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RNA Secondary Structures in Neurodegeneration

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Autism Spectrum Disorder and Alzheimer's Disease

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Abstract

RNA is hierarchically organized, and its 3D structure can be described at different levels. Instead of the long helices formed by two perfectly complementary strands of DNA, an RNA chain folds back on itself to form short stretches of helical regions interrupted by bulges, internal loops, hairpin loops, or multi-way junctions. While RNA plays a significant role in several biological processes, including translation, catalysis, and gene regulation, the RNA secondary structure’s prediction is crucial for the identification and formulation of the RNA functionality. The second level of RNA hierarchical structure is RNA acting as a key factor in the posttranscriptional regulation and the noncoding RNA functions. This chapter reviews the representation, visualization, and mathematical formulation mostly of RNA secondary structures, which can be viewed as steps toward the three-dimensional prediction modeling and their role in neurodegeneration.

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References

  • Akutsu T (2000) Dynamic programming algorithms for RNA secondary structure with pseudoknots. Discrete Appl Math 104:45–62

    Google Scholar 

  • Alexiou A, Nizami B, Khan FI, Soursou G, Vairaktarakis C, Chatzichronis S, Tsiamis V, Manztavinos V, Yarla NS, Ashraf GM (2018a) Mitochondrial dynamics and proteins related to neurodegenerative diseases. Curr Protein Pept Sci 19:850

    CAS  PubMed  Google Scholar 

  • Alexiou A, Soursou G, Chatzichronis S, Gasparatos E, Kamal MA, Yarla NS, Perveen A, Barreto G, Ashraf GM (2018b) GTPases role in the regulation of mitochondrial dynamics in Alzheimer’s disease and CNS related disorders. Mol Neurobiol 56(6):4530–4538

    PubMed  Google Scholar 

  • Alexiou A, Soursou G, Yarla NS, Ashraf GM (2018c) Proteins commonly linked to autism spectrum disorder and Alzheimer’s disease. Curr Protein Pept Sci 19:876

    CAS  PubMed  Google Scholar 

  • Alexiou A, Chatzichronis S, Asma P, Abdul H, Ashraf GM (2019) Algorithmic and stochastic representations of gene regulatory networks and protein-protein interactions. Curr Top Med Chem 19:1

    Google Scholar 

  • Alkan C, Karakoc E, Nadeau J, Sahinalp S, Zhang K (2006) RNA-RNA interaction prediction and antisense RNA target search. J Comput Biol 13(2):267–282

    CAS  PubMed  Google Scholar 

  • Ashraf GM, Ganash M, Alexiou A (2019) Computational analysis of non-coding RNAs in Alzheimer’s disease. Bioinformation 15(5):351–357

    PubMed  PubMed Central  Google Scholar 

  • Baillie JK, Barnett MW, Upton KR, Gerhardt DJ, Richmond TA, De Sapio F, Brennan PM, Rizzu P, Smith S, Fell M et al (2011) Somatic retrotransposition alters the genetic landscape of the human brain. Nature 479:534–537

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bellaousov S, Mathews DH (2010) ProbKnot: fast prediction of RNA secondary structure including pseudoknots. RNA 16:1870–1880

    CAS  PubMed  PubMed Central  Google Scholar 

  • Borghi R, Patriarca S, Traverso N et al (2007) The increased activity of BACE1 correlates with oxidative stress in Alzheimer’s disease. Neurobiol Aging 28(7):1009–1014

    CAS  PubMed  Google Scholar 

  • Briggs JA, Wolvetang EJ, Mattick JS et al (2015) Mechanisms of long non-coding RNAs in mammalian nervous system development, plasticity, disease, and evolution. Neuron 88(5):861–877

    CAS  PubMed  Google Scholar 

  • Ciarlo E, Massone S, Penna I et al (2013) An intronic ncRNA-dependent regulation of SORL1 expression affecting Abeta formation is upregulated in post-mortem Alzheimer’s disease brain samples. Dis Model Mech 6(2):424–433

    CAS  PubMed  Google Scholar 

  • Dash R, Emran TB, Uddin MM, Islam A, Junaid M (2014) Molecular docking of fisetin with AD associated AChE, ABAD and BACE1 proteins. Bioinformation 10(9):562–568

    PubMed  PubMed Central  Google Scholar 

  • Decourt B, Sabbagh MN (2011) BACE1 as a potential biomarker for Alzheimer’s disease. J Alzheimers Dis 24(Suppl 2):53–59

    CAS  PubMed  PubMed Central  Google Scholar 

  • Deininger PL, Batzer MA (1999) Alu repeats and human disease. Mol Genet Metab 67:183–193

