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Systems models of the ways transcription factor networks operate and evolve are essential for understanding cell identity, developmental commitment and regulatory variation. Terminologies from different techniques and disciplines may need to be adapted or put aside to make and test these models effectively.
Orchids have captured imaginations worldwide for hundreds of years. The publication of the moth orchid genome sequence opens the door to a greater understanding of orchid morphological evolution and physiological adaptation.
Bacterial whole-genome sequencing of longitudinally collected isolates enables the investigation of evolutionary trajectories, which may inform both the prevention and treatment of human-associated pathogen infections. A new study explores the adaptation of multiple lineages of Pseudomonas aeruginosa to the lungs of young patients with cystic fibrosis and finds evidence of convergent molecular evolution and historical contingencies.
Betalains are bright red and yellow pigments, which are produced in only one order of plants, the Caryophyllales, and replace the more familiar anthocyanin pigments. The evolutionary origin of betalain production is a mystery, but a new study has identified the first regulator of betalain production and discovered a previously unknown link between the two pigment pathways.
Jason Lieb and Sebastian Pott review the identification and composition of super-enhancers and ask whether super-enhancers are a new, conceptually distinct regulatory entity.
Giuseppe Testa and colleagues report the generation and transcriptional characterization of patient-derived induced pluripotent stem cells (iPSCs) with copy number variants at 7q11.23, which cause syndromes including neurocognitive phenotypes. They find that the dosage of the transcription factor gene GTF2I accounts for 10–20% of the transcriptional dysregulation observed in these cells.
Benjamin Raphael and colleagues report an analysis of altered subnetworks of somatic aberrations in TCGA pan-cancer data sets, including 3,281 samples from 12 cancer types, using a newly developed HotNet2 algorithm. They identify 16 significantly mutated subnetworks and provide a more comprehensive view into altered pathways, including those with known roles in cancer development.
Guido Sauter, Roland Eils, Christoph Plass, Raffaella Santoro and colleagues report that the gene encoding the epigenetic regulator BAZ2A is overexpressed in prostate cancer, where it interacts with EZH2 to induce aberrant gene silencing and cell proliferation. The authors find that BAZ2A levels are predictive of disease recurrence in patients with prostate cancer.
Roland Rad and colleagues report development of a new conditional piggyBac transposition system for performing insertional mutagenesis screens in mice. They apply the system to identify new oncogenic driver pathways for pancreatic cancer.
Martin Reincke, Martin Fassnacht and colleagues identify somatic mutations in the USP8 deubiquitinase gene in corticotroph adenomas in Cushing's disease. The mutations enhanced proteolytic cleavage and catalytic activity of USP8, which led to activation of EGF receptor signaling.
Emmanouil Dermitzakis, Alfonso Buil and colleagues measure transcriptome-wide expression in a sample of twins to measure the relative contribution of genetic and environmental effects on allele-specific expression and find substantial effects of gene × gene and gene × environment interactions.
Alan Lloyd and colleagues identify a MYB gene in beet that acts as a key regulator of the betalain red pigmentation pathway. They further show that this gene resides at the classical Y pigmentation locus and shares homology with MYB genes that encode positive regulators of the anthocyanin pigmentation pathway in other species.