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Evidence for natural antisense transcript-mediated inhibition of microRNA function

Faghihi, Mohammad Ali, Zhang, Ming, Huang, Jia, Modarresi, Farzaneh, Van der Brug, Marcel P, Nalls, Michael A, Cookson, Mark R, St-Laurent, Georges, Wahlestedt, Claes·2010·Genome Biology
DOI 10.1186/gb-2010-11-5-r56PMC PMC2898074
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Abstract

Background: MicroRNAs (miRNAs) have the potential to regulate diverse sets of mRNA targets. In addition, mammalian genomes contain numerous natural antisense transcripts, most of which appear to be non-protein-coding RNAs (ncRNAs). We have recently identified and characterized a highly conserved non-coding antisense transcript for beta-secretase-1 ( BACE1 ), a critical enzyme in Alzheimer's disease pathophysiology. The BACE1 -antisense transcript is markedly up-regulated in brain samples from Alzheimer's disease patients and promotes the stability of the (sense) BACE1 transcript. Results: We report here that BACE1 -antisense prevents miRNA-induced repression of BACE1 mRNA by masking the binding site for miR-485-5p. Indeed, miR-485-5p and BACE1 -antisense compete for binding within the same region in the open reading frame of the BACE1 mRNA. We observed opposing effects of BACE1 -antisense and miR-485-5p on BACE1 protein in vitro and showed that Locked Nucleic Acid-antimiR mediated knockdown of miR-485-5p as well as BACE1 -antisense over-expression can prevent the miRNA-induced BACE1 suppression. We found that the expression of BACE1 -antisense as well as miR-485-5p are dysregulated in RNA samples from Alzheimer's disease subjects compared to control individuals. Conclusions: Our data demonstrate an interface between two distinct groups of regulatory RNAs in the computation of BACE1 gene expression. Moreover, bioinformatics analyses revealed a theoretical basis for many other potential interactions between natural antisense transcripts and miRNAs at the binding sites of the latter.

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  • BACE1-AS stabilizes BACE1 through competitive binding of miR-485-5p which would otherwise repress BACE1 mRNA translation.

    “BACE1‐AS is reported to stabilize BACE1 through competitive binding of miR‐485‐5p which would otherwise repress BACE1 mRNA translation.”

    From BACE1: More than just a β‐secretase (2022) · cites this paper as [56]

  • miR-485-5p is significantly downregulated in the parietal lobe, cerebellum, entorhinal cortex and hippocampus.

    “Faghihi et al. [64] found that miR-485-5p was significantly downregulated in the parietal lobe, cerebellum, entorhinal cortex and hippocampus”

    From MicroRNAs in Extracellular Vesicles of Alzheimer’s Disease (2023) · cites this paper as [64]

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Research works printed but not linked: 52