    CAS  PubMed  Google Scholar 

  • Derrien T, Guigo R, Johnson R (2011) The long non-coding RNAs: a new (P)layer in the “Dark Matter”. Front Genet 2:107

    PubMed  Google Scholar 

  • Derrien T, Johnson R, Bussotti G et al (2012) The GENCODE v7 catalog of human long non-coding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22(9):1775–1789

    CAS  PubMed  PubMed Central  Google Scholar 

  • Deschenes A (2005) A genetic algorithm for RNA secondary structure prediction using stacking energy thermodynamic models. Master’s Thesis, Simon Fraser University, Burnaby, British Columbia, Canada

    Google Scholar 

  • Deutsch E, Shapiro L (2002) A bijection between ordered trees and 2-Motzkin paths and its many consequences. Discrete Math 256:655–670

    Google Scholar 

  • Dislich B, Lichtenthaler SF (2012) The membrane-bound aspartyl protease BACE1: molecular and functional properties in Alzheimer’s disease and beyond. Front Physiol 3:8

    CAS  PubMed  PubMed Central  Google Scholar 

  • Do CB, Woods DA, Batzoglou S (2006) CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics 22:e90–e98

    CAS  PubMed  Google Scholar 

  • Donaghey R, Shapiro LW (1977) Motzkin numbers. J Combin Theory A 23:291–301

    Google Scholar 

  • Doslic T, Veljan D (2007) Secondary structures, plane trees and Motzkin numbers. Math Commun 12:163–169

    Google Scholar 

  • Eddy S (2004) How do RNA folding algorithms work? Nat Biotechnol 22:1457–1458. https://doi.org/10.1038/nbt1104-1457

    Article  CAS  PubMed  Google Scholar 

  • Evin G, Hince C (2013) BACE1 as a therapeutic target in Alzheimer’s disease: rationale and current status. Drugs Aging 30(10):755–764

    CAS  PubMed  Google Scholar 

  • Faghihi MA, Modarresi F, Khalil AM et al (2008a) Expression of a non-coding RNA is elevated in Alzheimer’s disease and drives rapid feedforward regulation of beta-secretase. Nat Med 14(7):723–730

    CAS  PubMed  PubMed Central  Google Scholar 

  • Faghihi MA, Modarresi F, Khalil AM, Wood DE, Sahagan BG, Morgan TE, Finch CE, Laurent GS, Kenny PJ, Wahlestedt C (2008b) Expression of a non-coding RNA is elevated in Alzheimer’s disease and drives rapid feedforward regulation of beta-secretase. Nat Med 14:723–730

    CAS  PubMed  PubMed Central  Google Scholar 

  • Faghihi MA, Zhang M, Huang J, Modarresi F, Van der Brug MP, Nalls MA, Cookson MR, St-Laurent G, Wahlestedt C (2010) Evidence for natural antisense transcript-mediated inhibition of microRNA function. Genome Biol 11

    Google Scholar 

  • Fukumoto H, Cheung BS, Hyman BT, Irizarry MC (2002) Beta-secretase protein and activity are increased in the neocortex in Alzheimer disease. Arch Neurol 59:1381–1389

    PubMed  Google Scholar 

  • Gacy AM, Goellner G, Juranić N, Macura S, McMurray CT (1995) Trinucleotide repeats that expand in human disease form hairpin structures in vitro. Cell 81:533–540

    CAS  PubMed  Google Scholar 

  • Gavazzo P, Vassalli M, Costa D, Pagano A (2013) Novel ncRNAs transcribed by Pol III and elucidation of their functional relevance by biophysical approaches. Front Cell Neurosci 7:203

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hajiaghayi M, Condon A, Hoos HH (2012) Analysis of energy-based algorithms for RNA secondary structure prediction. BMC Bioinformatics 13:22

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hamada M (2015a) RNA secondary structure prediction from multi-aligned sequences. Methods Mol Biol 1269:17–38

    CAS  PubMed  Google Scholar 

  • Hamada M (2015b) RNA secondary structure prediction from multi-aligned sequences. In: Picardi E (ed) RNA bioinformatics. Humana Press Inc., Totowa, pp 17–38

    Google Scholar 

  • Harrow J, Frankish A, Gonzalez JM et al (2012) GENCODE: the reference human genome annotation for the ENCODE Project. Genome Res 22(9):1760–1774

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hendriks A (2005) A parallel evolutionary algorithm for RNA secondary structure prediction. Simon Fraser University, Burnaby

