Transcription Elongation and Tissue-Specific Somatic CAG Instability
The expansion of CAG/CTG repeats is responsible for many diseases, including Huntington's disease (HD) and myotonic dystrophy 1. CAG/CTG expansions are unstable in selective somatic tissues, which accelerates disease progression. The mechanisms underlying repeat instability are complex, and it remains unclear whether chromatin structure and/or transcription contribute to somatic CAG/CTG instability in vivo. To address these issues, we investigated the relationship between CAG instability, chromatin structure, and transcription at the HD locus using the R6/1 and R6/2 HD transgenic mouse lines. These mice express a similar transgene, albeit integrated at a different site, and recapitulate HD tissue-specific instability. We show that instability rates are increased in R6/2 tissues as compared to R6/1 matched-samples. High transgene expression levels and chromatin accessibility correlated with the increased CAG instability of R6/2 mice. Transgene mRNA and H3K4 trimethylation at the HD locus were increased, whereas H3K9 dimethylation was reduced in R6/2 tissues relative to R6/1 matched-tissues. However, the levels of transgene expression and these specific histone marks were similar in the striatum and cerebellum, two tissues showing very different CAG instability levels, irrespective of mouse line. Interestingly, the levels of elongating RNA Pol II at the HD locus, but not the initiating form of RNA Pol II, were tissue-specific and correlated with CAG instability levels. Similarly, H3K36 trimethylation, a mark associated with transcription elongation, was specifically increased at the HD locus in the striatum and not in the cerebellum. Together, our data support the view that transcription modulates somatic CAG instability in vivo. More specifically, our results suggest for the first time that transcription elongation is regulated in a tissue-dependent manner, contributing to tissue-selective CAG instability.
Vyšlo v časopise:
Transcription Elongation and Tissue-Specific Somatic CAG Instability. PLoS Genet 8(11): e32767. doi:10.1371/journal.pgen.1003051
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1003051
Souhrn
The expansion of CAG/CTG repeats is responsible for many diseases, including Huntington's disease (HD) and myotonic dystrophy 1. CAG/CTG expansions are unstable in selective somatic tissues, which accelerates disease progression. The mechanisms underlying repeat instability are complex, and it remains unclear whether chromatin structure and/or transcription contribute to somatic CAG/CTG instability in vivo. To address these issues, we investigated the relationship between CAG instability, chromatin structure, and transcription at the HD locus using the R6/1 and R6/2 HD transgenic mouse lines. These mice express a similar transgene, albeit integrated at a different site, and recapitulate HD tissue-specific instability. We show that instability rates are increased in R6/2 tissues as compared to R6/1 matched-samples. High transgene expression levels and chromatin accessibility correlated with the increased CAG instability of R6/2 mice. Transgene mRNA and H3K4 trimethylation at the HD locus were increased, whereas H3K9 dimethylation was reduced in R6/2 tissues relative to R6/1 matched-tissues. However, the levels of transgene expression and these specific histone marks were similar in the striatum and cerebellum, two tissues showing very different CAG instability levels, irrespective of mouse line. Interestingly, the levels of elongating RNA Pol II at the HD locus, but not the initiating form of RNA Pol II, were tissue-specific and correlated with CAG instability levels. Similarly, H3K36 trimethylation, a mark associated with transcription elongation, was specifically increased at the HD locus in the striatum and not in the cerebellum. Together, our data support the view that transcription modulates somatic CAG instability in vivo. More specifically, our results suggest for the first time that transcription elongation is regulated in a tissue-dependent manner, contributing to tissue-selective CAG instability.
Zdroje
1. Lopez CastelA, ClearyJD, PearsonCE (2010) Repeat instability as the basis for human diseases and as a potential target for therapy. Nat Rev Mol Cell Biol 11: 165–170.
2. Lopes-CendesI, MacielP, KishS, GasparC, RobitailleY, et al. (1996) Somatic mosaicism in the central nervous system in spinocerebellar ataxia type 1 and Machado-Joseph disease. Ann Neurol 40: 199–206.
