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The Fragile X Protein and Genome Function

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Abstract

The fragile X syndrome (FXS) arises from loss of expression or function of the FMR1 gene and is one of the most common monogenic forms of intellectual disability and autism. During the past two decades of FXS research, the fragile X mental retardation protein (FMRP) has been primarily characterized as a cytoplasmic RNA binding protein that facilitates transport of select RNA substrates through neural projections and regulation of translation within synaptic compartments, with the protein products of such mRNAs then modulating cognitive functions. However, the presence of a small fraction of FMRP in the nucleus has long been recognized. Accordingly, recent studies have uncovered several mechanisms or pathways by which FMRP influences nuclear gene expression and genome function. Some of these pathways appear to be independent of the classical role for FMRP as a regulator of translation and point to novel functions, including the possibility that FMRP directly participates in the DNA damage response and in the maintenance of genome stability. In this review, we highlight these advances and discuss how these new findings could contribute to our understanding of FMRP in brain development and function, the neural pathology of fragile X syndrome, and perhaps impact of future therapeutic considerations.

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References

  1. Ehninger D, Li W, Fox K, Stryker MP, Silva AJ (2008) Reversing neurodevelopmental disorders in adults. Neuron 60:950–960

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Scharf SH, Jaeschke G, Wettstein JG, Lindemann L (2015) Metabotropic glutamate receptor 5 as drug target for fragile X syndrome. Curr Opin Pharmacol 20:124–134

    Article  CAS  PubMed  Google Scholar 

  3. Siomi H, Siomi MC, Nussbaum RL, Dreyfuss G (1993) The protein product of the fragile X gene, FMR1, has characteristics of an RNA-binding protein. Cell 74:291–298

    Article  CAS  PubMed  Google Scholar 

  4. Khandjian EW, Corbin F, Woerly S, Rousseau F (1996) The fragile X mental retardation protein is associated with ribosomes. Nat Genet 12:91–93

    Article  CAS  PubMed  Google Scholar 

  5. Tamanini F, Meijer N, Verheij C, Willems PJ, Galjaard H, Oostra BA, Hoogeveen AT (1996) FMRP is associated to the ribosomes via RNA. Hum Mol Genet 5:809–813

    Article  CAS  PubMed  Google Scholar 

  6. Siomi MC, Zhang Y, Siomi H, Dreyfuss G (1996) Specific sequences in the fragile X syndrome protein FMR1 and the FXR proteins mediate their binding to 60S ribosomal subunits and the interactions among them. Mol Cell Biol 16:3825–3832

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Brown V, Jin P, Ceman S, Darnell JC, O'Donnell WT, Tenenbaum SA, Jin X, Feng Y et al (2001) Microarray identification of FMRP-associated brain mRNAs and altered mRNA translational profiles in fragile X syndrome. Cell 107:477–487

    Article  CAS  PubMed  Google Scholar 

  8. Darnell JC, Jensen KB, Jin P, Brown V, Warren ST, Darnell RB (2001) Fragile X mental retardation protein targets G quartet mRNAs important for neuronal function. Cell 107:489–499

    Article  CAS  PubMed  Google Scholar 

  9. Huber KM, Gallagher SM, Warren ST, Bear MF (2002) Altered synaptic plasticity in a mouse model of fragile X mental retardation. Proc Natl Acad Sci U S A 99:7746–7750

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Ashley CT Jr, Wilkinson KD, Reines D, Warren ST (1993) FMR1 protein: conserved RNP family domains and selective RNA binding. Science 262:563–566

    Article  CAS  PubMed  Google Scholar 

  11. Bear MF, Huber KM, Warren ST (2004) The mGluR theory of fragile X mental retardation. Trends Neurosci 27:370–377

    Article  CAS  PubMed  Google Scholar 

  12. Bassell GJ, Warren ST (2008) Fragile X syndrome: loss of local mRNA regulation alters synaptic development and function. Neuron 60:201–214

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. McBride SM, Choi CH, Wang Y, Liebelt D, Braunstein E, Ferreiro D, Sehgal A, Siwicki KK et al (2005) Pharmacological rescue of synaptic plasticity, courtship behavior, and mushroom body defects in a Drosophila model of fragile X syndrome. Neuron 45:753–764

