Advances in CLIP Technologies for Studies of Protein-RNA Interactions

RNA binding proteins (RBPs) regulate all aspects in the life cycle of RNA molecules. To elucidate the elements that guide RNA specificity, regulatory mechanisms, and functions of RBPs, methods that identify direct endogenous protein-RNA interactions are particularly valuable. UV crosslinking and immunoprecipitation (CLIP) purifies short RNA fragments that crosslink to a specific protein and then identifies these fragments by sequencing. When combined with high-throughput sequencing, CLIP can produce transcriptome-wide maps of RNA crosslink sites. The protocol is comprised of several dozen biochemical steps, and improvements made over the last 15 years have increased its resolution, sensitivity, and convenience. Adaptations of CLIP are also emerging in the epitranscriptomic field to map the positions of RNA modifications accurately. Here, we describe the rationale for each step in the protocol and discuss the impact of variations to help users determine the most suitable option

Subcellular mRNA Localization Regulates Ribosome Biogenesis in Migrating Cells

Translation of ribosomal protein-coding mRNAs (RP-mRNAs) constitutes a key step in ribosome biogenesis, but the mechanisms that modulate RP-mRNA translation in coordination with other cellular processes are poorly defined. Here, we show that subcellular localization of RP-mRNAs acts as a key regulator of their translation during cell migration. As cells migrate into their surroundings, RP-mRNAs localize to the actin-rich cell protrusions. This localization is mediated by La-related protein 6 (LARP6), an RNA-binding protein that is enriched in protrusions. Protrusions act as hotspots of translation for RP-mRNAs, enhancing RP synthesis, ribosome biogenesis, and the overall protein synthesis in migratory cells. In human breast carcinomas, epithelial-to-mesenchymal transition (EMT) upregulates LARP6 expression to enhance protein synthesis and support invasive growth. Our findings reveal LARP6-mediated mRNA localization as a key regulator of ribosome biogenesis during cell migration and demonstrate a role for this process in cancer progression downstream of EMT

RGS4 RNA secondary structure mediates Staufen2 RNP assembly in Neurons

RNA‐binding proteins (RBPs) act as posttranscriptional regulators controlling the fate of target mRNAs. Unraveling how RNAs are recognized by RBPs and in turn are assembled into neuronal RNA granules is therefore key to understanding the underlying mechanism. While RNA sequence elements have been extensively characterized, the functional impact of RNA secondary structures is only recently being explored. Here, we show that Staufen2 binds complex, long‐ranged RNA hairpins in the 3′‐untranslated region (UTR) of its targets. These structures are involved in the assembly of Staufen2 into RNA granules. Furthermore, we provide direct evidence that a defined Rgs4 RNA duplex regulates Staufen2‐dependent RNA localization to distal dendrites. Importantly, disrupting the RNA hairpin impairs the observed effects. Finally, we show that these secondary structures differently affect protein expression in neurons. In conclusion, our data reveal the importance of RNA secondary structure in regulating RNA granule assembly, localization and even-tually translation. It is therefore tempting to speculate that secondary structures represent an important code for cells to control the intracellular fate of their mRNAs

Bifurcation Boundary Conditions for Switching DC-DC Converters Under Constant On-Time Control

Sampled-data analysis and harmonic balance analysis are applied to analyze switching DC-DC converters under constant on-time control. Design-oriented boundary conditions for the period-doubling bifurcation and the saddle-node bifurcation are derived. The required ramp slope to avoid the bifurcations and the assigned pole locations associated with the ramp are also derived. The derived boundary conditions are more general and accurate than those recently obtained. Those recently obtained boundary conditions become special cases under the general modeling approach presented in this paper. Different analyses give different perspectives on the system dynamics and complement each other. Under the sampled-data analysis, the boundary conditions are expressed in terms of signal slopes and the ramp slope. Under the harmonic balance analysis, the boundary conditions are expressed in terms of signal harmonics. The derived boundary conditions are useful for a designer to design a converter to avoid the occurrence of the period-doubling bifurcation and the saddle-node bifurcation.Comment: Submitted to International Journal of Circuit Theory and Applications on August 10, 2011; Manuscript ID: CTA-11-016

Human resources issues and Australian Disaster Medical Assistance Teams: results of a national survey of team members