  1. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, et al: The transcriptional landscape of the mammalian genome. Science. 2005, 309: 1559-1563. 10.1126/science.1112014. · DOI
  2. Kapranov P, Drenkow J, Cheng J, Long J, Helt G, Dike S, Gingeras TR: Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res. 2005, 15: 987-997. 10.1101/gr.3455305. · DOI
  3. Gustincich S, Sandelin A, Plessy C, Katayama S, Simone R, Lazarevic D, Hayashizaki Y, Carninci P: The complexity of the mammalian transcriptome. J Physiol. 2006, 575: 321-332. 10.1113/jphysiol.2006.115568. · DOI
  4. Mehler MF, Mattick JS: Non-coding RNA in the nervous system. J Physiol. 2006, 575: 333-341. 10.1113/jphysiol.2006.113191. · DOI
  5. Faghihi MA, Wahlestedt C: RNA interference is not involved in natural antisense mediated regulation of gene expression in mammals. Genome Biol. 2006, 7: R38-10.1186/gb-2006-7-5-r38. · DOI
  6. Mattick JS, Makunin IV: Non-coding RNA. Hum Mol Genet. 2006, R17-29. 10.1093/hmg/ddl046. 15 Spec No 1 · DOI
  7. Wahlestedt C: Natural antisense and noncoding RNA transcripts as potential drug targets. Drug Discov Today. 2006, 11: 503-508. 10.1016/j.drudis.2006.04.013. · DOI
  8. Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, Suzuki H, Carninci P, Hayashizaki Y, Wells C, Frith M, Ravasi T, Pang KC, Hallinan J, Mattick J, Hume DA, Lipovich L, Batalov S, Engstrom PG, Mizuno Y, Faghihi MA, Sandelin A, Chalk AM, Mottagui-Tabar S, Liang Z, Lenhard B, et al: Antisense transcription in the mammalian transcriptome. Science. 2005, 309: 1564-1566. 10.1126/science.1112009. · DOI
  9. Engstrom PG, Suzuki H, Ninomiya N, Akalin A, Sessa L, Lavorgna G, Brozzi A, Luzi L, Tan SL, Yang L, Kunarso G, Ng EL, Batalov S, Wahlestedt C, Kai C, Kawai J, Carninci P, Hayashizaki Y, Wells C, Bajic VB, Orlando V, Reid JF, Lenhard B, Lipovich L: Complex Loci in human and mouse genomes. PLoS Genet. 2006, 2: e47-10.1371/journal.pgen.0020047. · DOI
  10. Faghihi MA, Modarresi F, Khalil AM, Wood DE, Sahagan BG, Morgan TE, Finch CE, St Laurent G, Kenny PJ, Wahlestedt C: Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase. Nat Med. 2008, 14: 723-730. 10.1038/nm1784. · DOI · Paper page
  11. Uchida T, Rossignol F, Matthay MA, Mounier R, Couette S, Clottes E, Clerici C: Prolonged hypoxia differentially regulates hypoxia-inducible factor (HIF)-1alpha and HIF-2alpha expression in lung epithelial cells: implication of natural antisense HIF-1alpha. J Biol Chem. 2004, 279: 14871-14878. 10.1074/jbc.M400461200. · DOI
  12. Cayre A, Rossignol F, Clottes E, Penault-Llorca F: aHIF but not HIF-1alpha transcript is a poor prognostic marker in human breast cancer. Breast Cancer Res. 2003, 5: R223-230. 10.1186/bcr652. · DOI
  13. Rossignol F, Vache C, Clottes E: Natural antisense transcripts of hypoxia-inducible factor 1alpha are detected in different normal and tumour human tissues. Gene. 2002, 299: 135-140. 10.1016/S0378-1119(02)01049-1. · DOI
  14. Rossignol F, de Laplanche E, Mounier R, Bonnefont J, Cayre A, Godinot C, Simonnet H, Clottes E: Natural antisense transcripts of HIF-1alpha are conserved in rodents. Gene. 2004, 339: 121-130. 10.1016/j.gene.2004.06.029. · DOI
  15. Capaccioli S, Quattrone A, Schiavone N, Calastretti A, Copreni E, Bevilacqua A, Canti G, Gong L, Morelli S, Nicolin A: A bcl-2/IgH antisense transcript deregulates bcl-2 gene expression in human follicular lymphoma t(14;18) cell lines. Oncogene. 1996, 13: 105-115.
  16. Leung AK, Sharp PA: Function and localization of microRNAs in mammalian cells. Cold Spring Harb Symp Quant Biol. 2006, 71: 29-38. 10.1101/sqb.2006.71.049. · DOI
  17. Bartel DP: MicroRNAs: target recognition and regulatory functions. Cell. 2009, 136: 215-233. 10.1016/j.cell.2009.01.002. · DOI · Paper page
  18. Laird FM, Cai H, Savonenko AV, Farah MH, He K, Melnikova T, Wen H, Chiang HC, Xu G, Koliatsos VE, Borchelt DR, Price DL, Lee HK, Wong PC: BACE1, a major determinant of selective vulnerability of the brain to amyloid-beta amyloidogenesis, is essential for cognitive, emotional, and synaptic functions. J Neurosci. 2005, 25: 11693-11709. 10.1523/JNEUROSCI.2766-05.2005. · DOI · Paper page