    Article  CAS  PubMed  Google Scholar 

  14. Yan QJ, Rammal M, Tranfaglia M, Bauchwitz RP (2005) Suppression of two major fragile X syndrome mouse model phenotypes by the mGluR5 antagonist MPEP. Neuropharmacology 49:1053–1066

    Article  CAS  PubMed  Google Scholar 

  15. Berry-Kravis E, Des Portes V, Hagerman R, Jacquemont S, Charles P, Visootsak J, Brinkman M, Rerat K et al (2016) Mavoglurant in fragile X syndrome: results of two randomized, double-blind, placebo-controlled trials. Sci Transl Med 8:321ra325

    Article  Google Scholar 

  16. Jeste SS, Geschwind DH (2016) Clinical trials for neurodevelopmental disorders: at a therapeutic frontier. Sci Transl Med 8:321fs321

    Article  Google Scholar 

  17. Eberhart DE, Malter HE, Feng Y, Warren ST (1996) The fragile X mental retardation protein is a ribonucleoprotein containing both nuclear localization and nuclear export signals. Hum Mol Genet 5:1083–1091

    Article  CAS  PubMed  Google Scholar 

  18. Fridell RA, Benson RE, Hua J, Bogerd HP, Cullen BR (1996) A nuclear role for the fragile X mental retardation protein. EMBO J 15:5408–5414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Sittler A, Devys D, Weber C, Mandel JL (1996) Alternative splicing of exon 14 determines nuclear or cytoplasmic localisation of fmr1 protein isoforms. Hum Mol Genet 5:95–102

    Article  CAS  PubMed  Google Scholar 

  20. Feng Y, Gutekunst CA, Eberhart DE, Yi H, Warren ST, Hersch SM (1997) Fragile X mental retardation protein: nucleocytoplasmic shuttling and association with somatodendritic ribosomes. J Neurosci 17:1539–1547

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Zhang Y, O'Connor JP, Siomi MC, Srinivasan S, Dutra A, Nussbaum RL, Dreyfuss G (1995) The fragile X mental retardation syndrome protein interacts with novel homologs FXR1 and FXR2. EMBO J 14:5358–5366

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Hu Y, Chen Z, Fu Y, He Q, Jiang L, Zheng J, Gao Y, Mei P et al (2015) The amino-terminal structure of human fragile X mental retardation protein obtained using precipitant-immobilized imprinted polymers. Nat Commun 6:6634

    Article  CAS  PubMed  Google Scholar 

  23. Pasciuto E, Bagni C (2014) SnapShot: FMRP interacting proteins. Cell 159(218–218):e211

    Google Scholar 

  24. Bhogal B, Jepson JE, Savva YA, Pepper AS, Reenan RA, Jongens TA (2011) Modulation of dADAR-dependent RNA editing by the Drosophila fragile X mental retardation protein. Nat Neurosci 14:1517–1524

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Shamay-Ramot A, Khermesh K, Porath HT, Barak M, Pinto Y, Wachtel C, Zilberberg A, Lerer-Goldshtein T et al (2015) Fmrp interacts with Adar and regulates RNA editing, synaptic density and locomotor activity in zebrafish. PLoS Genet 11:e1005702

    Article  PubMed  PubMed Central  Google Scholar 

  26. Filippini A, Bonini D, Lacoux C, Pacini L, Zingariello M, Sancillo L, Bosisio D, Salvi V et al (2017) Absence of the fragile X mental retardation protein results in defects of RNA editing of neuronal mRNAs in mouse. RNA Biol 14(11):1580–1591

  27. Zhou LT, Ye SH, Yang HX, Zhou YT, Zhao QH, Sun WW, Gao MM, Yi YH et al (2017) A novel role of fragile X mental retardation protein in pre-mRNA alternative splicing through RNA-binding protein 14. Neuroscience 349:64–75

    Article  CAS  PubMed  Google Scholar 

  28. Bardoni B, Schenck A, Mandel JL (1999) A novel RNA-binding nuclear protein that interacts with the fragile X mental retardation (FMR1) protein. Hum Mol Genet 8:2557–2566

    Article  CAS  PubMed  Google Scholar 

  29. Brown MR, Kronengold J, Gazula VR, Chen Y, Strumbos JG, Sigworth FJ, Navaratnam D, Kaczmarek LK (2010) Fragile X mental retardation protein controls gating of the sodium-activated potassium channel slack. Nat Neurosci 13:819–821

