Many RNA regulatory proteins controlling pre-mRNA splicing contain serine:arginine (SR) repeats. Here we found that these SR domains bound hydrogel droplets composed of fibrous polymers of the low-complexity domain of heterogeneous ribonucleoprotein A2 (hnRNPA2). Hydrogel binding was reversed upon phosphorylation of the SR domain by CDC2-like kinases 1 and 2 (CLK1/2). Mutated variants of the SR domains changing serine to glycine (SR-to-GR variants) also bound to hnRNPA2 hydrogels, but were not affected by CLK1/2. When expressed in mammalian cells, these variants bound nucleoli. The translation products of the sense and antisense transcripts of the expansion repeats associated with the C9ORF72 gene altered in neurodegenerative disease encode GR N and PR N repeat polypeptides. Both peptides bound to hnRNPA2 hydrogels independent of CLK1/2 activity. When applied to cultured cells, both peptides entered cells, migrated to the nucleus, bound nucleoli, and poisoned RNA biogenesis, which caused cell death.Among familial causes of amyotrophic lateral sclerosis (ALS) and/or frontotemporal dementia (FTD), between 25 and 40% of cases are attributed to a repeat expansion in a gene designated C9ORF72. The hexa-nucleotide repeat sequence GGGGCC normally present in 2 to 23 copies is expanded in affected patients to 700 to 1,600 copies (1, 2). The pattern of genetic inheritance of the C9ORF72 repeat expansion is dominant, and multiple lines of evidence suggest that the repeat expansion causes disease. Two theories have been advanced to explain repeat-generated toxicity. First, in situ hybridization assays have identified nuclear dots containing either sense or anti-sense repeat transcripts (3-5), leading to the idea that the nuclear-retained RNAs might themselves be toxic. More recently, equally clear evidence has been generated showing that both the sense and anti-sense transcripts of the * Corresponding author. steven.mcknight@utsouthwestern.edu. SUPPLEMENTARY MATERIALS www.sciencemag.org/cgi/content/full/science.1254917/DC1 Materials and Methods Figs. S1 to S6 Table S1 References (29)(30)(31)(32)(33)(34) HHS Public Access Author ManuscriptAuthor Manuscript Author ManuscriptAuthor Manuscript GGGGCC repeats associated with C9ORF72 can be translated in an ATG-independent manner known as repeat associated non-ATG (RAN) translation (6). Depending upon reading frame, the sense transcript of the repeats can be translated into glycine:alanine (GA N ), glycine:proline (GP N ), or glycine:arginine (GR N ) polymers. RAN translation of the anti-sense transcript of the GGGGCC repeats of C9ORF72 lead to the production of proline:alanine (PA N ), proline:glycine (PG N ) or proline:arginine (PR N ) polymers. These repeat-encoded polymers are expressed in disease tissue (5, 7-9). The disordered and hydrophobic nature of these polymers, at least the GA N , GP N , and PA N versions, properly predicted that they would aggregate into distinct foci within affected cells (5, 9). Another plausible explanation for repeat-generated toxicity ...

CLIP-seq is widely used to study genome-wide interactions between RNA-binding proteins and RNAs. However, there are few tools available to analyze CLIP-seq data, thus creating a bottleneck to the implementation of this methodology. Here, we present PIPE-CLIP, a Galaxy framework-based comprehensive online pipeline for reliable analysis of data generated by three types of CLIP-seq protocol: HITS-CLIP, PAR-CLIP and iCLIP. PIPE-CLIP provides both data processing and statistical analysis to determine candidate cross-linking regions, which are comparable to those regions identified from the original studies or using existing computational tools. PIPE-CLIP is available at http://pipeclip.qbrc.org/.

Co-expression analysis is widely used to predict gene function and to identify functionally related gene sets. However, co-expression analysis using human cancer transcriptomic data is confounded by somatic copy number alterations (SCNA), which produce co-expression signatures based on physical proximity rather than biological function. To better understand gene–gene co-expression based on biological regulation but not SCNA, we describe a method termed “Genomic Regression Analysis of Coordinated Expression” (GRACE) to adjust for the effect of SCNA in co-expression analysis. The results from analyses of TCGA, CCLE, and NCI60 data sets show that GRACE can improve our understanding of how a transcriptional network is re-wired in cancer. A user-friendly web database populated with data sets from The Cancer Genome Atlas (TCGA) is provided to allow customized query.

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PurposeTo identify incidence and risk factors of recurrence after discontinuation of successful antimuscarinic therapy in patients with overactive bladder (OAB).Materials and MethodsThis was a prospective, multicenter trial. Patients who had antimuscarinic agents for more than 12 weeks and showed successful response were enrolled. Successful response was defined as answering 'benefit' for patient perception of treatment benefit and answer lesser than 3 points in patient's perception of bladder condition (PPBC). The enrolled patients discontinued the antimuscarinics, and we evaluated their recurrence with PPBC and OAB symptom score (OABSS) at 1, 3, 6, and 12 months. Primary purpose was to identify the recurrence rate and secondary purpose was to reveal risk factors.ResultsFour hundred forty-one patients enrolled and 371 patients completed 6-month follow-up. The enrolled patients showed 1.6 points in PPBC, 2.9 points in OABSS and 1.4 points in IPSS (quality of life) which represented successful response after using antimuscarinics. The cumulative rates of recurrence were 25.6%, 42.3%, and 52.2% at 1, 3, 6 months, respectively. Among 177 patients who did not show recurrence at 6 months, 41 patients were followed up and 4 patients of the 41 patients (9.7%) showed recurrence at 12 months. On univariate and multivariate analyses of recurrence, OAB wet was the risk factor for recurrence after 6 months of discontinuation.ConclusionsDiscontinuation of antimuscarinic therapy after successful treatment resulted in high recurrence rate with time and OAB wet was the independent risk factor for recurrence.