    Google Scholar 

  • Hofacker IL (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31(13):3429–3431.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hu X, Hicks CW, He W et al (2006) Bace1 modulates myelination in the central and peripheral nervous system. Nat Neurosci 9(12):1520–1525

    CAS  PubMed  Google Scholar 

  • Iacoangeli A, Bianchi R, Tiedge H (2010) Regulatory RNAs in brain function and disorders. Brain Res 1338:36–47

    CAS  PubMed  PubMed Central  Google Scholar 

  • Iida A, Hosono N, Sano M, Kamei T, Oshima S, Tokuda T, Nakajima M, Kubo M, Nakamura Y, Ikegawa S (2012) Novel deletion mutations of OPTN in amyotrophic lateral sclerosis in Japanese. Neurobiol Aging 33:1843.e19–e1843.e24

    Google Scholar 

  • Iwakiri J, Hamada M, Asai K (2016) Bioinformatics tools for lncRNA research. Biochim Biophys Acta 1859(1):23–30

    CAS  PubMed  Google Scholar 

  • Jabbari H, Wark I, Montemagno C, Will S (2018) Knotty: efficient and accurate prediction of complex RNA pseudoknot structures. Bioinformatics 34:3849–3856

    CAS  PubMed  Google Scholar 

  • Jacobsen L, Madsen P, Moestrup SK et al (1996) Molecular characterization of a novel human hybrid-type receptor that binds the alpha2-macroglobulin receptor-associated protein. J Biol Chem 271(49):31379–31383

    CAS  PubMed  Google Scholar 

  • Janssen S, Giegerich R (2014) The RNA shapes studio. Bioinformatics 31:423–425

    PubMed  Google Scholar 

  • Jha NK, Jha SK, Kumar D, Kejriwal N, Sharma R, Ambasta RK, Kumar P (2015) Impact of insulin degrading enzyme and neprilysin in Alzheimer’s disease biology: characterization of putative cognates for therapeutic applications. J Alzheimers Dis 48(4):891–917

    CAS  PubMed  Google Scholar 

  • Jha SK, Jha NK, Kumar D, Ambasta RK, Kumar P (2017a) Linking mitochondrial dysfunction, metabolic syndrome and stress signaling in Neurodegeneration. Biochim Biophys Acta Mol Basis Dis 1863(5):1132–1146

    CAS  PubMed  Google Scholar 

  • Jha SK, Jha NK, Kumar D, Sharma R, Shrivastava A, Ambasta RK, Kumar P (2017b) Stress-induced synaptic dysfunction and neurotransmitter release in Alzheimer’s disease: can neurotransmitters and neuromodulators be potential therapeutic targets? J Alzheimers Dis 57(4):1017–1039

    CAS  PubMed  Google Scholar 

  • Jha NK, Jha SK, Sharma R, Kumar D, Ambasta RK, Kumar P (2018) Hypoxia-induced signaling activation in neurodegenerative diseases: targets for new therapeutic strategies. J Alzheimers Dis 62(1):15–38

    CAS  PubMed  Google Scholar 

  • Jha NK, Jha SK, Kar R, Nand P, Swati K, Goswami VK (2019a) Nuclear factor-kappa β as a therapeutic target for Alzheimer’s disease. J Neurochem 150(2):113–137

    CAS  PubMed  Google Scholar 

  • Jha NK, Kar R, Niranjan R (2019b) ABC transporters in neurological disorders: an important gateway for botanical compounds mediated neuro-therapeutics. Curr Top Med Chem 19(10):795–811

    CAS  PubMed  Google Scholar 

  • Jha NK, Sharma A, Jha SK, Ojha S, Chellappan DK, Gupta G, Kesari KK, Bhardwaj S, Shukla SD, Tambuwala MM, Ruokolainen J, Dua K, Singh SK (2020) Alzheimer’s disease-like perturbations in HIV-mediated neuronal dysfunctions: understanding mechanisms and developing therapeutic strategies. Open Biol 10(12):200286

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jiang T, Lin GH, Ma B, Zhang K (2002) A general edit distance between RNA structures. J Comput Biol 9(2):371–388

    CAS  PubMed  Google Scholar 

  • Khvotchev M, Sudhof TC (2004) Proteolytic processing of amyloid-beta precursor protein by secretases does not require cell surface transport. J Biol Chem 279(45):47101–47108

    CAS  PubMed  Google Scholar 

  • Kim J, Kim KM, Noh JH, Yoon J-H, Abdelmohsen K, Gorospe M (2016) Long non-coding RNAs in diseases of aging. Biochim Biophys Acta 1859(1):209–221. https://doi.org/10.1016/j.bbagrm.2015.06.013

