Tandem Stem-Loops in roX RNAs Act Together to Mediate X Chromosome Dosage Compensation in Drosophila

• Published in: Molecular cell Vol. 51; no. 2; pp. 156 - 173
• Main Authors: Ilik, Ibrahim Avsar, Quinn, Jeffrey J., Georgiev, Plamen, Tavares-Cadete, Filipe, Maticzka, Daniel, Toscano, Sarah, Wan, Yue, Spitale, Robert C., Luscombe, Nicholas, Backofen, Rolf, Chang, Howard Y., Akhtar, Asifa
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 25.07.2013
• Subjects: Animals; Animals, Genetically Modified; Base Pairing; Blotting, Western; Chromatin - genetics; Chromosomal Proteins, Non-Histone - genetics; Chromosomal Proteins, Non-Histone - metabolism; crosslinking; DNA Helicases - genetics; DNA Helicases - metabolism; dosage; Dosage Compensation, Genetic - genetics; Drosophila; Drosophila melanogaster - genetics; Drosophila melanogaster - growth & development; Drosophila melanogaster - metabolism; Drosophila Proteins - chemistry; Drosophila Proteins - genetics; Drosophila Proteins - metabolism; epigenetics; gene expression regulation; high-throughput nucleotide sequencing; Immunoprecipitation; Male; males; multiprotein complexes; mutation; Mutation - genetics; non-coding RNA; Nucleic Acid Conformation; RNA - chemistry; RNA - genetics; RNA - metabolism; RNA helicases; RNA-Binding Proteins - chemistry; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism; Tandem Repeat Sequences - genetics; transcription (genetics); Transcription Factors - chemistry; Transcription Factors - genetics; Transcription Factors - metabolism; Transcription, Genetic; ubiquitin-protein ligase; Ubiquitin-Protein Ligases - genetics; Ubiquitin-Protein Ligases - metabolism; X chromosome; X Chromosome - genetics; X Chromosome - metabolism
• ISSN: 1097-2765; 1097-4164; 1097-4164
• DOI: 10.1016/j.molcel.2013.07.001

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. [Display omitted] •roX RNAs contain conserved and structured domains formed by tandem stem loops•Structured domains in roX RNAs form hot spots for MLE and MSL2 interaction•MLE binds roX2 RNA in an ATP-independent manner and uses ATP for dynamic interaction•Combined action of conserved tandem stem loops in roX2 is crucial for male viability