From non-coding RNAs to histone demethylases: Identifying novel epigenetic regulators of the HOX loci in development and cancer

Epigenetics, the heritable changes in phenotype or gene expression caused by mechanisms other than the underlying DNA sequence, play an integral part in cell differentiation, development, and cancer. Recent discoveries of new classes of epigenetic regulators, such as noncoding RNAs (ncRNAs) and histone demethylases, have unlocked new molecules that not only shed light on complex mechanisms of regulation, but also provide potential therapeutic targets. We identified 231 ncRNAs in the HOX loci, genes essential in specifying positional identities of cells. We found that one of these ncRNAs, HOTAIR, reveals a novel mechanism of ncRNA guidance of transcriptional silencing via the Polycomb group (PcG) proteins in trans. PcG proteins regulate HOX expression and maintenance by trimethylating histone H3 on lysine 27 (H3K27me3), rendering the target transcriptionally silent. While regulation of HOX expression may influence the positional identity of cells and their differentiation, the mechanism downstream and putative targets remain poorly understood. We show that expression of HOXA13 is required and the transcriptional targets are sufficient to maintain epidermal inductive properties of distal fibroblasts.;The discovery of histone demethylases has challenged the original concept that histone methylation is a permanent and stable epigenetic mark, and has raised the question of the existence of a H3K27me3 demethylase. We and others demonstrate the related JmjC domain-containing UTX and JMJD3 catalyze demethylation of H3K27me3, and UTX regulates H3K27 methylation at the HOX gene locus, where its absence results in misregulation of HOX genes and a significant posterior developmental defect. H3K27me3 has also been shown to inhibit the transcription of tumor suppressor genes. One of the core PcG proteins, H3K27 methylase EZH2, is amplified or overexpressed in human breast, prostate, and melanocytic tumors, and is a strong predictor of cancer progression. Here we show that the H3K27me3 demethylase UTX is essential for cell cycle control. Genome-wide chromatin occupancy analysis revealed that UTX bound multiple genes encoding RB-binding proteins, and UDC is required to remove H3K27me3 and maintain expression of several RB-binding proteins. In human cancer samples, loss of UTX expression is a significant predictor of disease progression and worse survival. Proper demethylation of H3K27me3 by UTX enables the RB-dependent cell cycle checkpoint and guards against cancer.