Histone side chains are post-translationally modified at multiple sites, including at Lys36 on histone H3 (H3K36). Several enzymes from yeast and humans, including the methyltransferases SET domain-containing 2 (Set2) and nuclear receptor SET domain- containing 1 (NSD1), respectively, alter the methylation status of H3K36, and significant progress has been made in understanding how they affect chromatin structure and function. Although H3K36 methylation is most commonly associated with the transcription of active euchromatin, it has also been implicated in diverse processes, including alternative splicing, dosage compensation and transcriptional repression, as well as DNA repair and recombination. Disrupted placement of methylated H3K36 within the chromatin landscape can lead to a range of human diseases, underscoring the importance of this modification.

The canonical histone proteins are encoded by replication-dependent genes and must rapidly reach high levels of expression during S phase. In metazoans the genes that encode these proteins produce mRNAs that, instead of being polyadenylated, contain a unique 3' end structure. By contrast, the synthesis of the variant, replication-independent histones, which are encoded by polyadenylated mRNAs, persists outside of S phase. Accurate positioning of both histone types in chromatin is essential for proper transcriptional regulation, the demarcation of heterochromatic boundaries and the epigenetic inheritance of gene expression patterns. Recent results suggest that the coordinated synthesis of replication-dependent and variant histone mRNAs is achieved by signals that affect formation of the 3' end of the replication-dependent histone mRNAs.Histones are the primary protein component of chromatin. Although they were initially thought to be mainly involved in chromosomal DNA packaging in eukaryotes, it is now recognized that they also have a crucial role in regulating gene expression. Histones can be extensively modified after translation and these modifications play an important part in regulating gene expression. They are constantly being shifted, modified, evicted and re-deposited as chromatin is continually remodelled (reviewed in REF. 1 ). Thus, the cell must carefully coordinate the replication of DNA, the synthesis of an estimated 10 8 molecules of each histone type in mammalian cells and the rapid deposition of new and old histones to reform chromatin during each relatively short S phase 2,3 .In metazoans the bulk of the histone proteins, defined here as the canonical histone proteins, are encoded by a family of replication-dependent histone genes. Their mRNAs are the only known cellular non-polyadenylated mRNAs in eukaryotes 4 . These genes encode all four core histones -H2A, H2B, H3 and H4 -which make up the nucleosome, and the linker H1 histones, which are found between nucleosomes. In place of a poly(A) tail, replicationdependent histone mRNAs end in a 3′ stem-loop sequence that is crucial in their regulation (FIG. 1a), and is formed by endonu-cleolytic cleavage of the pre-mRNA (FIG. 1b). This novel 3′ end results in the requirement for a distinct set of factors for metabolism and regulation of these histone mRNAs. These mRNAs must be expressed rapidly at the beginning of S phase and must persist at high levels throughout S phase to coincide with the replication of DNA. They are destroyed at the conclusion of S phase or rapidly during S phase if DNA replication is halted.In addition to the canonical histones, there are several variant histones whose synthesis is not cell-cycle-regulated and whose mRNAs are polyadenylated and expressed throughout the cell cycle (replication-independent histone mRNAs). These histones include the H3.3 and Correspondence to W.F.M.

Alternative polyadenylation (APA) is a pervasive mechanism in the regulation of most human genes, and its implication in diseases including cancer is only beginning to be appreciated. Since conventional APA profiling has not been widely adopted, global cancer APA studies are very limited. Here we develop a novel bioinformatics algorithm (DaPars) for the de novo identification of dynamic APAs from standard RNA-seq. When applied to 358 TCGA Pan-Cancer tumor/normal pairs across 7 tumor types, DaPars reveals 1,346 genes with recurrent and tumor-specific APAs. Most APA genes (91%) have shorter 3′ UTRs in tumors that can avoid miRNA-mediated repression, including glutaminase (GLS), a key metabolic enzyme for tumor proliferation. Interestingly, selected APA events add strong prognostic power beyond common clinical and molecular variables, suggesting their potential as novel prognostic biomarkers. Finally, our results implicate CstF64, an essential polyadenylation factor, as a master regulator of 3′ UTR shortening across multiple tumor types.

Animal cells have recently been shown to express a range of approximately 22 nucleotide noncoding RNAs termed micro RNAs (miRNAs). Here, we show that the human mir-30 miRNA can be excised from irrelevant, endogenously transcribed mRNAs encompassing the predicted 71 nucleotide mir-30 precursor. Expression of the mir-30 miRNA specifically blocked the translation in human cells of an mRNA containing artificial mir-30 target sites. Similarly, designed miRNAs were also excised from transcripts encompassing artificial miRNA precursors and could inhibit the expression of mRNAs containing a complementary target site. These data indicate that novel miRNAs can be readily produced in vivo and can be designed to specifically inactivate the expression of selected target genes in human cells.

The global shortening of mRNAs through alternative polyadenylation (APA) that occurs during enhanced cellular proliferation represents an important, yet poorly understood mechanism of regulated gene expression1,2. The 3′UTR truncation of growth promoting mRNA transcripts that relieves intrinsic microRNA- and AU-rich element-mediated repression has been observed to correlate with cellular transformation3; however, the importance to tumorigenicity of RNA 3′ end processing factors that potentially govern APA is unknown. Here, we have identified CFIm25 as a broad repressor of proximal poly(A) site usage that, when depleted, increases cell proliferation. Applying a regression model on standard RNA-seq data for novel APA events, we identified at least 1,450 genes with shortened 3′UTRs after CFIm25 knockdown, representing 11% of significantly expressed mRNA in HeLa cells. Dramatic increases in expression of several known oncogenes including Cyclin D1 are observed as a consequence of CFIm25 depletion. Importantly, we identified a subset of CFIm25-regulated APA genes with shortened 3′UTRs in glioblastoma (GBM) tumors that have reduced CFIm25 expression. Downregulation of CFIm25 expression in glioblastoma cells enhances their tumorigenic properties and increases tumor size while CFIm25 overexpression reduces these properties and inhibits tumor growth. These findings identify a pivotal role of the CFIm25 in governing APA and reveal a previously unknown connection between CFIm25 and glioblastoma tumorigenicity.