Synergistic lethality between BRCA1 and H3K9me2 loss reflects satellite derepression

Genes Dev. 2019 Apr 1;33(7-8):436-451. doi: 10.1101/gad.322495.118. Epub 2019 Feb 25.

Abstract

Caenorhabditis elegans has two histone H3 Lys9 methyltransferases, MET-2 (SETDB1 homolog) and SET-25 (G9a/SUV39H1 related). In worms, we found simple repeat sequences primarily marked by H3K9me2, while transposable elements and silent tissue-specific genes bear H3K9me3. RNA sequencing (RNA-seq) in histone methyltransferase (HMT) mutants shows that MET-2-mediated H3K9me2 is necessary for satellite repeat repression, while SET-25 silences a subset of transposable elements and tissue-specific genes through H3K9me3. A genome-wide synthetic lethality screen showed that RNA processing, nuclear RNA degradation, the BRCA1/BARD1 complex, and factors mediating replication stress survival are necessary for germline viability in worms lacking MET-2 but not SET-25. Unlike set-25 mutants, met-2-null worms accumulated satellite repeat transcripts, which form RNA:DNA hybrids on repetitive sequences, additively with the loss of BRCA1 or BARD1. BRCA1/BARD1-mediated H2A ubiquitination and MET-2 deposited H3K9me2 on satellite repeats are partially interdependent, suggesting both that the loss of silencing generates BRCA-recruiting DNA damage and that BRCA1 recruitment by damage helps silence repeats. The artificial induction of MSAT1 transcripts can itself trigger damage-induced germline lethality in a wild-type background, arguing that the synthetic sterility upon BRCA1/BARD1 and H3K9me2 loss is directly linked to the DNA damage provoked by unscheduled satellite repeat transcription.

Keywords: BRCA1 complex; DNA repeats; RNA:DNA hybrids; genome instability; heterochromatin; histone H3K9 methylation; satellite repeats; transcriptional silencing.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • BRCA1 Protein / genetics*
  • BRCA1 Protein / metabolism
  • Caenorhabditis elegans / embryology*
  • Caenorhabditis elegans / genetics*
  • Caenorhabditis elegans Proteins / genetics*
  • Caenorhabditis elegans Proteins / metabolism
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • DNA Transposable Elements / genetics
  • Embryo, Nonmammalian
  • Fertility / genetics
  • Gene Expression Regulation, Developmental / genetics*
  • Histone-Lysine N-Methyltransferase / genetics
  • Histone-Lysine N-Methyltransferase / metabolism
  • Histones / genetics*
  • Microsatellite Repeats / genetics
  • Mutation
  • RNA Processing, Post-Transcriptional / genetics
  • Temperature

Substances

  • BRCA1 Protein
  • Caenorhabditis elegans Proteins
  • DNA Transposable Elements
  • Histones
  • Histone-Lysine N-Methyltransferase
  • Met-2 protein, C elegans
  • SET-25 protein, C elegans