Is a Modifier of Mutations in Retinitis Pigmentosa with Incomplete Penetrance

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Heterozygous mutations in the PRPF31 gene cause autosomal dominant retinitis pigmentosa (adRP), a hereditary disorder leading to progressive blindness. In some cases, such mutations display incomplete penetrance, implying that certain carriers develop retinal degeneration while others have no symptoms at all. Asymptomatic carriers are protected from the disease by a higher than average expression of the PRPF31 allele that is not mutated, mainly through the action of an unknown modifier gene mapping to chromosome 19q13.4. We investigated a large family with adRP segregating an 11-bp deletion in PRPF31. The analysis of cell lines derived from asymptomatic and affected individuals revealed that the expression of only one gene among a number of candidates within the 19q13.4 interval significantly correlated with that of PRPF31, both at the mRNA and protein levels, and according to an inverse relationship. This gene was CNOT3, encoding a subunit of the Ccr4-not transcription complex. In cultured cells, siRNA–mediated silencing of CNOT3 provoked an increase in PRPF31 expression, confirming a repressive nature of CNOT3 on PRPF31. Furthermore, chromatin immunoprecipitation revealed that CNOT3 directly binds to a specific PRPF31 promoter sequence, while next-generation sequencing of the CNOT3 genomic region indicated that its variable expression is associated with a common intronic SNP. In conclusion, we identify CNOT3 as the main modifier gene determining penetrance of PRPF31 mutations, via a mechanism of transcriptional repression. In asymptomatic carriers CNOT3 is expressed at low levels, allowing higher amounts of wild-type PRPF31 transcripts to be produced and preventing manifestation of retinal degeneration.

Vyšlo v časopise: Is a Modifier of Mutations in Retinitis Pigmentosa with Incomplete Penetrance. PLoS Genet 8(11): e32767. doi:10.1371/journal.pgen.1003040
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003040

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Zdroje

1. AhluwaliaJK, HariharanM, BargajeR, PillaiB, BrahmachariV (2009) Incomplete penetrance and variable expressivity: is there a microRNA connection? Bioessays 31: 981–992.

2. ZlotogoraJ (2003) Penetrance and expressivity in the molecular age. Genet Med 5: 347–352.

3. BersonEL (1993) Retinitis pigmentosa. The Friedenwald Lecture. Invest Ophthalmol Vis Sci 34: 1659–1676.

4. HartongDT, BersonEL, DryjaTP (2006) Retinitis pigmentosa. Lancet 368: 1795–1809.

5. EvansK, al-MaghthehM, FitzkeFW, MooreAT, JayM, et al. (1995) Bimodal expressivity in dominant retinitis pigmentosa genetically linked to chromosome 19q. Br J Ophthalmol 79: 841–846.

6. MooreAT, FitzkeF, JayM, ArdenGB, InglehearnCF, et al. (1993) Autosomal dominant retinitis pigmentosa with apparent incomplete penetrance: a clinical, electrophysiological, psychophysical, and molecular genetic study. Br J Ophthalmol 77: 473–479.

7. BersonEL, SimonoffEA (1979) Dominant retinitis pigmentosa with reduced penetrance. Further studies of the electroretinogram. Arch Ophthalmol 97: 1286–1291.

8. BersonEL, GourasP, GunkelRD, MyrianthopoulosNC (1969) Dominant retinitis pigmentosa with reduced penetrance. Arch Ophthalmol 81: 226–234.

9. RoseAM, MukhopadhyayR, WebsterAR, BhattacharyaSS, WaseemNH (2011) A 112 kb deletion in chromosome 19q13.42 leads to retinitis pigmentosa. Invest Ophthalmol Vis Sci 52: 6597–6603.

10. Rio FrioT, WadeNM, RansijnA, BersonEL, BeckmannJS, et al. (2008) Premature termination codons in PRPF31 cause retinitis pigmentosa via haploinsufficiency due to nonsense-mediated mRNA decay. J Clin Invest 118: 1519–1531.

11. WaseemNH, VaclavikV, WebsterA, JenkinsSA, BirdAC, et al. (2007) Mutations in the gene coding for the pre-mRNA splicing factor, PRPF31, in patients with autosomal dominant retinitis pigmentosa. Invest Ophthalmol Vis Sci 48: 1330–1334.

12. Abu-SafiehL, VithanaEN, MantelI, HolderGE, PelosiniL, et al. (2006) A large deletion in the adRP gene PRPF31: evidence that haploinsufficiency is the cause of disease. Mol Vis 12: 384–388.

13. SullivanLS, BowneSJ, SeamanCR, BlantonSH, LewisRA, et al. (2006) Genomic rearrangements of the PRPF31 gene account for 2.5% of autosomal dominant retinitis pigmentosa. Invest Ophthalmol Vis Sci 47: 4579–4588.

14. VithanaEN, Abu-SafiehL, AllenMJ, CareyA, PapaioannouM, et al. (2001) A human homolog of yeast pre-mRNA splicing gene, PRP31, underlies autosomal dominant retinitis pigmentosa on chromosome 19q13.4 (RP11). Mol Cell 8: 375–381.

15. TanackovicG, RansijnA, ThibaultP, Abou ElelaS, KlinckR, et al. (2011) PRPF mutations are associated with generalized defects in spliceosome formation and pre-mRNA splicing in patients with retinitis pigmentosa. Hum Mol Genet 20: 2116–2130.

