This process was continued until at most 10 significant terms were identified. OLIG2 regulates PDGFRA (47), which was also a Group 2 bivalent gene highly expressed in proneural samples, and although it is required for gliomagenesis (48), its expression is associated with an improved prognosis (49). To the backdrop of the JD Knockouts’ softball game, Connor explains, “I think the camaraderie in a lab makes a really, really big difference. Finally, transcriptome-aware alignment was performed with TopHat2 (v2.1.0; ref. In this system, we observed a baseline of ∼75% GFP-positive cells after induction in the presence of a negative control sgRNA, which was reduced to near 0% by an on-target sgRNA disrupting GFP expression (SI Appendix, Fig. The resulting cell lines were then further transduced with a vector expressing a GFP-targeting or negative control sgRNA and an associated mCherry fluorescence marker. By comparing our enhancer annotations to 5hmC data from GBM tumors (24), we found that GBM enhancers were enriched for 5hmC compared with promoters (P = 6.212e−07, t test), bivalent regions (P = 4.08e−09), polycomb silenced regions (P = 1.866e−09), and background 5hmC levels in the genome (P = 2.778e−12; Supplementary Fig. Duplicate sequences were flagged using the Picard MarkDuplicates tool (v1.123; http://broadinstitute.github.io/picard). Transcribed genes such as calmodulin (CALM1) displayed active histone modifications (Fig. Sonication continued for four 10-minute cycles; then, samples were centrifuged to pellet-insoluble particles. Thank you for sharing this Cancer Research article. Interestingly, although the genes nearest enhancers were highly expressed, the enhancers themselves were highly methylated (Fig. If they can do that, they will have more control over the gene editing process, and ultimately its outcome. Our study raises the possibility that targeting epigenetic states with small-molecule modulators, in combination with agents that target Wnt and hedgehog signaling pathways, might be a fruitful approach for exploring subtype-specific therapy in GBM. S1). However, creating “designer” inhibitors for specific gene editors and editing scenarios is very challenging, as Acr proteins are small and lack any sequence and structural conservation to use for direct identification of desired modalities. More than 500 terrestrial vertebrate species are on the brink of extinction, likely driven by human activities in biodiversity hotspots, a study suggests. Postdoctoral Scholar CRISPR-Cas enzymes are RNA-guided bacterial proteins widely used for genome editing and genetic manipulation in a wide range of cell types. Iyer). In addition, if active and repressive marks occurred in different populations of cells, the expectation is that such loci would show expression levels that are intermediate between the active and repressed state. Iyer, Administrative, technical, or material support (i.e., reporting or organizing data, constructing databases): A.M. Battenhouse, M.C. S5A). For example, PODXL (Podocalyxin-like) promotes cell migration, and its overexpression in GSCs is associated with a poor outcome (34); MMP11 (matrix metalloprotease 11) cleaves ECM, promotes tumorigenesis, and cellular invasion (35); S100A16 (a Ca++ binding protein) promotes the epithelial-to-mesenchymal transition (EMT) in breast cancer (36); the protein kinase FAM20C is a marker of mesenchymal GSCs and promotes proliferation in triple-negative breast cancer (37); LMO2 (LIM Domain Only 2) promotes angiogenesis (38), and is a marker of GSCs (32, 33).