3. DuyaoM, AmbroseC, MyersR, NovellettoA, PersichettiF, et al. (1993) Trinucleotide repeat length instability and age of onset in Huntington's disease. Nat Genet 4: 387–392.
4. TeleniusH, KremerB, GoldbergYP, TheilmannJ, AndrewSE, et al. (1994) Somatic and gonadal mosaicism of the Huntington disease gene CAG repeat in brain and sperm. Nat Genet 6: 409–414.
5. GrohWJ, GrohMR, ShenC, MoncktonDG, BodkinCL, et al. (2011) Survival and CTG repeat expansion in adults with myotonic dystrophy type 1. Muscle Nerve 43: 648–651.
6. ShelbournePF, Keller-McGandyC, BiWL, YoonSR, DubeauL, et al. (2007) Triplet repeat mutation length gains correlate with cell-type specific vulnerability in Huntington disease brain. Hum Mol Genet 16: 1133–1142.
7. SwamiM, HendricksAE, GillisT, MassoodT, MysoreJ, et al. (2009) Somatic expansion of the Huntington's disease CAG repeat in the brain is associated with an earlier age of disease onset. Hum Mol Genet 18: 3039–3047.
8. AnvretM, AhlbergG, GrandellU, HedbergB, JohnsonK, et al. (1993) Larger expansions of the CTG repeat in muscle compared to lymphocytes from patients with myotonic dystrophy. Hum Mol Genet 2: 1397–1400.
9. WongLJ, AshizawaT, MoncktonDG, CaskeyCT, RichardsCS (1995) Somatic heterogeneity of the CTG repeat in myotonic dystrophy is age and size dependent. Am J Hum Genet 56: 114–122.
10. Lopez CastelA, NakamoriM, TomeS, ChitayatD, GourdonG, et al. (2011) Expanded CTG repeat demarcates a boundary for abnormal CpG methylation in myotonic dystrophy patient tissues. Hum Mol Genet 20: 1–15.
11. De BiaseI, RasmussenA, EndresD, Al-MahdawiS, MonticelliA, et al. (2007) Progressive GAA expansions in dorsal root ganglia of Friedreich's ataxia patients. Ann Neurol 61: 55–60.
12. ClarkRM, De BiaseI, MalykhinaAP, Al-MahdawiS, PookM, et al. (2007) The GAA triplet-repeat is unstable in the context of the human FXN locus and displays age-dependent expansions in cerebellum and DRG in a transgenic mouse model. Hum Genet 120: 633–640.
13. PanigrahiGB, LauR, MontgomerySE, LeonardMR, PearsonCE (2005) Slipped (CTG)*(CAG) repeats can be correctly repaired, escape repair or undergo error-prone repair. Nat Struct Mol Biol 12: 654–662.
14. GacyAM, GoellnerG, JuranicN, MacuraS, McmurrayCT (1995) Trinucleotide repeats that expand in human disease form hairpin structures in vitro. Cell 81: 533–540.
15. LinY, WilsonJH (2007) Transcription-induced CAG repeat contraction in human cells is mediated in part by transcription-coupled nucleotide excision repair. Mol Cell Biol 27: 6209–6217.
16. ManleyK, ShirleyTL, FlahertyL, MesserA (1999) Msh2 deficiency prevents in vivo somatic instability of the CAG repeat in Huntington disease transgenic mice. Nat Genet 23: 471–473.
17. KovtunIV, LiuY, BjorasM, KlunglandA, WilsonSH, et al. (2007) OGG1 initiates age-dependent CAG trinucleotide expansion in somatic cells. Nature 447: 447–452.
18. DragilevaE, HendricksA, TeedA, GillisT, LopezET, et al. (2009) Intergenerational and striatal CAG repeat instability in Huntington's disease knock-in mice involve different DNA repair genes. Neurobiol Dis 33: 37–47.