    Article  CAS  PubMed  Google Scholar 

  • Knauss JL, Sun T (2013) Regulatory mechanisms of long non-coding RNAs in vertebrate central nervous system development and function. Neuroscience 235:200–214

    CAS  PubMed  Google Scholar 

  • Knudsen B, Hein J (2003) Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res 31:3423–3428

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kovtun IV, McMurray CT (2008) Features of trinucleotide repeat instability in vivo. Cell Res 18:198–213

    CAS  PubMed  Google Scholar 

  • Kraus TF, Greiner A, Guibourt V, Lisec K, Kretzschmar HA (2015) Identification of stably expressed incRNAs as valid endogenous controls for profiling of human glioma. J Cancer 6(2):111–119

    PubMed  PubMed Central  Google Scholar 

  • Kumar P, Jha NK, Jha SK, Ramani K, Ambasta RK (2015) Tau phosphorylation, molecular chaperones, and ubiquitin E3 ligase: clinical relevance in Alzheimer’s disease. J Alzheimers Dis 43(2):341–361

    CAS  PubMed  Google Scholar 

  • Kumar P, Kumar D, Jha SK, Jha NK, Ambasta RK (2016) Ion channels in neurological disorders. Adv Protein Chem Struct Biol 103:97–136

    CAS  PubMed  Google Scholar 

  • Laird FM, Cai H, Savonenko AV et al (2005) BACE1, a major determinant of selective vulnerability of the brain to amyloid-beta amyloidogenesis, is essential for cognitive, emotional, and synaptic functions. J Neurosci 25(50):11693–11709

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W et al (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921

    CAS  PubMed  Google Scholar 

  • Lee JH, Barral S, Reitz C (2008) The neuronal sortilin-related receptor gene SORL1 and late-onset Alzheimer’s disease. Curr Neurol Neurosci Rep 8(5):384–391

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lee S, Liu B, Lee S, Huang SX, Shen B, Qian SB (2012) Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution. Proc Natl Acad Sci U S A 109:E2424–E2432

    CAS  PubMed  PubMed Central  Google Scholar 

  • Li K, Rahman R, Gupta A, Siddavatam P, Gribskov M (2008) Pattern matching in RNA structures. Springer, ISBRA 2008. LNBI 4983:317–330

    CAS  Google Scholar 

  • Li AX, Qin J, Marz M, Reidys CM (2011) RNA–RNA interaction prediction based on multiple sequence alignments. Bioinformatics 27(4):456–463. https://doi.org/10.1093/bioinformatics/btq659

    Article  CAS  PubMed  Google Scholar 

  • Li D, Zhang J, Li X, Chen Y, Yu F, Liu Q (2020) Insights into lncRNAs in Alzheimer’s disease mechanisms. RNA Biol 14:1–11

    CAS  Google Scholar 

  • Lin D, Pestova TV, Hellen CU, Tiedge H (2008) Translational control by a small RNA: dendritic BC1 RNA targets the eukaryotic initiation factor 4A helicase mechanism. Mol Cell Biol 28(9):3008–3019

    CAS  PubMed  PubMed Central  Google Scholar 

  • Liu G, Chen X, Bissler JJ, Sinden RR, Leffak M (2010) Replication-dependent instability at (CTG)·(CAG) repeat hairpins in human cells. Nat Chem Biol 6:652–659

    CAS  PubMed  PubMed Central  Google Scholar 

  • Liu T, Huang Y, Chen J et al (2014) Attenuated ability of BACE1 to cleave the amyloid precursor protein via silencing long non-coding RNA BACE1AS expression. Mol Med Rep 10(3):1275–1281

    CAS  PubMed  PubMed Central  Google Scholar 

  • Liu Q, Sun S, Yu W et al (2015) Altered expression of long non-coding RNAs during genotoxic stress-induced cell death in human glioma cells. J Neurooncol 122(2):283–292

    CAS  PubMed  Google Scholar 

  • LĂłpez Castel A, Cleary JD, Pearson CE (2010) Repeat instability as the basis for human diseases and as a potential target for therapy. Nat Rev Mol Cell Biol 11:165–170

    PubMed  Google Scholar 

  • Lorenz R et al (2011) Vienna RNA package 2.0. algorithms. Mol Biol 6:26

    Google Scholar 

  • Lorenz R, Wolfinger MT, Tanzer A, Hofacker IL (2016) Predicting RNA secondary structures from sequence and probing data. Methods 103:86–98

