Epigenetic control is an important aspect of gene regulation. Despite detailed understanding of protein-coding gene expression, the transcription of non-coding RNA genes by RNA polymerase (pol) III is less well characterized. Here we profile the epigenetic features of pol III target genes throughout the human genome. This reveals that the chromatin landscape of pol III-transcribed genes resembles that of pol II templates in many ways, although there are also clear differences. Our analysis also discovered an entirely unexpected phenomenon, namely that pol II is present at the majority of genomic loci that are bound by pol III.

Histidine phosphorylation, the so-called hidden phosphoproteome, is a poorly characterized post-translational modification of proteins. Here we describe a role of histidine phosphorylation in tumorigenesis. Proteomic analysis of 12 tumours from an mTOR-driven hepatocellular carcinoma mouse model revealed that NME1 and NME2, the only known mammalian histidine kinases, were upregulated. Conversely, expression of the putative histidine phosphatase LHPP was downregulated specifically in the tumours. We demonstrate that LHPP is indeed a protein histidine phosphatase. Consistent with these observations, global histidine phosphorylation was significantly upregulated in the liver tumours. Sustained, hepatic expression of LHPP in the hepatocellular carcinoma mouse model reduced tumour burden and prevented the loss of liver function. Finally, in patients with hepatocellular carcinoma, low expression of LHPP correlated with increased tumour severity and reduced overall survival. Thus, LHPP is a protein histidine phosphatase and tumour suppressor, suggesting that deregulated histidine phosphorylation is oncogenic.

Transfer of quiescent Saccharomyces cerevisiae cells to fresh medium rapidly induces hundreds of genes needed for growth. A large subset of these genes is regulated via a DNA sequence motif known as the ribosomal RNA processing element (RRPE). However, no RRPE-binding proteins have been identified. We screened a panel of 6144 glutathione S-transferase-open reading frame fusions for RRPE-binding proteins and identified Stb3 as a specific RRPE-binding protein, both in vitro and in vivo. Chromatin immunoprecipitation experiments showed that glucose increases Stb3 binding to RRPE-containing promoters.Microarray experiments demonstrated that the loss of Stb3 inhibits the transcriptional response to fresh glucose, especially for genes with RRPE motifs. However, these experiments also showed that not all genes containing RRPEs were dependent on Stb3 for expression. Overall our data support a model in which Stb3 plays an important but not exclusive role in the transcriptional response to growth conditions. Evolutionary pressures make it imperative that quiescent yeast cells respond rapidly to fresh medium. By the same token, the cell must cease growth with precision as nutrients become depleted (1, 2). Saccharomyces cerevisiae cells have developed elaborate and redundant pathways for sensing glucose (3,4). Early microarray work established that specific gene sets are regulated as cells deplete glucose and pass through the diauxic shift (5). More recent work has focused on the transition from quiescence in poor or depleted medium to rapid growth in fresh glucose medium. Nutrient repletion produces a very rapid induction of genes involved in protein synthesis, mass accumulation, and cell division (6 -9).A significant portion of genes that are rapidly induced by fresh medium encode ribosomal proteins (RPs). 2 RP genes frequently contain binding sites for the Rap1 and Abf1 transcriptionalregulators(10,11).Inaddition,theTORkinaseandcAMPdependent protein kinase nutrient signaling pathways converge on the Sfp1 and Crf1 transcriptional regulators to control RP gene transcription (12)(13)(14). The Rap1 cofactor Gcr1 appears to regulate the nuclear location and the expression of RP genes (15). The nutrient controlled kinases Sch9 and Yak1 also play a role in RP gene regulation (14,16).However, many of the growth-related genes induced by fresh medium do not encode ribosomal proteins but instead encode other gene products needed for rapid growth, including transcription factors, components involved in ribosome assembly, and translation factors (6,14,17). We refer to this set as non-RP growth genes (9). Little is known about the control of this gene set. In addition to being induced by fresh medium, these genes are negatively regulated by a wide variety of stresses (8, 18 -20). As with the RP genes, induction of the non-RP growth genes by fresh medium involves the cAMP-dependent protein kinase and TOR kinase pathways. However, it is clear that there are key differences between the regulation of the RP and non-RP growth genes. Induct...

Nutrient repletion leads to substantial restructuring of the transcriptome in Saccharomyces cerevisiae. The expression levels of approximately one-third of all S. cerevisiae genes are altered at least twofold when a nutrient-depleted culture is transferred to fresh medium. Several nutrient-sensing pathways are known to play a role in this process, but the relative contribution that each pathway makes to the total response has not been determined. To better understand this, we used a chemical-genetic approach to block the protein kinase A (PKA), TOR (target of rapamycin), and glucose transport pathways, alone and in combination. Of the three pathways, we found that loss of PKA produced the largest effect on the transcriptional response; however, many genes required both PKA and TOR for proper nutrient regulation. Those genes that did not require PKA or TOR for nutrient regulation were dependent on glucose transport for either nutrient induction or repression. Therefore, loss of these three pathways is sufficient to prevent virtually the entire transcriptional response to fresh medium. In the absence of fresh medium, activation of the cyclic AMP/PKA pathway does not induce cellular growth; nevertheless, PKA activation induced a substantial fraction of the PKA-dependent genes. In contrast, the absence of fresh medium strongly limited gene repression by PKA. These results account for the signals needed to generate the transcriptional responses to glucose, including induction of growth genes required for protein synthesis and repression of stress genes, as well as the classical glucose repression and hexose transporter responses.

Target of rapamycin (TOR) is a highly conserved protein kinase that plays a key role in mediating cell growth and homeostasis. It is activated by nutrients, growth factors, and cellular energy levels to control a number of anabolic and catabolic processes. It is a validated drug target implicated in a variety of diseases. In this review, we describe the molecular mode of action of TOR in the context of cellular and organismal physiology. We focus on mammalian TOR (mTOR) signaling in cancer and neurological disease and discuss usage of TOR inhibitors in the clinic.