Locus specific reduction of L1 expression in the cortices of individuals with amyotrophic lateral sclerosis

Mejzini R, Flynn LL, Pitout IL, Fletcher S, Wilton SD, Akkari PA. ALS genetics, mechanisms, and therapeutics: where are we now? Front Neurosci. 2019;13:1310.

Article  Google Scholar 

van Es MA, Hardiman O, Chio A, Al-Chalabi A, Pasterkamp RJ, Veldink JH, et al. Amyotrophic lateral sclerosis. Lancet. 2017;390(10107):2084–98.

Article  Google Scholar 

Savage AL, Schumann GG, Breen G, Bubb VJ, Al-Chalabi A, Quinn JP. Retrotransposons in the development and progression of amyotrophic lateral sclerosis. J Neurol Neurosurg Psychiatry. 2019;90(3):284–93.

Article  Google Scholar 

Andrews WD, Tuke PW, Al-Chalabi A, Gaudin P, Ijaz S, Parton MJ, et al. Detection of reverse transcriptase activity in the serum of patients with motor neurone disease. J Med Virol. 2000;61(4):527–32.

CAS  Article  Google Scholar 

Steele AJ, Al-Chalabi A, Ferrante K, Cudkowicz ME, Brown RH Jr, Garson JA. Detection of serum reverse transcriptase activity in patients with ALS and unaffected blood relatives. Neurology. 2005;64(3):454–8.

CAS  Article  Google Scholar 

Douville R, Liu J, Rothstein J, Nath A. Identification of active loci of a human endogenous retrovirus in neurons of patients with amyotrophic lateral sclerosis. Ann Neurol. 2011;69(1):141–51.

CAS  Article  Google Scholar 

Li W, Lee MH, Henderson L, Tyagi R, Bachani M, Steiner J, et al. Human endogenous retrovirus-K contributes to motor neuron disease. Sci Transl Med. 2015;7(307):307ra153.

Article  Google Scholar 

Garson JA, Usher L, Al-Chalabi A, Huggett J, Day EF, McCormick AL. Quantitative analysis of human endogenous retrovirus-K transcripts in postmortem premotor cortex fails to confirm elevated expression of HERV-K RNA in amyotrophic lateral sclerosis. Acta Neuropathol Commun. 2019;7(1):45.

Article  Google Scholar 

Mayer J, Harz C, Sanchez L, Pereira GC, Maldener E, Heras SR, et al. Transcriptional profiling of HERV-K(HML-2) in amyotrophic lateral sclerosis and potential implications for expression of HML-2 proteins. Mol Neurodegener. 2018;13(1):39.

Article  Google Scholar 

Prudencio M, Gonzales PK, Cook CN, Gendron TF, Daughrity LM, Song Y, et al. Repetitive element transcripts are elevated in the brain of C9orf72 ALS/FTLD patients. Hum Mol Genet. 2017;26(17):3421–31.

CAS  Article  Google Scholar 

Tam OH, Rozhkov NV, Shaw R, Kim D, Hubbard I, Fennessey S, et al. Postmortem cortex samples identify distinct molecular subtypes of ALS: retrotransposon activation, oxidative stress, and activated glia. Cell Rep. 2019;29(5):1164–77.

CAS  Article  Google Scholar 

Pereira GC, Sanchez L, Schaughency PM, Rubio-Roldan A, Choi JA, Planet E, et al. Properties of LINE-1 proteins and repeat element expression in the context of amyotrophic lateral sclerosis. Mob DNA. 2018;9:35.

CAS  Article  Google Scholar 

Mackenzie IR, Bigio EH, Ince PG, Geser F, Neumann M, Cairns NJ, et al. Pathological TDP-43 distinguishes sporadic amyotrophic lateral sclerosis from amyotrophic lateral sclerosis with SOD1 mutations. Ann Neurol. 2007;61(5):427–34.

CAS  Article  Google Scholar 

Li W, Jin Y, Prazak L, Hammell M, Dubnau J. Transposable elements in TDP-43-mediated neurodegenerative disorders. PLoS ONE. 2012;7(9):e44099.

CAS  Article  Google Scholar 

Liu EY, Russ J, Cali CP, Phan JM, Amlie-Wolf A, Lee EB. Loss of Nuclear TDP-43 Is Associated with Decondensation of LINE Retrotransposons. Cell Rep. 2019;27(5):1409–21.

CAS  Article  Google Scholar 

Brouha B, Schustak J, Badge RM, Lutz-Prigge S, Farley AH, Moran JV, et al. Hot L1s account for the bulk of retrotransposition in the human population. Proc Natl Acad Sci U S A. 2003;100(9):5280–5.

