Journal Article

Role for perinuclear chromosome tethering in maintenance of genome stability

Gygi, Steven P., Moazed, Danesh, Seebacher, Jan, Mekhail, Karim

2008

Overview

Chromsomes tethered for stability Suppressing the homologous recombination of repetitive DNA sequences is important for maintaining genome stability, and packaging of repeat DNA into silent chromatin was generally thought to protect it from recombination. Here, yeast ribosomal DNA (rDNA) repetitive sequences are shown to associate with the nuclear periphery via inner nuclear membrane proteins, and this tethering is required for rDNA stability. Sir2-dependent silencing is not sufficient to inhibit rDNA recombination. The inner nuclear membrane proteins involved are conserved and have been implicated in chromosome organization in metazoans. These results therefore reveal an ancient mechanism in which interactions between inner nuclear membrane proteins and chromosomal proteins ensure genome stability. Suppressing the homologous recombination of repetitive DNA sequences is important for maintaining genome stability, and packaging of repeat DNA into silent chromatin was generally thought to protect it from recombination. Yeast ribosomal DNA (rDNA) repetitive sequences are shown to associate with the nuclear periphery via inner nuclear membrane proteins, and this tethering is required for rDNA stability. Sir2-dependent silencing is not sufficient to inhibit rDNA recombination. Repetitive DNA sequences, which constitute half the genome in some organisms, often undergo homologous recombination. This can instigate genomic instability resulting from a gain or loss of DNA 1 . Assembly of DNA into silent chromatin is generally thought to serve as a mechanism ensuring repeat stability by limiting access to the recombination machinery 2 . Consistent with this notion is the observation, in the budding yeast Saccharomyces cerevisiae , that stability of the highly repetitive ribosomal DNA (rDNA) sequences requires a Sir2-containing chromatin silencing complex that also inhibits transcription from foreign promoters and transposons inserted within the repeats by a process called rDNA silencing 2 , 3 , 4 , 5 . Here we describe a protein network that stabilizes rDNA repeats of budding yeast by means of interactions between rDNA-associated silencing proteins and two proteins of the inner nuclear membrane (INM). Deletion of either the INM or silencing proteins reduces perinuclear rDNA positioning, disrupts the nucleolus–nucleoplasm boundary, induces the formation of recombination foci, and destabilizes the repeats. In addition, artificial targeting of rDNA repeats to the INM suppresses the instability observed in cells lacking an rDNA-associated silencing protein that is typically required for peripheral tethering of the repeats. Moreover, in contrast to Sir2 and its associated nucleolar factors, the INM proteins are not required for rDNA silencing, indicating that Sir2-dependent silencing is not sufficient to inhibit recombination within the rDNA locus. These findings demonstrate a role for INM proteins in the perinuclear localization of chromosomes and show that tethering to the nuclear periphery is required for the stability of rDNA repeats. The INM proteins studied here are conserved and have been implicated in chromosome organization in metazoans 6 , 7 . Our results therefore reveal an ancient mechanism in which interactions between INM proteins and chromosomal proteins ensure genome stability.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: Biological and medical sciences / Cell membranes / Chromosomal Position Effects / Chromosomal Proteins, Non-Histone - metabolism / Chromosome Positioning / Chromosomes / Chromosomes, Fungal - genetics / Chromosomes, Fungal - metabolism / DNA, Ribosomal - genetics / DNA, Ribosomal - metabolism / Electric fields / Fundamental and applied biological sciences. Psychology / Gene Expression Regulation, Fungal / Gene Silencing / Genetic research / Genetics / Genic rearrangement. Recombination. Transposable element / Genomes / Genomic Instability - genetics / Humanities and Social Sciences / letter / Mass spectrometry / Metazoa / Molecular and cellular biology / Molecular genetics / multidisciplinary / Nuclear Envelope - chemistry / Nuclear Envelope - genetics / Nuclear Envelope - metabolism / Nucleotide sequence / Protein Binding / Protein research / Proteins / Recombination, Genetic - genetics / Repetitive Sequences, Nucleic Acid - genetics / RNA polymerase / Saccharomyces cerevisiae / Saccharomyces cerevisiae - cytology / Saccharomyces cerevisiae - genetics / Science / Yeasts