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Deng PY, Rotman Z, Blundon JA, Cho Y, Cui J, Cavalli V, Zakharenko SS, Klyachko VA (2013) FMRP regulates neurotransmitter release and synaptic information transmission by modulating action potential duration via BK channels. Neuron 77:696–711

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Alpatov R, Lesch BJ, Nakamoto-Kinoshita M, Blanco A, Chen S, Stutzer A, Armache KJ, Simon MD et al (2014) A chromatin-dependent role of the fragile X mental retardation protein FMRP in the DNA damage response. Cell 157:869–881

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Blokhuis AM, Koppers M, Groen EJ, van den Heuvel DM, Dini Modigliani S, Anink JJ, Fumoto K, van Diggelen F et al (2016) Comparative interactomics analysis of different ALS-associated proteins identifies converging molecular pathways. Acta Neuropathol 132:175–196

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. He Q, Ge W (2017) The tandem Agenet domain of fragile X mental retardation protein interacts with FUS. Sci Rep 7:962

    Article  PubMed  PubMed Central  Google Scholar 

  34. Raj B, Blencowe BJ (2015) Alternative splicing in the mammalian nervous system: recent insights into mechanisms and functional roles. Neuron 87:14–27

    Article  CAS  PubMed  Google Scholar 

  35. Didiot MC, Tian Z, Schaeffer C, Subramanian M, Mandel JL, Moine H (2008) The G-quartet containing FMRP binding site in FMR1 mRNA is a potent exonic splicing enhancer. Nucleic Acids Res 36:4902–4912

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Brooks AN, Duff MO, May G, Yang L, Bolisetty M, Landolin J, Wan K, Sandler J et al (2015) Regulation of alternative splicing in Drosophila by 56 RNA binding proteins. Genome Res 25:1771–1780

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Stoiber MH, Olson S, May GE, Duff MO, Manent J, Obar R, Guruharsha KG, Bickel PJ et al (2015) Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila. Genome Res 25:1692–1702

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Tapial J, Ha KCH, Sterne-Weiler T, Gohr A, Braunschweig U, Hermoso-Pulido A, Quesnel-Vallieres M, Permanyer J et al (2017) An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms. Genome Res 27:1759–1768

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Lein E, Borm LE, Linnarsson S (2017) The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing. Science 358:64–69

    Article  CAS  PubMed  Google Scholar 

  40. Lai D, Sakkas D, Huang Y (2006) The fragile X mental retardation protein interacts with a distinct mRNA nuclear export factor NXF2. RNA 12:1446–1449

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Zhang M, Wang Q, Huang Y (2007) Fragile X mental retardation protein FMRP and the RNA export factor NXF2 associate with and destabilize Nxf1 mRNA in neuronal cells. Proc Natl Acad Sci U S A 104:10057–10062

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Kim M, Bellini M, Ceman S (2009) Fragile X mental retardation protein FMRP binds mRNAs in the nucleus. Mol Cell Biol 29:214–228

    Article  CAS  PubMed  Google Scholar 

  43. Rosenthal JJ, Seeburg PH (2012) A-to-I RNA editing: effects on proteins key to neural excitability. Neuron 74:432–439

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Darnell JC, Van Driesche SJ, Zhang C, Hung KY, Mele A, Fraser CE, Stone EF, Chen C et al (2011) FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism. Cell 146:247–261

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Ascano M Jr, Mukherjee N, Bandaru P, Miller JB, Nusbaum JD, Corcoran DL, Langlois C, Munschauer M et al (2012) FMRP targets distinct mRNA sequence elements to regulate protein expression. Nature 492:382–386

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Korb E, Herre M, Zucker-Scharff I, Gresack J, Allis CD, Darnell RB (2017) Excess translation of epigenetic regulators contributes to fragile X syndrome and is alleviated by Brd4 inhibition. Cell 170(1209–1223):e1220

    Google Scholar 

  47. McConnell MJ, Moran JV, Abyzov A, Akbarian S, Bae T, Cortes-Ciriano I, Erwin JA, Fasching L et al (2017) Intersection of diverse neuronal genomes and neuropsychiatric disease: the brain somatic mosaicism network. Science 356:eaal1641

