Chromatin allows the eukaryotic cell to package its DNA efficiently. To understand how chromatin structure is controlled across the Saccharomyces cerevisiae genome, we have investigated the role of the ATP-dependent chromatin remodelling complex Isw2 in positioning nucleosomes. We find that Isw2 functions adjacent to promoter regions where it repositions nucleosomes at the interface between genic and intergenic sequences. Nucleosome repositioning by Isw2 is directional and results in increased nucleosome occupancy of the intergenic region. Loss of Isw2 activity leads to inappropriate transcription, resulting in the generation of both coding and noncoding transcripts. Here we show that Isw2 repositions nucleosomes to enforce directionality on transcription by preventing transcription initiation from cryptic sites. Our analyses reveal how chromatin is organized on a global scale and advance our understanding of how transcription is regulated.

Gliomas harboring mutations in isocitrate dehydrogenase 1/2 (IDH1/2) have the CpG island methylator phenotype (CIMP) and significantly longer patient survival time than wild-type IDH1/2 (wtIDH1/2) tumors. Although there are many factors underlying the differences in survival between these two tumor types, immune-related differences in cell content are potentially important contributors. In order to investigate the role of IDH mutations in immune response, we created a syngeneic pair mouse model for mutant IDH1 (muIDH1) and wtIDH1 gliomas and demonstrated that muIDH1 mice showed many molecular and clinical similarities to muIDH1 human gliomas, including a 100-fold higher concentration of 2-hydroxygluratate (2-HG), longer survival time, and higher CpG methylation compared with wtIDH1. Also, we showed that IDH1 mutations caused down-regulation of leukocyte chemotaxis, resulting in repression of the tumor-associated immune system. Given that significant infiltration of immune cells such as macrophages, microglia, monocytes, and neutrophils is linked to poor prognosis in many cancer types, these reduced immune infiltrates in muIDH1 glioma tumors may contribute in part to the differences in aggressiveness of the two glioma types.

During development cells monitor and adjust their rates of accumulation to produce predeterminedsize organs; however, responsible for this mechanisms remain unknown. We show here that central nervous system-specific deletion of the essential adherens junction gene, αE-catenin, causes abnormal activation of the hedgehog pathway resulting in shortening of the cell cycle, decreased apoptosis and subsequent massive cortical hyperplasia. We propose that αE-catenin connects celldensity-dependent adherens junctions with the developmental hedgehog pathway and this connection may provide a negative feedback loop controlling the size of developing cerebral cortex.Keywords mammalian brain development; hedgehog pathway; neural progenitor cells During brain development, proliferation of neural progenitor cells is tightly controlled to produce the organ of predetermined size. We hypothesized that cell-cell adhesion structures may be involved in this function because they can provide cells with information concerning the density of their cellular neighborhood. Intercellular adhesion in neural progenitors is mediated primarily by adherens junctions, which contain cadherins, β-and α-catenins (1). We found that progenitors express αE(epithelial)-catenin, while differentiated neurons express αN(neural)-catenin ( Fig. S1A-D). Since α-catenin is critical for the formation of adherens junctions (2,3), we decided to determine the role of these adhesion structures in neural progenitor cells by generating mice with CNS-specific deletion of αE-catenin. Mice with a conditional αE-catenin allele (αE-catenin loxP/loxP ) (4) were crossed with mice carrying nestinpromoter-driven Cre recombinase (Nestin-Cre +/− ), which is expressed in CNS stem/neural progenitors starting at embryonic day E10.5 (5) (Fig. S1E). The resulting αE-catenin loxP/loxP / Nestin-Cre +/− animals displayed loss of αE-catenin in neural progenitor cells and its presence in the blood vessels not targeted by Nestin-Cre (Figs. 2D-F, S1F).While no phenotype was observed in heterozygous αE-catenin loxP/+ /Nestin-Cre +/− mice, the knockout αE-catenin loxP/loxP /Nestin-Cre +/− mice were born with bodies similar to their littermates, but with enlarged heads (Fig. S2A). After birth, the heads of these animals continued to grow, but their bodies were developmentally-retarded generating abnormal large-

SUMMARY To identify therapeutic targets for Glioblastoma (GBM), we performed genome-wide CRISPR-Cas9 "knockout" (KO) screens in patient-derived GBM stem-like cells (GSCs) and human neural stem/progenitors (NSCs), non-neoplastic stem cell controls, for genes required for their in vitro growth. Surprisingly, the vast majority GSC-lethal hits were found outside of molecular networks commonly altered in GBM and GSCs (e.g., oncogenic drivers). In vitro and in vivo validation of GSC-specific targets revealed several strong hits, including the wee1-like kinase, PKMYT1/Myt1. Mechanistic studies demonstrated that PKMYT1 acts redundantly with WEE1 to inhibit Cyclin B-CDK1 activity via CDK1-Y15 phosphorylation and to promote timely completion of mitosis in NSCs. However, in GSCs, this redundancy is lost, likely as a result of oncogenic signaling, causing GBM-specific lethality.