CAPRI enables comparison of evolutionary conserved RNA interacting regions

RNA-protein complexes play essential regulatory roles at nearly all levels of gene expression. Using in vivo crosslinking and RNA capture, we report a comprehensive RNA-protein interactome in a metazoan at four levels of resolution: single amino acids, domains, proteins and multisubunit complexes. We devise CAPRI, a method to map RNA-binding domains (RBDs) by simultaneous identification of RNA interacting crosslinked peptides and peptides adjacent to such crosslinked sites. CAPRI identifies more than 3000 RNA proximal peptides in Drosophila and human proteins with more than 45% of them forming new interaction interfaces. The comparison of orthologous proteins enables the identification of evolutionary conserved RBDs in globular domains and intrinsically disordered regions (IDRs). By comparing the sequences of IDRs through evolution, we classify them based on the type of motif, accumulation of tandem repeats, conservation of amino acid composition and high sequence divergence

The long noncoding RNA mimi scaffolds neuronal granules to maintain nervous system maturity

RNA binding proteins and messenger RNAs (mRNAs) assemble into ribonucleoprotein granules that regulate mRNA trafficking, local translation, and turnover. The dysregulation of RNA-protein condensation disturbs synaptic plas-ticity and neuron survival and has been widely associated with human neurological disease. Neuronal granules are thought to condense around particular proteins that dictate the identity and composition of each granule type. Here, we show in Drosophila that a previously uncharacterized long noncoding RNA, mimi, is required to scaffold large neuronal granules in the adult nervous system. Neuronal ELAV-like proteins directly bind mimi and mediate granule assembly, while Staufen maintains condensate integrity. mimi granules contain mRNAs and proteins involved in synaptic processes; granule loss in mimi mutant flies impairs nervous system maturity and neuropeptide-mediated signaling and causes phenotypes of neurodegeneration. Our work reports an architectural RNA for a neuronal granule and provides a handle to interrogate functions of a condensate independently of those of its constituent proteins

The Development of a Point of Care Clinical Guidelines Mobile Application Following a User-Centred Design Approach

This paper describes the development of a point of care clinical guidelines mobile application. A user-centred design approach was utilised to inform the design of a smartphone application, this included: Observations; a survey; focus groups and an analysis of popular apps utilised by clinicians in a UK NHS Trust. Usability testing was conducted to inform iterations of the application, which presents clinicians with a variety of integrated tools to aid in decision making and information retrieval. The study found that clinicians use a mixture of technology to retrieve information, which is often inefficient or has poor usability. It also shows that smartphone application development for use in UK hospitals needs to consider the variety of users and their clinical knowledge and work pattern. This study highlights the need for applying user-centred design methods in the design of information presented to clinicians and the need for clinical information delivery that is efficient and easy to use at the bedside

Evaluation of learning approaches in physiotherapy students: A valuable insight

INTRODUCTION: Every individual has different learning approaches in acquisition and processing of knowledge. Physiotherapy, an evolving allied health science profession, is developing rapidly. Exploration of learning approaches among physiotherapy students will help the academicians to enrich the quality of learning. This study aimed to analyze the learning approaches among physiotherapy students. MATERIALS AND METHODS: A cross-sectional study was carried out among 435 physiotherapy students. The Approaches and Study Skills Inventory for Students questionnaire was used to evaluate learning approaches in both preclinical and clinical students. Data were analyzed using the Statistical Package for the Social Sciences software version 21. Statistical significance was set at P < 0.05. RESULTS: A total of 435 participants, 233 (53.56%) in preclinical phase and 202 (46.44%) in clinical phase with a mean age of 19.01 ± 1.01 and 22.03 ± 1.43 years, respectively, participated in the study. Among the 435 students, 411 (94.49%) adopted the deep approach, while only 21 (4.83%) and 3 (0.69%) adopted strategic approach and surface approach, respectively. Preclinical students had significantly higher mean scores for strategic and surface approaches than clinical (P = 0.000) and (P = 0.000) using independent t-test, respectively. Out of the 435 students, 50 (11.45%) were male and 385 (88.51%) were female. Male students appeared less likely to adopt the deep learning approach than female students (P = 0.013). CONCLUSIONS: Assessment of learning approaches will assist the academicians to develop teaching and learning strategies and effective curriculum depending on the perspectives of students. Multiple methodologies focused on interactive student-centric approach should be utilized to enhance positive learning outcomes

RNA nucleation by MSL2 induces selective X chromosome compartmentalization

Confinement of the X chromosome to a territory for dosage compensation is a prime example of how subnuclear compartmental-ization is used to regulate transcription at the megabase scale. In Drosophila melano-gaster, two sex-specific non-coding RNAs (roX1 and roX2) are transcribed from the X chromosome. They associate with the male-specific lethal (MSL) complex, which acetylates histone H4 lysine 16 and thereby induces an approximately twofold increase in expression of male X-linked genes. Current models suggest that X-over-autosome specificity is achieved by the recognition of cis-regulatory DNA high-affinity sites (HAS) by the MSL2 subunit. However, HAS motifs are also found on autosomes, indicating that additional factors must stabilize the association of the MSL complex with the X chromosome. Here we show that the low-complexity C-terminal domain (CTD) of MSL2 renders its recruitment to the X chromosome sensitive to roX non-coding RNAs. roX non-coding RNAs and the MSL2 CTD form a stably condensed state, and functional analyses in Drosophila and mammalian cells show that their interactions are crucial for dosage compensation in vivo. Replacing the CTD of mammalian MSL2 with that from Drosophila and expressing roX in cis is sufficient to nucleate ectopic dosage compensation in mammalian cells. Thus, the condensing nature of roX-MSL2CTD is the primary determinant for specific compartmentalization of the X chromosome in Drosophila

MOF Acetyl Transferase Regulates Transcription and Respiration in Mitochondria

A functional crosstalk between epigenetic regulators and metabolic control could provide a mechanism to adapt cellular responses to environmental cues. We report that the well-known nuclear MYST family acetyl transferase MOF and a subset of its non-specific lethal complex partners reside in mitochondria. MOF regulates oxidative phosphorylation by controlling expression of respiratory genes from both nuclear and mtDNA in aerobically respiring cells. MOF binds mtDNA, and this binding is dependent on KANSL3. The mitochondrial pool of MOF, but not a catalytically deficient mutant, rescues respiratory and mtDNA transcriptional defects triggered by the absence of MOF. Mof conditional knockout has catastrophic consequences for tissues with high-energy consumption, triggering hypertrophic cardiomyopathy and cardiac failure in murine hearts; cardiomyocytes show severe mitochondrial degeneration and deregulation of mitochondrial nutrient metabolism and oxidative phosphorylation pathways. Thus, MOF is a dual-transcriptional regulator of nuclear and mitochondrial genomes connecting epigenetics and metabolism

Chemical RNA digestion enables robust RNA-binding site mapping at single amino acid resolution

© 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. RNA-binding sites (RBSs) can be identified by liquid chromatography and tandem mass spectrometry analyses of the protein-RNA conjugates created by crosslinking, but RBS mapping remains highly challenging due to the complexity of the formed RNA adducts. Here, we introduce RBS-ID, a method that uses hydrofluoride to fully cleave RNA into mono-nucleosides, thereby minimizing the search space to drastically enhance coverage and to reach single amino acid resolution. Moreover, the simple mono-nucleoside adducts offer a confident and quantitative measure of direct RNA-protein interaction. Using RBS-ID, we profiled similar to 2,000 human RBSs and probedStreptococcus pyogenesCas9 to discover residues important for genome editing11sci