    CAS  PubMed  Google Scholar 

  • Luo Q, Chen Y (2016) Long non-coding RNAs and Alzheimer’s disease. Clin Interv Aging 11:867–872. https://doi.org/10.2147/CIA.S107037

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ma H, Lesne S, Kotilinek L et al (2007) Involvement of beta-site APP cleaving enzyme 1 (BACE1) in amyloid precursor protein-mediated enhancement of memory and activity-dependent synaptic plasticity. Proc Natl Acad Sci U S A 104(19):8167–8172

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ma QL, Galasko DR, Ringman JM et al (2009) Reduction of SorLA/LR11, a sorting protein limiting beta-amyloid production, in Alzheimer disease cerebrospinal fluid. Arch Neurol 66(4):448–457

    PubMed  PubMed Central  Google Scholar 

  • Magistri M, Faghihi MA, St Laurent G III, Wahlestedt C (2012) Regulation of chromatin structure by long non-coding RNAs: focus on natural antisense transcripts. Trends Genet 28(8):389–396

    CAS  PubMed  PubMed Central  Google Scholar 

  • Massone S, Vassallo I, Fiorino G et al (2011) 17A, a novel non-coding RNA, regulates GABA B alternative splicing and signaling in response to inflammatory stimuli and in Alzheimer disease. Neurobiol Dis 41(2):308–317

    CAS  PubMed  Google Scholar 

  • Massone S, Ciarlo E, Vella S et al (2012) NDM29, a RNA polymerase III-dependent non coding RNA, promotes amyloidogenic processing of APP and amyloid beta secretion. Biochim Biophys Acta 1823(7):1170–1177

    CAS  PubMed  Google Scholar 

  • Mathews DH, Turner DH (2002) Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. J Mol Biol 317:191–203

    CAS  PubMed  Google Scholar 

  • Melissari MT, Grote P (2016) Roles for long non-coding RNAs in physiology and disease. Pflugers Arch. Epub 2016 Mar 5

    Google Scholar 

  • Mirkin SM (2007) Expandable DNA repeats and human disease. Nature 447:932–940

    CAS  PubMed  Google Scholar 

  • Modarresi F, Faghihi MA, Patel NS, Sahagan BG, Wahlestedt C, Lopez-Toledano MA (2011) Knockdown of BACE1-AS nonprotein-coding transcript modulates beta-amyloid-related hippocampal neurogenesis. Int J Alzheimers Dis 2011:929042

    PubMed  PubMed Central  Google Scholar 

  • Mulder SD, van der Flier WM, Verheijen JH et al (2010) BACE1 activity in cerebrospinal fluid and its relation to markers of AD pathology. J Alzheimer’s Dis 20(1):253–260

    CAS  Google Scholar 

  • Mus E, Hof PR, Tiedge H (2007) Dendritic BC200 RNA in aging and in Alzheimer’s disease. Proc Natl Acad Sci U S A 104(25):10679–10684

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nakayama T, Ogiwara I, Ito K, Kaneda M, Mazaki E, Osaka H, Ohtani H, Inoue Y, Fujiwara T, Uematsu M et al (2010) Deletions of SCN1A 5′ genomic region with promoter activity in Dravet syndrome. Hum Mutat 31:820–829

    CAS  PubMed  Google Scholar 

  • Nebel ME (2001) Combinatorial properties of RNA secondary structures. J Comput Biol 9:541–573

    Google Scholar 

  • Ng S-Y, Lin L, Soh BS et al (2013) Long non-coding RNAs in development and disease of the central nervous system. Trends Genet 29:461–468

    CAS  PubMed  Google Scholar 

  • Nowakowski J, Tinoco I (1997) RNA structure and stability. Semin Virol 8:153–165

    CAS  Google Scholar 

  • Pagani F, Baralle FE (2004) Genomic variants in exons and introns: identifying the splicing spoilers. Nat Rev Genet 5:389–396

    CAS  PubMed  Google Scholar 

  • Parenti R, Paratore S, Torrisi A, Cavallaro S (2007) A natural antisense transcript against Rad18, specifically expressed in neurons and upregulated during beta-amyloid-induced apoptosis. Eur J Neurosci 26(9):2444–2457

    PubMed  Google Scholar 

  • Parisien M, Major F (2008) The MC-fold and MC-sym pipeline infers RNA structure from sequence data. Nature 452:51–55

    CAS  PubMed  Google Scholar 

  • Perneczky R, Alexopoulos P (2014) Cerebrospinal fluid BACE1 activity and markers of amyloid precursor protein metabolism and axonal degeneration in Alzheimer’s disease. Alzheimer’s Dement 10(5 Suppl):S425–S429.e421