19. HubertLJr, LinY, DionV, WilsonJH (2011) Xpa deficiency reduces CAG trinucleotide repeat instability in neuronal tissues in a mouse model of SCA1. Hum Mol Genet 20: 4822–4830.
20. LinY, DionV, WilsonJH (2006) Transcription promotes contraction of CAG repeat tracts in human cells. Nat Struct Mol Biol 13: 179–180.
21. Salinas-RiosV, BelotserkovskiiBP, HanawaltPC (2011) DNA slip-outs cause RNA polymerase II arrest in vitro: potential implications for genetic instability. Nucleic Acids Res 39: 7444–7454.
22. LinY, DentSY, WilsonJH, WellsRD, NapieralaM (2010) R loops stimulate genetic instability of CTG.CAG repeats. Proc Natl Acad Sci U S A 107: 692–697.
23. ReddyK, TamM, BowaterRP, BarberM, TomlinsonM, et al. (2010) Determinants of R-loop formation at convergent bidirectionally transcribed trinucleotide repeats. Nucleic Acids Res 39: 1749–1762.
24. NakamoriM, PearsonCE, ThorntonCA (2011) Bidirectional transcription stimulates expansion and contraction of expanded (CTG)*(CAG) repeats. Hum Mol Genet 20: 580–588.
25. DureLSt, LandwehrmeyerGB, GoldenJ, McNeilSM, GeP, et al. (1994) IT15 gene expression in fetal human brain. Brain Res 659: 33–41.
26. BhidePG, DayM, SappE, SchwarzC, ShethA, et al. (1996) Expression of normal and mutant huntingtin in the developing brain. J Neurosci 16: 5523–5535.
27. LiaAS, SeznecH, Hofmann-RadvanyiH, RadvanyiF, DurosC, et al. (1998) Somatic instability of the CTG repeat in mice transgenic for the myotonic dystrophy region is age dependent but not correlated to the relative intertissue transcription levels and proliferative capacities. Hum Mol Genet 7: 1285–1291.
28. KouzaridesT (2007) Chromatin modifications and their function. Cell 128: 693–705.
29. DionV, WilsonJH (2009) Instability and chromatin structure of expanded trinucleotide repeats. Trends Genet 25: 288–297.
30. SavelievA, EverettC, SharpeT, WebsterZ, FestensteinR (2003) DNA triplet repeats mediate heterochromatin-protein-1-sensitive variegated gene silencing. Nature 422: 909–913.
31. ChoDH, ThienesCP, MahoneySE, AnalauE, FilippovaGN, et al. (2005) Antisense transcription and heterochromatin at the DM1 CTG repeats are constrained by CTCF. Mol Cell 20: 483–489.
32. MangiariniL, SathasivamK, SellerM, CozensB, HarperA, et al. (1996) Exon 1 of the HD gene with an expanded CAG repeat is sufficient to cause a progressive neurological phenotype in transgenic mice. Cell 87: 493–506.
33. ChiangC, JacobsenJC, ErnstC, HanscomC, HeilbutA, et al. (2012) Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration. Nat Genet 44: 390–397, S391.
34. CowinRM, BuiN, GrahamD, GreenJR, GrueningerS, et al. (2011) Onset and progression of behavioral and molecular phenotypes in a novel congenic R6/2 line exhibiting intergenerational CAG repeat stability. PLoS ONE 6: e28409 doi:10.1371/journal.pone.0028409
35. MangiariniL, SathasivamK, MahalA, MottR, SellerM, et al. (1997) Instability of highly expanded CAG repeats in mice transgenic for the Huntington's disease mutation [see comments]. Nat Genet 15: 197–200.
36. GoulaAV, BerquistBR, WilsonDM3rd, WheelerVC, TrottierY, et al. (2009) Stoichiometry of base excision repair proteins correlates with increased somatic CAG instability in striatum over cerebellum In Huntington's disease transgenic mice. PLoS Genet 5: e1000749 doi:10.1371/journal.pgen.1000749
37. KimE, NapieralaM, DentSY (2011) Hyperexpansion of GAA repeats affects post-initiation steps of FXN transcription in Friedreich's ataxia. Nucleic Acids Res 39: 8366–8377.