16. Rio FrioT, CivicN, RansijnA, BeckmannJS, RivoltaC (2008) Two trans-acting eQTLs modulate the penetrance of PRPF31 mutations. Hum Mol Genet 17: 3154–3165.

17. RivoltaC, McGeeTL, Rio FrioT, JensenRV, BersonEL, et al. (2006) Variation in retinitis pigmentosa-11 (PRPF31 or RP11) gene expression between symptomatic and asymptomatic patients with dominant RP11 mutations. Hum Mutat 27: 644–653.

18. VithanaEN, Abu-SafiehL, PelosiniL, WinchesterE, HornanD, et al. (2003) Expression of PRPF31 mRNA in patients with autosomal dominant retinitis pigmentosa: a molecular clue for incomplete penetrance? Invest Ophthalmol Vis Sci 44: 4204–4209.

19. McGeeTL, DevotoM, OttJ, BersonEL, DryjaTP (1997) Evidence that the penetrance of mutations at the RP11 locus causing dominant retinitis pigmentosa is influenced by a gene linked to the homologous RP11 allele. Am J Hum Genet 61: 1059–1066.

20. al-MaghthehM, InglehearnCF, KeenTJ, EvansK, MooreAT, et al. (1994) Identification of a sixth locus for autosomal dominant retinitis pigmentosa on chromosome 19. Hum Mol Genet 3: 351–354.

21. CollartMA, PanasenkoOO (2012) The Ccr4–not complex. Gene 492: 42–53.

22. MoritaM, OikeY, NagashimaT, KadomatsuT, TabataM, et al. (2011) Obesity resistance and increased hepatic expression of catabolism-related mRNAs in Cnot3+/− mice. EMBO J 30: 4678–4691.

23. HuG, KimJ, XuQ, LengY, OrkinSH, et al. (2009) A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal. Genes Dev 23: 837–848.

24. ChakarovaCF, CherninkovaS, TournevI, WaseemN, KanevaR, et al. (2006) Molecular genetics of retinitis pigmentosa in two Romani (Gypsy) families. Mol Vis 12: 909–914.

25. GratzerW (1994) Human genetics. Silence speaks in spectrin. Nature 372: 620–621.

26. GouyaL, PuyH, RobreauAM, BourgeoisM, LamorilJ, et al. (2002) The penetrance of dominant erythropoietic protoporphyria is modulated by expression of wildtype FECH. Nat Genet 30: 27–28.

27. GouyaL, PuyH, RobreauAM, LyoumiS, LamorilJ, et al. (2004) Modulation of penetrance by the wild-type allele in dominantly inherited erythropoietic protoporphyria and acute hepatic porphyrias. Hum Genet 114: 256–262.

28. IvingsL, TownsKV, MatinMA, TaylorC, PonchelF, et al. (2008) Evaluation of splicing efficiency in lymphoblastoid cell lines from patients with splicing-factor retinitis pigmentosa. Mol Vis 14: 2357–2366.

29. Rio FrioT, McGeeTL, WadeNM, IseliC, BeckmannJS, et al. (2009) A single-base substitution within an intronic repetitive element causes dominant retinitis pigmentosa with reduced penetrance. Hum Mutat 30: 1340–1347.

30. WinklerGS, MulderKW, BardwellVJ, KalkhovenE, TimmersHT (2006) Human Ccr4-Not complex is a ligand-dependent repressor of nuclear receptor-mediated transcription. EMBO J 25: 3089–3099.

31. CollartMA, StruhlK (1994) NOT1(CDC39), NOT2(CDC36), NOT3, and NOT4 encode a global-negative regulator of transcription that differentially affects TATA-element utilization. Genes Dev 8: 525–537.

32. LauNC, KolkmanA, van SchaikFM, MulderKW, PijnappelWW, et al. (2009) Human Ccr4-Not complexes contain variable deadenylase subunits. Biochem J 422: 443–453.

33. AlbertTK, LemaireM, van BerkumNL, GentzR, CollartMA, et al. (2000) Isolation and characterization of human orthologs of yeast CCR4-NOT complex subunits. Nucleic Acids Res 28: 809–817.

34. KerrSC, AzzouzN, FuchsSM, CollartMA, StrahlBD, et al. (2011) The Ccr4-Not complex interacts with the mRNA export machinery. PLoS ONE 6: e18302 doi:10.1371/journal.pone.0018302

35. ZwartjesCG, JayneS, van den BergDL, TimmersHT (2004) Repression of promoter activity by CNOT2, a subunit of the transcription regulatory Ccr4-not complex. J Biol Chem 279: 10848–10854.

36. RoseAM, ShahAZ, WaseemNH, ChakarovaCF, AlfanoG, et al. (2012) Expression of PRPF31 and TFPT: regulation in health and retinal disease. Hum Mol Genet In press.

37. Al-MaghthehM, VithanaE, TarttelinE, JayM, EvansK, et al. (1996) Evidence for a major retinitis pigmentosa locus on 19q13.4 (RP11) and association with a unique bimodal expressivity phenotype. Am J Hum Genet 59: 864–871.

38. OberleyMJ, InmanDR, FarnhamPJ (2003) E2F6 negatively regulates BRCA1 in human cancer cells without methylation of histone H3 on lysine 9. J Biol Chem 278: 42466–42476.