    Google Scholar 

  • Puton T, Kozlowski LP, Rother KM, Bujnicki JM (2013) CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction. Nucleic Acids Res 41:4307–4323

    CAS  PubMed  PubMed Central  Google Scholar 

  • QIAGEN CLC Main Workbench Software (n.d.). clcbio.com

  • Rastegari B, Condon A (2005) Linear time algorithm for parsing RNA secondary structure. Springer WABI 2005(3692):341–352

    Google Scholar 

  • Reeder J, Giegerich R (2004) Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics 5:104

    PubMed  PubMed Central  Google Scholar 

  • Reuter JS, Mathews DH (2010) RNA structure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics 11:129

    PubMed  PubMed Central  Google Scholar 

  • Rogaeva E, Meng Y, Lee JH et al (2007) The neuronal sortilin-related receptor SORL1 is genetically associated with Alzheimer disease. Nat Genet 39(2):168–177

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sato K, Hamada M, Asai K, Mituyama T (2009) CentroidFold: a web server for RNA secondary structure prediction. Nucleic Acids Res 37:W277–W280

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sato K, Kato Y, Hamada M, Akutsu T, Asai K (2011) IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Bioinformatics 27:i85–i93

    CAS  PubMed  PubMed Central  Google Scholar 

  • Saus E, Willis JR, Pryszcz LP, Hafez A, Llorens C, Himmelbauer H, Gabaldn T (2018) nextPARS: parallel probing of RNA structures in Illumina. RNA 24:609–619

    CAS  PubMed  PubMed Central  Google Scholar 

  • Schroeder SJ (2009) Advances in RNA structure prediction from sequence: new tools for generating hypotheses about viral RNA structure-function relationships. J f Virol 83(13):6326–6334. https://doi.org/10.1128/JVI.00251-09

    Article  CAS  Google Scholar 

  • Seetin MG, Mathews DH (2012) RNA structure prediction: an overview of methods. In: Keiler KC (ed) Bacterial regulatory RNA: methods and protocols. Humana Press, Totowa, NJ, pp 99–122. https://doi.org/10.1007/978-1-61779-949-5_8

    Chapter  Google Scholar 

  • Senior A, Evans R, Jumper J, Kirkpatrick J, Sifre L, Green T, Qin C, Žídek A, Nelson A, Bridgland A, Penedones H, Petersen S, Simonyan K, Crossan S, Kohli P, Jones D, Silver D, Kavukcuoglu K, Hassabis D (2019) Protein structure prediction using multiple deep neural networks in CASP13. Proteins 87. https://doi.org/10.1002/prot.25834

  • Senior AW, Evans R, Jumper J et al (2020) Improved protein structure prediction using potentials from deep learning. Nature 577:706–710. https://doi.org/10.1038/s41586-019-1923-7

    Article  CAS  PubMed  Google Scholar 

  • Singh J, Hanson J, Paliwal K et al (2019) RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning. Nat Commun 10:5407. https://doi.org/10.1038/s41467-019-13395-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Slavoff SA, Mitchell AJ, Schwaid AG, Cabili MN, Ma J, Levin JZ, Karger AD, Budnik BA, Rinn JL, Saghatelian A (2013) Peptidomic discovery of short open reading frame-encoded peptides in human cells. Nat Chem Biol 9:59–64

    CAS  PubMed  Google Scholar 

  • Sloane N (n.d.) The online-encyclopedia of integer sequences, published electronically at www.research.att.com/~njas/sequences/

  • Sloma MF, Mathews DH (2017) Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs. PLoS Comput Biol 13:1–23

    Google Scholar 

  • Smola MJ, Weeks KM (2018) In-cell RNA structure probing with SHAPE-MaP. Nat Protoc 13:1181–1195

    CAS  PubMed  PubMed Central  Google Scholar 

  • Stein PR, Waterman MS (1978) On some new sequences generalizing the Catalan and Motzkin numbers. Discrete Math 26:261–272

    Google Scholar 

  • Stern-Ginossar N, Weisburd B, Michalski A, Le VTK, Hein MY, Huang SX, Ma M, Shen B, Qian SB, Hengel H et al (2012) Decoding human cytomegalovirus. Science 338:1088–1093

    CAS  PubMed  Google Scholar 

  • Stockley JH, O’Neill C (2008) Understanding BACE1: essential protease for amyloid-beta production in Alzheimer’s disease. Cell Mol Life Sci 65(20):3265–3289

    CAS  PubMed  Google Scholar 

  • Sun M, Nie FQ, Wang ZX, De W (2016) Involvement of incRNA dysregulation in gastric cancer. Histol Histopathol 31(1):33–39