38. KumariD, BiacsiRE, UsdinK (2011) Repeat expansion affects both transcription initiation and elongation in friedreich ataxia cells. J Biol Chem 286: 4209–4215.
39. KumariD, UsdinK (2010) The distribution of repressive histone modifications on silenced FMR1 alleles provides clues to the mechanism of gene silencing in fragile X syndrome. Hum Mol Genet 19: 4634–4642.
40. KaplanN, MooreIK, Fondufe-MittendorfY, GossettAJ, TilloD, et al. (2009) The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458: 362–366.
41. BarskiA, CuddapahS, CuiK, RohTY, SchonesDE, et al. (2007) High-resolution profiling of histone methylations in the human genome. Cell 129: 823–837.
42. BesseS, VigneronM, PichardE, Puvion-DutilleulF (1995) Synthesis and maturation of viral transcripts in herpes simplex virus type 1 infected HeLa cells: the role of interchromatin granules. Gene Expr 4: 143–161.
43. NechaevS, AdelmanK (2011) Pol II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation. Biochim Biophys Acta 1809: 34–45.
44. MuseGW, GilchristDA, NechaevS, ShahR, ParkerJS, et al. (2007) RNA polymerase is poised for activation across the genome. Nat Genet 39: 1507–1511.
45. GuentherMG, LevineSS, BoyerLA, JaenischR, YoungRA (2007) A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130: 77–88.
46. BannisterAJ, SchneiderR, MyersFA, ThorneAW, Crane-RobinsonC, et al. (2005) Spatial distribution of di- and tri-methyl lysine 36 of histone H3 at active genes. J Biol Chem 280: 17732–17736.
47. StrongTV, TagleDA, ValdesJM, ElmerLW, BoehmK, et al. (1993) Widespread expression of the human and rat Huntington's disease gene in brain and nonneural tissues. Nature Genet 5: 259–265.
48. LiS-H, SchillingG, YoungWSIII, LiX-J, MargolisRL, et al. (1993) Huntington's disease gene (IT15) is widely expressed in human and rat tissues. Neuron 11: 985–993.
49. KumariD, UsdinK (2009) Chromatin remodeling in the noncoding repeat expansion diseases. J Biol Chem 284: 7413–7417.
50. Al-MahdawiS, PintoRM, IsmailO, VarshneyD, LymperiS, et al. (2008) The Friedreich ataxia GAA repeat expansion mutation induces comparable epigenetic changes in human and transgenic mouse brain and heart tissues. Hum Mol Genet 17: 735–746.
51. HermanD, JenssenK, BurnettR, SoragniE, PerlmanSL, et al. (2006) Histone deacetylase inhibitors reverse gene silencing in Friedreich's ataxia. Nat Chem Biol 2: 551–558.
52. De BiaseI, ChutakeYK, RindlerPM, BidichandaniSI (2009) Epigenetic silencing in Friedreich ataxia is associated with depletion of CTCF (CCCTC-binding factor) and antisense transcription. PLoS ONE 4: e7914 doi:10.1371/journal.pone.0007914
53. BiacsiR, KumariD, UsdinK (2008) SIRT1 inhibition alleviates gene silencing in Fragile X mental retardation syndrome. PLoS Genet 4: e1000017 doi:10.1371/journal.pgen.1000017
54. PungaT, BuhlerM (2010) Long intronic GAA repeats causing Friedreich ataxia impede transcription elongation. EMBO Mol Med 2: 120–129.
