA LINC00689 overexpression contributes to osteosarcoma progression via the miR‐655/SOX18 axis. European Review for Medical and Pharmacological Sciences, 24(5), 2205–2217. https://doi.org/10.26355/eurrev_202003_20486
Xue,, Z., Hennelly,, S., Doyle,, B., Gulati,, A. A., Novikova,, I. V., Sanbonmatsu,, K. Y., & Boyer,, L. A. (2016). A G‐rich motif in the lncRNA Braveheart interacts with a zinc‐finger transcription factor to specify the cardiovascular lineage. Molecular Cell, 64(1), 37–50. https://doi.org/10.1016/j.molcel.2016.08.010
Yadava,, R. S., Foff,, E. P., Yu,, Q., Gladman,, J. T., Kim,, Y. K., Bhatt,, K. S., … Mahadevan,, M. S. (2015). TWEAK/Fn14, a pathway and novel therapeutic target in myotonic dystrophy. Human Molecular Genetics, 24(7), 2035–2048. https://doi.org/10.1093/hmg/ddu617
Yamazaki,, T., Nakagawa,, S., & Hirose,, T. (2020). Architectural RNAs for Membraneless nuclear body formation. Cold Spring Harbor Symposia on Quantitative Biology, 039404, 227–237. https://doi.org/10.1101/sqb.2019.84.039404
Yang,, F., Deng,, X., Ma,, W., Berletch,, J. B., Rabaia,, N., Wei,, G., … Disteche,, C. M. (2015). The lncRNA firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation. Genome Biology, 16(1), 52. https://doi.org/10.1186/s13059-015-0618-0
Yeasmin,, F., Yada,, T., & Akimitsu,, N. (2018). Micropeptides encoded in transcripts previously identified as long noncoding RNAs: A new chapter in transcriptomics and proteomics. Frontiers in Genetics, 9, 144. https://doi.org/10.3389/fgene.2018.00144
Yoon,, J.‐H., Abdelmohsen,, K., Kim,, J., Yang,, X., Martindale,, J. L., Tominaga‐Yamanaka,, K., … Gorospe,, M. (2013). Scaffold function of long non‐coding RNA HOTAIR in protein ubiquitination. Nature Communications, 4(1), 2939. https://doi.org/10.1038/ncomms3939
Yu,, Z., Teng,, X., & Bonini,, N. M. (2011). Triplet repeat–derived siRNAs enhance RNA–mediated toxicity in a Drosophila model for myotonic dystrophy. PLoS Genetics, 7(3), e1001340. https://doi.org/10.1371/journal.pgen.1001340
Yuan,, G., Liu,, B., Han,, W., & Zhao,, D. (2019). LncRNA‐MIR17HG mediated upregulation of miR‐17 and miR‐18a promotes colon cancer progression via activating Wnt/β‐catenin signaling. Translational Cancer Research, 8(4), 1097–1108. https://doi.org/10.21037/tcr.2019.06.20
Zhang,, K., Donnelly,, C. J., Haeusler,, A. R., Grima,, J. C., Machamer,, J. B., Steinwald,, P., … Rothstein,, J. D. (2015). The C9orf72 repeat expansion disrupts nucleocytoplasmic transport. Nature, 525(7567), 56–61. https://doi.org/10.1038/nature14973
Zhang,, Y.‐J., Gendron,, T. F., Grima,, J. C., Sasaguri,, H., Jansen‐West,, K., Xu,, Y.‐F., … Petrucelli,, L. (2016). C9ORF72 poly(GA) aggregates sequester and impair HR23 and nucleocytoplasmic transport proteins. Nature Neuroscience, 19(5), 668–677. https://doi.org/10.1038/nn.4272
Zhao,, Z., Sentürk,, N., Song,, C., & Grummt,, I. (2018). lncRNA PAPAS tethered to the rDNA enhancer recruits hypophosphorylated CHD4/NuRD to repress rRNA synthesis at elevated temperatures. Genes %26 Development, 32(11–12), 836–848. https://doi.org/10.1101/gad.311688.118
Zhou,, W., Ye,, X., Xu,, J., Cao,, M.‐G., Fang,, Z.‐Y., Li,, L.‐Y., … Xie,, D. (2017). The lncRNA H19 mediates breast cancer cell plasticity during EMT and MET plasticity by differentially sponging miR‐200b/c and let‐7b. Science Signaling, 10(483), eaak9557. https://doi.org/10.1126/scisignal.aak9557
Zongaro,, S., Hukema,, R., D`Antoni,, S., Davidovic,, L., Barbry,, P., Catania,, M. V., … Bardoni,, B. (2013). The 3′ UTR of FMR1 mRNA is a target of miR‐101, miR‐129‐5p and miR‐221: Implications for the molecular pathology of FXTAS at the synapse. Human Molecular Genetics, 22(10), 1971–1982. https://doi.org/10.1093/hmg/ddt044
Zu,, T., Cleary,, J. D., Liu,, Y., Bañez‐Coronel,, M., Bubenik,, J. L., Ayhan,, F., … Ranum,, L. P. W. (2017). RAN translation regulated by Muscleblind proteins in myotonic dystrophy type 2. Neuron, 95(6), 1292–1305. https://doi.org/10.1016/j.neuron.2017.08.039
Zu,, T., Gibbens,, B., Doty,, N. S., Gomes‐Pereira,, M., Huguet,, A., Stone,, M. D., … Ranum,, L. P. W. (2011). Non‐ATG–initiated translation directed by microsatellite expansions. Proceedings of the National Academy of Sciences, 108(1), 260–265. https://doi.org/10.1073/pnas.1013343108
Zumwalt,, M., Ludwig,, A., Hagerman,, P. J., & Dieckmann,, T. (2007). Secondary structure and dynamics of the r(CGG) repeat in the mRNA of the fragile X mental retardation 1(FMR1) gene. RNA Biology, 4(2), 93–100. https://doi.org/10.4161/rna.4.2.5039