Long noncoding RNA as regulatory switch of protein turnover

Long intervening noncoding RNAs (lincRNAs) are prevalent genes with poorly understood functions. Here we discover a pathway of lincRNA-regulated proteolysis. The enhancer-like lincRNA HOTTIP extends the half-life of its binding protein WDR5, a subunit of the MLL H3K4 methylase complex, resulting in increased chromatin occupancy and gene activation. LincRNA-mediated stabilization requires direct RNA-protein interaction in a long RNA context, and blocks turnover at a step after target protein poly-ubiquitination. We elucidate the lincRNA binding interface on WDR5. A WDR5 mutant that selectively abrogates lincRNA binding becomes unstable, and is defective in gene activation, maintenance of histone H3 lysine 4 trimethylation, and embryonic stem cell self renewal. The ability to modulate protein turnover may allow lincRNAs to control the lifespan of molecular interactions at chromatin and elsewhere, broadening their scope in epigenetics and cell fate control. Gene expression analysis: To establish a differentiation signature for mouse V6.5 ES cells infected with anti mouse WDR5 shRNA, rescued with doxycycline inducible WDR5 WT or WDR5 F266A, total RNA was isolated in biologic duplicate from cells in different conditions and hybridized to Affymetrix Mouse 430 2.0 arrays.