CNOT3 is a modifier of PRPF31 mutations in retinitis pigmentosa with incomplete penetrance

PLoS Genet. 2012;8(11):e1003040. doi: 10.1371/journal.pgen.1003040. Epub 2012 Nov 8.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Eye Proteins / genetics*
  • Eye Proteins / metabolism
  • Gene Expression Regulation
  • Heterozygote
  • Humans
  • Penetrance*
  • Polymorphism, Single Nucleotide
  • Promoter Regions, Genetic
  • RNA, Small Interfering
  • Retinitis Pigmentosa* / genetics
  • Retinitis Pigmentosa* / metabolism
  • Sequence Deletion
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism

Substances

  • CNOT3 protein, human
  • Eye Proteins
  • PRPF31 protein, human
  • RNA, Small Interfering
  • Transcription Factors

Grant support

This work was supported by the Swiss National Science Foundation (grants 320030-121929 and 310030_138346), the Gebert Rüf Foundation (Rare Diseases - New Technologies grant), the Rosetrees Trust, and Fight for Sight. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.