    Article  PubMed  PubMed Central  Google Scholar 

  48. Megosh HB, Cox DN, Campbell C, Lin H (2006) The role of PIWI and the miRNA machinery in Drosophila germline determination. Curr Biol 16:1884–1894

    Article  CAS  PubMed  Google Scholar 

  49. Bozzetti MP, Specchia V, Cattenoz PB, Laneve P, Geusa A, Sahin HB, Di Tommaso S, Friscini A et al (2015) The Drosophila fragile X mental retardation protein participates in the piRNA pathway. J Cell Sci 128:2070–2084

    Article  CAS  PubMed  Google Scholar 

  50. Jiang F, Lu F, Li P, Liu W, Zhao L, Wang Q, Cao X, Zhang L et al (2016) Drosophila homolog of FMRP maintains genome integrity by interacting with Piwi. J Genet Genomics 43:11–24

    Article  PubMed  Google Scholar 

  51. Zhang W, Cheng Y, Li Y, Chen Z, Jin P, Chen D (2014) A feed-forward mechanism involving Drosophila fragile X mental retardation protein triggers a replication stress-induced DNA damage response. Hum Mol Genet 23:5188–5196

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Peters L, Meister G (2007) Argonaute proteins: mediators of RNA silencing. Mol Cell 26:611–623

    Article  CAS  PubMed  Google Scholar 

  53. Jin P, Zarnescu DC, Ceman S, Nakamoto M, Mowrey J, Jongens TA, Nelson DL, Moses K et al (2004) Biochemical and genetic interaction between the fragile X mental retardation protein and the microRNA pathway. Nat Neurosci 7:113–117

    Article  CAS  PubMed  Google Scholar 

  54. Caudy AA, Myers M, Hannon GJ, Hammond SM (2002) Fragile X-related protein and VIG associate with the RNA interference machinery. Genes Dev 16:2491–2496

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Ishizuka A, Siomi MC, Siomi H (2002) A Drosophila fragile X protein interacts with components of RNAi and ribosomal proteins. Genes Dev 16:2497–2508

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Iwasaki YW, Siomi MC, Siomi H (2015) PIWI-interacting RNA: Its biogenesis and functions. Annu Rev Biochem 84:405–433

    Article  CAS  PubMed  Google Scholar 

  57. Sienski G, Donertas D, Brennecke J (2012) Transcriptional silencing of transposons by Piwi and maelstrom and its impact on chromatin state and gene expression. Cell 151:964–980

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Rajasethupathy P, Antonov I, Sheridan R, Frey S, Sander C, Tuschl T, Kandel ER (2012) A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity. Cell 149:693–707

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Perrat PN, DasGupta S, Wang J, Theurkauf W, Weng Z, Rosbash M, Waddell S (2013) Transposition-driven genomic heterogeneity in the Drosophila brain. Science 340:91–95

    Article  CAS  PubMed  Google Scholar 

  60. Liu W, Jiang F, Bi X, Zhang YQ (2012) Drosophila FMRP participates in the DNA damage response by regulating G2/M cell cycle checkpoint and apoptosis. Hum Mol Genet 21:4655–4668

    Article  CAS  PubMed  Google Scholar 

  61. Collins SC, Bray SM, Suhl JA, Cutler DJ, Coffee B, Zwick ME, Warren ST (2010) Identification of novel FMR1 variants by massively parallel sequencing in developmentally delayed males. Am J Med Genet A 152A:2512–2520

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Myrick LK, Deng PY, Hashimoto H, Oh YM, Cho Y, Poidevin MJ, Suhl JA, Visootsak J et al (2015) Independent role for presynaptic FMRP revealed by an FMR1 missense mutation associated with intellectual disability and seizures. Proc Natl Acad Sci U S A 112:949–956

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Huyen Y, Zgheib O, Ditullio RA Jr, Gorgoulis VG, Zacharatos P, Petty TJ, Sheston EA, Mellert HS et al (2004) Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks. Nature 432:406–411

    Article  CAS  PubMed  Google Scholar 

  64. Francia S, Michelini F, Saxena A, Tang D, de Hoon M, Anelli V, Mione M, Carninci P et al (2012) Site-specific DICER and DROSHA RNA products control the DNA-damage response. Nature 488:231–235

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Wei W, Ba Z, Gao M, Wu Y, Ma Y, Amiard S, White CI, Rendtlew Danielsen JM et al (2012) A role for small RNAs in DNA double-strand break repair. Cell 149:101–112