Background: Calls for disaster medical assistance teams (DMATs) are likely to continue in response to international disasters. As part of a national survey, this study was designed to evaluate Australian DMAT experience in relation to the human resources issues associated with deployment.\ud \ud Methods: Data was collected via an anonymous mailed survey distributed via State and Territory representatives on the Australian Health Protection Committee, who identified team members associated with Australian DMAT deployments from the 2004 South East Asian Tsunami disaster.\ud \ud Results: The response rate for this survey was 50% (59/118). Most personnel had deployed to the Asian Tsunami affected areas with DMAT members having significant clinical and international experience. While all except one respondent stated they received a full orientation prior to deployment, only 34% of respondents (20/59) felt their role was clearly defined pre deployment. Approximately 56% (33/59) felt their actual role matched their intended role and that their clinical background was well suited to their tasks. Most respondents were prepared to be available for deployment for 1 month (34%, 20/59). The most common period of notice needed to deploy was 6–12 hours for 29% (17/59) followed by 12–24 hours for 24% (14/59). The preferred period of overseas deployment was 14–21 days (46%, 27/59) followed by 1 month (25%, 15/59) and the optimum shift period was felt to be 12 hours by 66% (39/59). The majority felt that there was both adequate pay (71%, 42/59) and adequate indemnity (66%, 39/59). Almost half (49%, 29/59) stated it was better to work with people from the same hospital and, while most felt their deployment could be easily covered by staff from their workplace (56%, 33/59) and caused an inconvenience to their colleagues (51%, 30/59), it was less likely to interrupt service delivery in their workplace (10%, 6/59) or cause an inconvenience to patients (9%, 5/59). Deployment was felt to benefit the affected community by nearly all (95%, 56/59) while less (42%, 25/59) felt that there was a benefit for their own local community. Nearly all felt their role was recognised on return (93%, 55/59) and an identical number (93%, 55/59) enjoyed the experience. All stated they would volunteer again, with 88% strongly agreeing with this statement.\ud \ud Conclusions: This study of Australian DMAT members provides significant insights into a number of human resources issues and should help guide future deployments. The preferred 'on call' arrangements, notice to deploy, period of overseas deployment and shift length are all identified. This extended period of operations needs to be supported by planning and provision of rest cycles, food, temporary accommodation and rest areas for staff. The study also suggests that more emphasis should be placed on team selection and clarification of roles. While the majority felt that there was both adequate pay and adequate indemnity, further work clarifying this, based on national conditions of service should be, and are, being explored currently by the state based teams in Australia. Importantly, the deployment was viewed positively by team members who all stated they would volunteer again, which allows the development of an experienced cohort of team members

miR-182 Regulates Slit2-Mediated Axon Guidance by Modulating the Local Translation of a Specific mRNA

During brain wiring, cue-induced axon behaviors such as directional steering and branching are aided by localized mRNA translation. Different guidance cues elicit translation of subsets of mRNAs that differentially regulate the cytoskeleton, yet little is understood about how specific mRNAs are selected for translation. MicroRNAs (miRNAs) are critical translational regulators that act through a sequence-specific mechanism. Here, we investigate the local role of miRNAs in mRNA-specific translation during pathfinding of $\textit{Xenopus laevis }$ retinal ganglion cell (RGC) axons. Among a rich repertoire of axonal miRNAs, miR-182 is identified as the most abundant. Loss of miR-182 causes RGC axon targeting defects in vivo and impairs Slit2-induced growth cone (GC) repulsion. We find that miR-182 targets cofilin-1 mRNA, silencing its translation, and Slit2 rapidly relieves the repression without causing miR-182 degradation. Our data support a model whereby miR-182 reversibly gates the selection of transcripts for fast translation depending on the extrinsic cue.This study was supported by EMBO ( ALTF992-2011 ) and HFSP fellowships ( LT000136/2012 ) (to A.B.), University of Trento PhD studentship (to A.I.), Wellcome Trust Programme ( 085314/Z/08/Z ) (to C.E.H.), and Marie Curie Career Integration ( 618969 GUIDANCE-miR ), G. Armenise-Harvard Foundation Career, and MIUR SIR ( RBSI144NZ4 ) grants (to M.-L.B.)

Cross-Regulation between TDP-43 and Paraspeckles Promotes Pluripotency-Differentiation Transition

RNA-binding proteins (RBPs) and long non-coding RNAs (lncRNAs) are key regulators of gene expression, but their joint functions in coordinating cell fate decisions are poorly understood. Here we show that the expression and activity of the RBP TDP-43 and the long isoform of the lncRNA Neat1, the scaffold of the nuclear compartment "paraspeckles," are reciprocal in pluripotent and differentiated cells because of their cross-regulation. In pluripotent cells, TDP-43 represses the formation of paraspeckles by enhancing the polyadenylated short isoform of Neat1. TDP-43 also promotes pluripotency by regulating alternative polyadenylation of transcripts encoding pluripotency factors, including Sox2, which partially protects its 3' UTR from miR-21-mediated degradation. Conversely, paraspeckles sequester TDP-43 and other RBPs from mRNAs and promote exit from pluripotency and embryonic patterning in the mouse. We demonstrate that cross-regulation between TDP-43 and Neat1 is essential for their efficient regulation of a broad network of genes and, therefore, of pluripotency and differentiation

Purification of cross-linked RNA-protein complexes by phenol-toluol extraction

Recent methodological advances allowed the identification of an increasing number of RNA-binding proteins (RBPs) and their RNA-binding sites. Most of those methods rely, however, on capturing proteins associated to polyadenylated RNAs which neglects RBPs bound to non-adenylate RNA classes (tRNA, rRNA, pre-mRNA) as well as the vast majority of species that lack poly-A tails in their mRNAs (including all archea and bacteria). We have developed the Phenol Toluol extraction (PTex) protocol that does not rely on a specific RNA sequence or motif for isolation of cross-linked ribonucleoproteins (RNPs), but rather purifies them based entirely on their physicochemical properties. PTex captures RBPs that bind to RNA as short as 30 nt, RNPs directly from animal tissue and can be used to simplify complex workflows such as PAR-CLIP. Finally, we provide a global RNA-bound proteome of human HEK293 cells and the bacterium Salmonella Typhimurium