    CAS  PubMed  Google Scholar 

  • Tsiamis V, Vairaktarakis M, Alexiou A, Ashraf GM (2016) Protein-protein interaction (PPI) network: recent advances in drug discovery. Curr Drug Metabol 18(1):5–10

    Google Scholar 

  • Underwood JG, Uzilov AV, Katzman S, Onodera CS, Mainzer JE, Mathews DH, Lowe TM, Salama SR, Haussler D (2010) FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat Methods 7:995–1001

    CAS  PubMed  PubMed Central  Google Scholar 

  • Vassar R, Kandalepas PC (2011) The beta-secretase enzyme BACE1 as a therapeutic target for Alzheimer’s disease. Alzheimer’s Res Ther 3(3):20

    CAS  Google Scholar 

  • Vella S, Penna I, Longo L et al (2015) Perhexiline maleate enhances antitumor efficacy of cisplatin in neuroblastoma by inducing over-expression of NDM29 ncRNA. Sci Rep 5:18144

    CAS  PubMed  PubMed Central  Google Scholar 

  • Vervoort R, Gitzelmann R, Lissens W, Liebaers I (1998) A mutation (IVS8+0.6kbdelTC) creating a new donor splice site activates a cryptic exon in an Alu-element in intron 8 of the human β-glucuronidase gene. Hum Genet 103:686–693

    CAS  PubMed  Google Scholar 

  • Viennot G, Vauchaussade de Chaumont M (1985) Enumeration of RNA secondary structures by complexity. Math Med Biol Lecture Notes Biomath 57:360–365

    CAS  Google Scholar 

  • Wan P, Su W, Zhuo Y (2017) The role of long non-coding RNAs in neurodegenerative diseases. Mol Neurobiol 54(3):2012–2021. Epub 2016 Feb 24

    CAS  PubMed  Google Scholar 

  • Wang L, Liu Y, Zhong X, Liu H, Lu C, Li C, Zhang H (2019) DMfold: a novel method to predict RNA secondary structure with pseudoknots based on deep learning and improved base pair maximization principle. Front Genet 10:143. https://doi.org/10.3389/fgene.2019.00143

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Warf MB, Berglund JA (2010) Role of RNA structure in regulating pre-mRNA splicing. Trends Biochem Sci 35:169–178

    CAS  PubMed  Google Scholar 

  • Washietl S, Kellis M, Garber M (2014) Evolutionary dynamics and tissue specificity of human long non-coding RNAs in six mammals. Genome Res 24(4):616–628

    CAS  PubMed  PubMed Central  Google Scholar 

  • Waterman MS (1987) Secondary structure of single-stranded nucleic acids. Adv Math 1(Suppl):167–212

    Google Scholar 

  • Westhof E, Fritsch V (2000) RNA folding: beyond Watson-Crick pairs. Structure 8:R55–R65

    CAS  PubMed  Google Scholar 

  • Wilk R, Hu J, Blotsky D, Krause HM (2016) Diverse and pervasive subcellular distributions for both coding and long non-coding RNAs. Genes Dev 30(5):594–609

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wu P, Zuo X, Deng H, Liu X, Liu L, Ji A (2013) Roles of long non-coding RNAs in brain development, functional diversification and neurodegenerative diseases. Brain Res Bull 97:69–80

    CAS  PubMed  Google Scholar 

  • Xu X, Chen S-J (2015) Physics-based RNA structure prediction. Biophys Rep 1:2–13

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yamazaki H, Bujo H, Saito Y (1997) A novel member of the LDL receptor gene family with eleven binding repeats is structurally related to neural adhesion molecules and a yeast vacuolar protein sorting receptor. J Atheroscler Thromb 4(1):20–26

    CAS  PubMed  Google Scholar 

  • Yan K, Arfat Y, Li D, Zhao F, Chen Z, Yin C, Sun Y, Hu L, Yang T, Qian A (2016) Structure prediction: new insights into decrypting long non-coding RNAs. Int J Mol Sci 17:132

    PubMed Central  Google Scholar 

  • Yu B, Lu Y, Zhang QC et al (2020) Prediction and differential analysis of RNA secondary structure. Quant Biol 8:109–118. https://doi.org/10.1007/s40484-020-0205-6

    Article  CAS  Google Scholar 

  • Yuan J, Venkatraman S, Zheng Y, McKeever BM, Dillard LW, Singh SB (2013) Structure-based design of beta-site APP cleaving enzyme 1 (BACE1) inhibitors for the treatment of Alzheimer’s disease. J Med Chem 56(11):4156–4180

