SUMMARY The discovery of long non-coding RNA (lncRNA) has dramatically altered our understanding of cancer. Here, we describe a comprehensive analysis of lncRNA alterations at transcriptional, genomic, and epigenetic levels in 5,037 human tumor specimens across 13 cancer types from the Cancer Genome Atlas (TCGA). Our results suggest that the expression and dysregulation of lncRNAs are highly cancer-type specific compared to protein-coding genes. Using the integrative data generated by this analysis, we present a clinically guided small interfering RNA screening strategy and a co-expression analysis approach to identify cancer driver lncRNAs and predict their functions. This provides a resource for investigating lncRNAs in cancer and lays the groundwork for the development of new diagnostics and treatments.

TDP-43 pathology is a disease hallmark that characterizes amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD-TDP). Although a critical role for TDP-43 as an RNA-binding protein has emerged, the regulation of TDP-43 function is poorly understood. Here we identify lysine acetylation as a novel post-translational modification controlling TDP-43 function and aggregation. We provide evidence that TDP-43 acetylation impairs RNA-binding and promotes accumulation of insoluble, hyper-phosphorylated TDP-43 species that largely resemble pathological inclusions in ALS and FTLD-TDP. Moreover, biochemical and cell-based assays identify oxidative stress as a signaling cue that promotes acetylated TDP-43 aggregates that are readily engaged by the cellular defense machinery. Importantly, acetylated TDP-43 lesions are found in ALS patient spinal cord, indicating that aberrant TDP-43 acetylation and loss of RNA binding are linked to TDP-43 proteinopathy. Thus, modulating TDP-43 acetylation represents a plausible strategy to fine-tune TDP-43 activity, which could provide new therapeutic avenues for TDP-43 proteinopathies.

The TRAP220 component of the TRAP/SMCC complex, a mammalian homologof the yeast Mediator that shows diverse coactivation functions, interacts directly with nuclear receptors. Ablation of the murine Trap220 gene revealed that null mutants die during an early gestational stage with heart failure and exhibit impaired neuronal development with extensive apoptosis. Primary embryonic fibroblasts derived from null mutants show an impaired cell cycle regulation and a prominent decrease of thyroid hormone receptor function that is restored by ectopic TRAP220 but no defect in activation by Gal4-RARalpha/RXRalpha, p53, or VP16. Moreover, haploinsufficient animals show growth retardation, pituitary hypothyroidism, and widely impaired transcription in certain organs. These results indicate that TRAP220 is essential for a wide range of physiological processes but also that it has gene- and activator-selective functions.

RNA polymerase II holoenzyme ͉ transcriptional regulation ͉ TRAP ͉ electron microscopy A Mediator complex with Ϸ20 polypeptide components is involved in regulation of RNA polymerase II transcription in the yeast Saccharomyces cerevisiae (1, 2). A number of complexes containing subunits homologous to those of the yeast Mediator have been identified in higher organisms. These related complexes include a murine Mediator (3), human thyroid hormone receptor-associated protein (TRAP) complex, a coactivator associated with the thyroid hormone nuclear receptor, and other human complexes (4-9). Mediator and related complexes interact with RNA polymerase II to form holoenzymes and confer on the polymerase both enhanced activity in basal transcription and responsiveness to transcriptional activators. Evidence of direct Mediator-activator interaction has come from the physical isolation of TRAP as a complex with thyroid hormone receptor from hormone-induced but not uninduced cells. Other human Mediators have been isolated as complexes with activators or isolated by activator-affinity chromatography.Initial structural analysis of yeast, murine Mediators, and holoenzymes was performed by averaging a small number (Ͻ100) of electron-microscope images of the complexes viewed in a single orientation in projection. Despite rather limited sequence homology, the yeast and murine complexes appeared remarkably alike in size, shape, and conformational changes associated with Mediator-polymerase interaction (10). Here we present three-dimensional (3-D) structures of yeast and murine Mediators and of human TRAP complex, obtained by averaging hundreds of electron-microscope images from views in random orientations. Beyond confirming the overall similarity of yeast and murine Mediators and extending this result to TRAP, the structures reveal details of surface and internal organization, disclosing further similarities and also notable differences. Materials and MethodsSample Preparation and Data Collection. Yeast Mediator purified from commercial yeast as described (11), mouse Mediator purified as described (3), and human TRAP complex immunopurified from HeLa cells as described (12) were diluted to a concentration of 15-25 g͞ml and applied to specimen grids covered with a thin amorphous carbon film. Because of their relatively low abundance, the amounts of murine Mediator and of the human TRAP complex available for our structural studies were not sufficient for the preparation of unstained specimens; thus, individual particles were imaged in negative stain. The carbon film substrate was glow discharged before preparation of the samples to facilitate adhesion of the molecules and aid staining by making the film surface more hydrophilic. The particles were negatively stained by using a 1% solution of uranyl acetate. After staining, a second, prestained carbon layer was placed over the specimen to ensure complete coverage of the particles by the stain. Samples were examined by using a Philips CM120 electron microscope, equipped with a LaB 6 f...