Tandem stem-loops in roX RNAs act together to mediate X chromosome dosage compensation in Drosophila

Mol Cell. 2013 Jul 25;51(2):156-73. doi: 10.1016/j.molcel.2013.07.001.

Abstract

Dosage compensation in Drosophila is an epigenetic phenomenon utilizing proteins and long noncoding RNAs (lncRNAs) for transcriptional upregulation of the male X chromosome. Here, by using UV crosslinking followed by deep sequencing, we show that two enzymes in the Male-Specific Lethal complex, MLE RNA helicase and MSL2 ubiquitin ligase, bind evolutionarily conserved domains containing tandem stem-loops in roX1 and roX2 RNAs in vivo. These domains constitute the minimal RNA unit present in multiple copies in diverse arrangements for nucleation of the MSL complex. MLE binds to these domains with distinct ATP-independent and ATP-dependent behavior. Importantly, we show that different roX RNA domains have overlapping function, since only combinatorial mutations in the tandem stem-loops result in severe loss of dosage compensation and consequently male-specific lethality. We propose that repetitive structural motifs in lncRNAs could provide plasticity during multiprotein complex assemblies to ensure efficient targeting in cis or in trans along chromosomes.

Publication types

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

MeSH terms

  • Animals
  • Animals, Genetically Modified
  • Base Pairing
  • Blotting, Western
  • Chromatin / genetics
  • Chromosomal Proteins, Non-Histone / genetics
  • Chromosomal Proteins, Non-Histone / metabolism
  • DNA Helicases / genetics
  • DNA Helicases / metabolism
  • Dosage Compensation, Genetic / genetics*
  • Drosophila Proteins / chemistry
  • Drosophila Proteins / genetics*
  • Drosophila Proteins / metabolism
  • Drosophila melanogaster / genetics*
  • Drosophila melanogaster / growth & development
  • Drosophila melanogaster / metabolism
  • Immunoprecipitation
  • Male
  • Mutation / genetics
  • Nucleic Acid Conformation
  • RNA / chemistry
  • RNA / genetics*
  • RNA / metabolism
  • RNA-Binding Proteins / chemistry
  • RNA-Binding Proteins / genetics*
  • RNA-Binding Proteins / metabolism
  • Tandem Repeat Sequences / genetics
  • Transcription Factors / chemistry
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism
  • Transcription, Genetic
  • Ubiquitin-Protein Ligases / genetics
  • Ubiquitin-Protein Ligases / metabolism
  • X Chromosome / genetics*
  • X Chromosome / metabolism

Substances

  • Chromatin
  • Chromosomal Proteins, Non-Histone
  • Drosophila Proteins
  • Pabp2 protein, Drosophila
  • RNA-Binding Proteins
  • Transcription Factors
  • mle protein, Drosophila
  • roX1 protein, Drosophila
  • RNA
  • Ubiquitin-Protein Ligases
  • DNA Helicases