    Article  CAS  PubMed  Google Scholar 

  66. d'Adda di Fagagna F (2014) A direct role for small non-coding RNAs in DNA damage response. Trends Cell Biol 24:171–178

    Article  CAS  PubMed  Google Scholar 

  67. Dutertre M, Lambert S, Carreira A, Amor-Gueret M, Vagner S (2014) DNA damage: RNA-binding proteins protect from near and far. Trends Biochem Sci 39:141–149

    Article  CAS  PubMed  Google Scholar 

  68. Dutertre M, Vagner S (2017) DNA-damage response RNA-binding proteins (DDRBPs): perspectives from a new class of proteins and their RNA targets. J Mol Biol 429:3139–3145

    Article  CAS  PubMed  Google Scholar 

  69. Guo W, Allan AM, Zong R, Zhang L, Johnson EB, Schaller EG, Murthy AC, Goggin SL et al (2011) Ablation of Fmrp in adult neural stem cells disrupts hippocampus-dependent learning. Nat Med 17:559–565

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. el Bekay R, Romero-Zerbo Y, Decara J, Sanchez-Salido L, Del Arco-Herrera I, Rodriguez-de Fonseca F, de Diego-Otero Y (2007) Enhanced markers of oxidative stress, altered antioxidants and NADPH-oxidase activation in brains from fragile X mental retardation 1-deficient mice, a pathological model for fragile X syndrome. Eur J Neurosci 26:3169–3180

    Article  PubMed  Google Scholar 

  71. Davidovic L, Navratil V, Bonaccorso CM, Catania MV, Bardoni B, Dumas ME (2011) A metabolomic and systems biology perspective on the brain of the fragile X syndrome mouse model. Genome Res 21:2190–2202

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Weisz ED, Towheed A, Monyak RE, Toth MS, Wallace DC, Jongens TA (2018) Loss of Drosophila FMRP leads to alterations in energy metabolism and mitochondrial function. Hum Mol Genet 27:95–106

    Article  CAS  PubMed  Google Scholar 

  73. Rousseau F, Heitz D, Tarleton J, MacPherson J, Malmgren H, Dahl N, Barnicoat A, Mathew C et al (1994) A multicenter study on genotype-phenotype correlations in the fragile X syndrome, using direct diagnosis with probe StB12.3: the first 2,253 cases. Am J Hum Genet 55:225–237

    CAS  PubMed  PubMed Central  Google Scholar 

  74. Fong YW, Cattoglio C, Tjian R (2013) The intertwined roles of transcription and repair proteins. Mol Cell 52:291–302

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Le May N, Fradin D, Iltis I, Bougneres P, Egly JM (2012) XPG and XPF endonucleases trigger chromatin looping and DNA demethylation for accurate expression of activated genes. Mol Cell 47:622–632

    Article  PubMed  Google Scholar 

  76. Suberbielle E, Sanchez PE, Kravitz AV, Wang X, Ho K, Eilertson K, Devidze N, Kreitzer AC et al (2013) Physiologic brain activity causes DNA double-strand breaks in neurons, with exacerbation by amyloid-beta. Nat Neurosci 16:613–621

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Madabhushi R, Gao F, Pfenning AR, Pan L, Yamakawa S, Seo J, Rueda R, Phan TX et al (2015) Activity-induced DNA breaks govern the expression of neuronal early-response genes. Cell 161:1592–1605

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Rutenberg-Schoenberg M, Sexton AN, Simon MD (2016) The properties of long noncoding RNAs that regulate chromatin. Annu Rev Genomics Hum Genet 17:69–94

    Article  CAS  PubMed  Google Scholar 

  79. Kopp F, Mendell JT (2018) Functional classification and experimental dissection of long noncoding RNAs. Cell 172:393–407

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

The authors apologize for omission of any relevant works due to space constraints.

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Support from NIH MH108956 and past support from NIH and FRAXA Research Foundation are gratefully acknowledged.

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Correspondence to Thomas C. Dockendorff or Mariano Labrador.

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Dockendorff, T.C., Labrador, M. The Fragile X Protein and Genome Function. Mol Neurobiol 56, 711–721 (2019). https://doi.org/10.1007/s12035-018-1122-9

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