  19. Hu X, Hicks CW, He W, Wong P, Macklin WB, Trapp BD, Yan R: Bace1 modulates myelination in the central and peripheral nervous system. Nat Neurosci. 2006, 9: 1520-1525. 10.1038/nn1797. · DOI · Paper page
  20. Roberson ED, Mucke L: 100 years and counting: prospects for defeating Alzheimer's disease. Science. 2006, 314: 781-784. 10.1126/science.1132813. · DOI
  21. Vassar R: Beta-secretase (BACE) as a drug target for Alzheimer's disease. Adv Drug Deliv Rev. 2002, 54: 1589-1602. 10.1016/S0169-409X(02)00157-6. · DOI
  22. Vassar R: The beta-secretase, BACE: a prime drug target for Alzheimer's disease. J Mol Neurosci. 2001, 17: 157-170. 10.1385/JMN:17:2:157. · DOI
  23. Ghosh AK, Kumaragurubaran N, Tang J: Recent developments of structure based beta-secretase inhibitors for Alzheimer's disease. Curr Top Med Chem. 2005, 5: 1609-1622. 10.2174/156802605775009711. · DOI
  24. Zimmermann M, Gardoni F, Di Luca M: Molecular rationale for the pharmacological treatment of Alzheimer's disease. Drugs Aging. 2005, 22 (Suppl 1): 27-37. 10.2165/00002512-200522001-00003. · DOI
  25. Li R, Lindholm K, Yang LB, Yue X, Citron M, Yan R, Beach T, Sue L, Sabbagh M, Cai H, Wong P, Price D, Shen Y: Amyloid beta peptide load is correlated with increased beta-secretase activity in sporadic Alzheimer's disease patients. Proc Natl Acad Sci USA. 2004, 101: 3632-3637. 10.1073/pnas.0205689101. · DOI
  26. Holsinger RM, McLean CA, Collins SJ, Masters CL, Evin G: Increased beta-Secretase activity in cerebrospinal fluid of Alzheimer's disease subjects. Ann Neurol. 2004, 55: 898-899. 10.1002/ana.20144. · DOI
  27. Fukumoto H, Cheung BS, Hyman BT, Irizarry MC: Beta-secretase protein and activity are increased in the neocortex in Alzheimer disease. Arch Neurol. 2002, 59: 1381-1389. 10.1001/archneur.59.9.1381. · DOI · Paper page
  28. Rossner S, Sastre M, Bourne K, Lichtenthaler SF: Transcriptional and translational regulation of BACE1 expression - implications for Alzheimer's disease. Prog Neurobiol. 2006, 79: 95-111. 10.1016/j.pneurobio.2006.06.001. · DOI
  29. Holsinger RM, McLean CA, Beyreuther K, Masters CL, Evin G: Increased expression of the amyloid precursor beta-secretase in Alzheimer's disease. Ann Neurol. 2002, 51: 783-786. 10.1002/ana.10208. · DOI · Paper page
  30. Chin LJ, Ratner E, Leng S, Zhai R, Nallur S, Babar I, Muller RU, Straka E, Su L, Burki EA, Crowell RE, Patel R, Kulkarni T, Homer R, Zelterman D, Kidd KK, Zhu Y, Christiani DC, Belinsky SA, Slack FJ, Weidhaas JB: A SNP in a let-7 microRNA complementary site in the KRAS 3' untranslated region increases non-small cell lung cancer risk. Cancer Res. 2008, 68: 8535-8540. 10.1158/0008-5472.CAN-08-2129. · DOI
  31. Mishra PJ, Humeniuk R, Longo-Sorbello GS, Banerjee D, Bertino JR: A miR-24 microRNA binding-site polymorphism in dihydrofolate reductase gene leads to methotrexate resistance. Proc Natl Acad Sci USA. 2007, 104: 13513-13518. 10.1073/pnas.0706217104. · DOI
  32. Mishra PJ, Banerjee D, Bertino JR: MiRSNPs or MiR-polymorphisms, new players in microRNA mediated regulation of the cell: introducing microRNA pharmacogenomics. Cell Cycle. 2008, 7: 853-858. · DOI
  33. Abelson JF, Kwan KY, O'Roak BJ, Baek DY, Stillman AA, Morgan TM, Mathews CA, Pauls DL, Rasin MR, Gunel M, Davis NR, Ercan-Sencicek AG, Guez DH, Spertus JA, Leckman JF, Dure LSt, Kurlan R, Singer HS, Gilbert DL, Farhi A, Louvi A, Lifton RP, Sestan N, State MW: Sequence variants in SLITRK1 are associated with Tourette's syndrome. Science. 2005, 310: 317-320. 10.1126/science.1116502. · DOI · Paper page
  34. Arteaga-Vazquez M, Caballero-Perez J, Vielle-Calzada JP: A family of microRNAs present in plants and animals. Plant Cell. 2006, 18: 3355-3369. 10.1105/tpc.106.044420. · DOI