55. GottesfeldJM (2007) Small molecules affecting transcription in Friedreich ataxia. Pharmacol Ther 116: 236–248.
56. DebackerK, FrizzellA, GleesonO, Kirkham-McCarthyL, MertzT, et al. (2012) Histone deacetylase complexes promote trinucleotide repeat expansions. PLoS Biol 10: e1001257 doi:10.1371/journal.pbio.1001257
57. PearsonCE, SindenRR (1996) Alternative structures in duplex DNA formed within the trinucleotide repeats of the myotonic dystrophy and fragile X loci. Biochemistry 35: 5041–5053.
58. WheelerVC, LebelLA, VrbanacV, TeedA, te RieleH, et al. (2003) Mismatch repair gene Msh2 modifies the timing of early disease in Hdh(Q111) striatum. Hum Mol Genet 12: 273–281.
59. SavouretC, Garcia-CordierC, MegretJ, te RieleH, JunienC, et al. (2004) MSH2-dependent germinal CTG repeat expansions are produced continuously in spermatogonia from DM1 transgenic mice. Mol Cell Biol 24: 629–637.
60. van den BroekWJ, NelenMR, WansinkDG, CoerwinkelMM, te RieleH, et al. (2002) Somatic expansion behaviour of the (CTG)n repeat in myotonic dystrophy knock-in mice is differentially affected by Msh3 and Msh6 mismatch-repair proteins. Hum Mol Genet 11: 191–198.
61. SaundersA, CoreLJ, LisJT (2006) Breaking barriers to transcription elongation. Nat Rev Mol Cell Biol 7: 557–567.
62. AdelmanK, MarrMT, WernerJ, SaundersA, NiZ, et al. (2005) Efficient release from promoter-proximal stall sites requires transcript cleavage factor TFIIS. Mol Cell 17: 103–112.
63. YamadaT, YamaguchiY, InukaiN, OkamotoS, MuraT, et al. (2006) P-TEFb-mediated phosphorylation of hSpt5 C-terminal repeats is critical for processive transcription elongation. Mol Cell 21: 227–237.
64. LiuCR, ChangCR, ChernY, WangTH, HsiehWC, et al. (2012) Spt4 is selectively required for transcription of extended trinucleotide repeats. Cell 148: 690–701.
65. StineOC, LiSH, PleasantN, WagsterMV, HedreenJC, et al. (1995) Expression of the mutant allele of IT-15 (the HD gene) in striatum and cortex of Huntington's disease patients. HumMolGenet 4: 15–18.
66. CasanovaE, Alonso-LlamazaresA, ZamanilloD, GarateC, CalvoP, et al. (1996) Identification of a long huntingtin mRNA transcript in mouse brain. Brain Res 743: 320–323.
67. LinB, RommensJM, GrahamRK, KalchmanM, MacDonaldH, et al. (1993) Differential 3′ polyadenylation of the Huntington disease gene results in two mRNA species with variable tissue expression. Hum Mol Genet 2: 1541–1545.
68. ZenklusenD, LarsonDR, SingerRH (2008) Single-RNA counting reveals alternative modes of gene expression in yeast. Nat Struct Mol Biol 15: 1263–1271.
69. KaernM, ElstonTC, BlakeWJ, CollinsJJ (2005) Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet 6: 451–464.
70. RajalaT, HakkinenA, HealyS, Yli-HarjaO, RibeiroAS (2010) Effects of transcriptional pausing on gene expression dynamics. PLoS Comput Biol 6: e1000704 doi:10.1371/journal.pcbi.1000704
71. BelotserkovskiiBP, LiuR, TornalettiS, KrasilnikovaMM, MirkinSM, et al. (2010) Mechanisms and implications of transcription blockage by guanine-rich DNA sequences. Proc Natl Acad Sci U S A 107: 12816–12821.
72. LinY, LengM, WanM, WilsonJH (2010) Convergent transcription through a long CAG tract destabilizes repeats and induces apoptosis. Mol Cell Biol 30: 4435–4451.
73. HanawaltPC, SpivakG (2008) Transcription-coupled DNA repair: two decades of progress and surprises. Nat Rev Mol Cell Biol 9: 958–970.
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Genetika Reprodukčná medicínaČlánok vyšiel v časopise
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