CAS  Article  Google Scholar 

Penzkofer T, Jager M, Figlerowicz M, Badge R, Mundlos S, Robinson PN, et al. L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes. Nucleic Acids Res. 2017;45(D1):D68–73.

CAS  Article  Google Scholar 

Feng Q, Moran JV, Kazazian HH Jr, Boeke JD. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell. 1996;87(5):905–16.

CAS  Article  Google Scholar 

Khazina E, Weichenrieder O. Non-LTR retrotransposons encode noncanonical RRM domains in their first open reading frame. Proc Natl Acad Sci U S A. 2009;106(3):731–6.

CAS  Article  Google Scholar 

Mathias SL, Scott AF, Kazazian HH Jr, Boeke JD, Gabriel A. Reverse transcriptase encoded by a human transposable element. Science. 1991;254(5039):1808–10.

CAS  Article  Google Scholar 

Gardner EJ, Lam VK, Harris DN, Chuang NT, Scott EC, Pittard WS, et al. The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology. Genome Res. 2017;27(11):1916–29.

CAS  Article  Google Scholar 

Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F, Demeulemeester J, et al. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nat Genet. 2020;52(3):306–19.

CAS  Article  Google Scholar 

Saleh A, Macia A, Muotri AR. Transposable elements, inflammation, and neurological disease. Front Neurol. 2019;10:894.

Article  Google Scholar 

Tam OH, Ostrow LW, Gale HM. Diseases of the nERVous system: retrotransposon activity in neurodegenerative disease. Mob DNA. 2019;10:32.

Article  Google Scholar 

Savage AL, Lopez AI, Iacoangeli A, Bubb VJ, Smith B, Troakes C, et al. Frequency and methylation status of selected retrotransposition competent L1 loci in amyotrophic lateral sclerosis. Mol Brain. 2020;13(1):154.

CAS  Article  Google Scholar 

Pfaff AL, Bubb VJ, Quinn JP, Koks S. An Increased Burden of Highly Active Retrotransposition Competent L1s Is Associated with Parkinson’s Disease Risk and Progression in the PPMI Cohort. Int J Mol Sci. 2020;21:18.

Article  Google Scholar 

McKerrow W, Fenyo D. L1EM: a tool for accurate locus specific LINE-1 RNA quantification. Bioinformatics. 2020;36(4):1167–73.

CAS  Article  Google Scholar 

Jeong HH, Yalamanchili HK, Guo C, Shulman JM, Liu Z. An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data. Pac Symp Biocomput. 2018;23:168–79.

PubMed  Google Scholar 

Rausch T, Zichner T, Schlattl A, Stutz AM, Benes V, Korbel JO. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics. 2012;28(18):i333–9.

CAS  Article  Google Scholar 

Penzkofer T, Dandekar T, Zemojtel T. L1Base: from functional annotation to prediction of active LINE-1 elements. Nucleic Acids Res. 2005;33:D498-500.

CAS  Article  Google Scholar 

Jones AR, Iacoangeli A, Adey BN, Bowles H, Shatunov A, Troakes C, et al. A HML6 endogenous retrovirus on chromosome 3 is upregulated in amyotrophic lateral sclerosis motor cortex. Sci Rep. 2021;11(1):14283.

CAS  Article  Google Scholar 

Bachiller S, Del-Pozo-Martin Y, Carrion AM. L1 retrotransposition alters the hippocampal genomic landscape enabling memory formation. Brain Behav Immun. 2017;64:65–70.

CAS  Article  Google Scholar 

Deininger P, Morales ME, White TB, Baddoo M, Hedges DJ, Servant G, et al. A comprehensive approach to expression of L1 loci. Nucleic Acids Res. 2017;45(5):e31.

Article  Google Scholar 

Kaul T, Morales ME, Sartor AO, Belancio VP, Deininger P. Comparative analysis on the expression of L1 loci using various RNA-Seq preparations. Mob DNA. 2020;11:2.

CAS  Article  Google Scholar 

Kaul T, Morales ME, Smither E, Baddoo M, Belancio VP, Deininger P. RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level. J Vis Exp. 2019;147:8.

Google Scholar 

Philippe C, Vargas-Landin DB, Doucet AJ, van Essen D, Vera-Otarola J, Kuciak M, et al. Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci. Elife. 2016;5:e99.

Article  Google Scholar 

Tubio JMC, Li Y, Ju YS, Martincorena I, Cooke SL, Tojo M, et al. Mobile DNA in cancer Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes. Science. 2014;345(6196):1251343.

Article  Google Scholar 

Ewing AD, Smits N, Sanchez-Luque FJ, Faivre J, Brennan PM, Richardson SR, et al. Nanopore sequencing enables comprehensive transposable element epigenomic profiling. Mol Cell. 2020;80(5):915–28.

CAS  Article  Google Scholar 

留言 (0)

沒有登入
gif