  35. Lytle JR, Yario TA, Steitz JA: Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5' UTR as in the 3' UTR. Proc Natl Acad Sci USA. 2007, 104: 9667-9672. 10.1073/pnas.0703820104. · DOI
  36. Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP: Prediction of plant microRNA targets. Cell. 2002, 110: 513-520. 10.1016/S0092-8674(02)00863-2. · DOI
  37. Forman JJ, Legesse-Miller A, Coller HA: A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence. Proc Natl Acad Sci USA. 2008, 105: 14879-14884. 10.1073/pnas.0803230105. · DOI · Paper page
  38. Duursma AM, Kedde M, Schrier M, le Sage C, Agami R: miR-148 targets human DNMT3b protein coding region. RNA. 2008, 14: 872-877. 10.1261/rna.972008. · DOI
  39. Prasanth KV, Prasanth SG, Xuan Z, Hearn S, Freier SM, Bennett CF, Zhang MQ, Spector DL: Regulating gene expression through RNA nuclear retention. Cell. 2005, 123: 249-263. 10.1016/j.cell.2005.08.033. · DOI
  40. Leung AK, Sharp PA: microRNAs: a safeguard against turmoil?. Cell. 2007, 130: 581-585. 10.1016/j.cell.2007.08.010. · DOI
  41. Bhattacharyya SN, Habermacher R, Martine U, Closs EI, Filipowicz W: Relief of microRNA-mediated translational repression in human cells subjected to stress. Cell. 2006, 125: 1111-1124. 10.1016/j.cell.2006.04.031. · DOI
  42. St Laurent G, Wahlestedt C: Noncoding RNAs: couplers of analog and digital information in nervous system function?. Trends Neurosci. 2007, 30: 612-621. 10.1016/j.tins.2007.10.002. · DOI
  43. Borghi R, Patriarca S, Traverso N, Piccini A, Storace D, Garuti A, Cirmena G, Odetti P, Tabaton M: The increased activity of BACE1 correlates with oxidative stress in Alzheimer's disease. Neurobiol Aging. 2007, 28: 1009-1014. 10.1016/j.neurobiolaging.2006.05.004. · DOI
  44. Tong Y, Zhou W, Fung V, Christensen MA, Qing H, Sun X, Song W: Oxidative stress potentiates BACE1 gene expression and Abeta generation. J Neural Transm. 2005, 112: 455-469. 10.1007/s00702-004-0255-3. · DOI
  45. Tamagno E, Bardini P, Guglielmotto M, Danni O, Tabaton M: The various aggregation states of beta-amyloid 1-42 mediate different effects on oxidative stress, neurodegeneration, and BACE-1 expression. Free Radic Biol Med. 2006, 41: 202-212. 10.1016/j.freeradbiomed.2006.01.021. · DOI
  46. Harkany T, Abraham I, Konya C, Nyakas C, Zarandi M, Penke B, Luiten PG: Mechanisms of beta-amyloid neurotoxicity: perspectives of pharmacotherapy. Rev Neurosci. 2000, 11: 329-382. · DOI
  47. Yatin SM, Aksenova M, Aksenov M, Markesbery WR, Aulick T, Butterfield DA: Temporal relations among amyloid beta-peptide-induced free-radical oxidative stress, neuronal toxicity, and neuronal defensive responses. J Mol Neurosci. 1998, 11: 183-197. 10.1385/JMN:11:3:183. · DOI
  48. Li Y, Zhou W, Tong Y, He G, Song W: Control of APP processing and Abeta generation level by BACE1 enzymatic activity and transcription. Faseb J. 2006, 20: 285-292. 10.1096/fj.05-4986com. · DOI
  49. Hackenberg M, Sturm M, Langenberger D, Falcon-Perez JM, Aransay AM: miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res. 2009, 37: W68-76. 10.1093/nar/gkp347. · DOI
  50. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ: miRBase: tools for microRNA genomics. Nucleic Acids Res. 2008, 36: D154-158. 10.1093/nar/gkm952. · DOI
  51. Zhang Z, Schwartz S, Wagner L, Miller W: A greedy algorithm for aligning DNA sequences. J Comput Biol. 2000, 7: 203-214. 10.1089/10665270050081478. · DOI
  52. John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS: Human microRNA targets. PLoS Biol. 2004, 2: e363-10.1371/journal.pbio.0020363. · DOI · Paper page

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Metadata

Authors
Faghihi, M. A., Zhang, M., Huang, J., Modarresi, F., Van der Brug, M. P., Nalls, M. A., Cookson, M. R., St-Laurent, G., & Wahlestedt, C.
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2010-05-27
Volume
11
Issue
5
ISSN
1474-760X
DOI
10.1186/gb-2010-11-5-r56
PMC
PMC2898074
Cited by
473
References
3
Language
en
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