    CAS  PubMed  Google Scholar 

  • Zakov S, Goldberg Y, Elhadad M, Ziv-ukelson M (2011) Rich parameterization improves RNA structure prediction. J Comput Biol 18:1525–1542

    CAS  PubMed  Google Scholar 

  • Zeng C, Yu X, Lai J, Yang L, Chen S, Li Y (2015) Overexpression of the long non-coding RNA PVT1 is correlated with leukemic cell proliferation in acute promyelocytic leukemia. J Hematol Oncol 8(1):126

    PubMed  PubMed Central  Google Scholar 

  • Zhan Y, Guo M (2005) A permutation-based genetic algorithm for predicting RNA secondary structure-a practicable approach, vol 13. Springer, Berlin, pp 861–864

    Google Scholar 

  • Zhou X, Xu J (2015) Identification of Alzheimer’s disease-associated long non-coding RNAs. Neurobiol Aging 36(11):2925–2931

    CAS  PubMed  Google Scholar 

  • Zhou J, Li P, Zeng W et al (2020) IRIS: a method for predicting in vivo RNA secondary structures using PARIS data. Quant Biol. https://doi.org/10.1007/s40484-020-0223-4

  • Zhu J, Fu H, Wu Y, Zheng X (2013) Function of lncRNAs and approaches to lncRNA-protein interactions. Sci China Life Sci 56(10):876–885

    CAS  PubMed  Google Scholar 

  • zu Siederdissen CH, Bernhart SH, Stadler PF, Hofacker IL (2011) A folding algorithm for extended RNA secondary structures. Bioinformatics 27:i129–i136

    PubMed Central  Google Scholar 

  • Zu T, Gibbens B, Doty NS, Gomes-Pereira M, Huguet A, Stone MD, Margolis J, Peterson M, Markowski TW, Ingram MAC et al (2011) Non-ATG-initiated translation directed by microsatellite expansions. Proc Natl Acad Sci U S A 108:260–265

    CAS  PubMed  Google Scholar 

  • Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31:3406–3415

    CAS  PubMed  PubMed Central  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, Uttar Pradesh, India

    Niraj Kumar Jha

  2. Faculty of Medicine, University of Thessaly, Larissa, Greece

    Anna Maria Louka

  3. Novel Global Community Educational Foundation, Hebersham, NSW, Australia

    Anna Maria Louka, Christos Tsagkaris, Filia Alexiou, Panagiota Simou & Mohammad A. Kamal

  4. Faculty of Medicine, University of Crete, Heraklion, Greece

    Christos Tsagkaris

  5. Department of Pathophysiology, Medical School, National University of Athens, Athens, Greece

    Panagiotis Christoforou

  6. Department of Physics and Computer Science, Wilfrid Laurier University, Waterloo, ON, Canada

    Ioannis Haranas

  7. Department of Mathematics, Northern Virginia Community College, Annandale, VA, USA

    Ioannis Gkigkitzis

  8. School of Human Sciences, College of Life and Natural Sciences, University of Derby, Derby, UK

    Georgios Zouganelis

  9. Department of Pharmacy, Southeast University, Dhaka, Bangladesh

    Md. Sahab Uddin

  10. Pharmakon Neuroscience Research Network, Dhaka, Bangladesh

    Md. Sahab Uddin

  11. Pre-Clinical Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia

    Ghulam Md Ashraf

  12. King Fahd Medical Research Center, Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia

    Ghulam Md Ashraf

  13. West China School of Nursing/Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China

    Mohammad A. Kamal

  14. King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia

    Mohammad A. Kamal

  15. Enzymoics, Peterlee Place, Hebersham, NSW, Australia

    Mohammad A. Kamal

  16. Department of Science and Engineering, Novel Global Community Educational Foundation, Sydney, Australia

    Athanasios Alexiou

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  1. Niraj Kumar Jha
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  13. Athanasios Alexiou
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Editors and Affiliations

  1. King Fahd Medical Research Center Department of Medical Laboratory Sciences Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia

    Ghulam Md Ashraf

  2. Department of Science and Engineering, Novel Global Community Educational Foundation, Sydney, Australia

    Athanasios Alexiou

Appendix: Secondary Structure Prediction

Appendix: Secondary Structure Prediction

Table 2
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Jha, N.K. et al. (2021). RNA Secondary Structures in Neurodegeneration. In: Md Ashraf, G., Alexiou, A. (eds) Autism Spectrum Disorder and Alzheimer's Disease . Springer, Singapore. https://doi.org/10.1007/978-981-16-4558-7_10

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