Rapidly Growing Protein-Centric Technologies to Extensively Identify Protein-RNA Interactions: Application to the Analysis of Co-Transcriptional RNA Processing.

During mRNA transcription, diverse RNA-binding proteins (RBPs) are recruited to RNA polymerase II (RNAP II) transcription machinery. These RBPs bind to distinct sites of nascent RNA to co-transcriptionally operate mRNA processing. Recent studies have revealed a close relationship between transcription and co-transcriptional RNA processing, where one affects the other's activity, indicating an essential role of protein-RNA interactions for the fine-tuning of mRNA production. Owing to their limited amount in cells, the detection of protein-RNA interactions specifically assembled on the transcribing RNAP II machinery still remains challenging. Currently, cross-linking and immunoprecipitation (CLIP) has become a standard method to detect in vivo protein-RNA interactions, although it requires a large amount of input materials. Several improved methods, such as infrared-CLIP (irCLIP), enhanced CLIP (eCLIP), and target RNA immunoprecipitation (tRIP), have shown remarkable enhancements in the detection efficiency. Furthermore, the utilization of an RNA editing mechanism or proximity labeling strategy has achieved the detection of faint protein-RNA interactions in cells without depending on crosslinking. This review aims to explore various methods being developed to detect endogenous protein-RNA interaction sites and discusses how they may be applied to the analysis of co-transcriptional RNA processing.

La megalina es el receptor para la endocitosis mediada por caveolas de la albúmina y se requiere para la síntesis del factor neurotrófico ácido oleico / Megalin is the receptor for caveola-mediated endocytosis of albumin and it’s required for the synthesis of the neurotrophic factor oleic acid

Objetivo: Estudiar el mecanismo de endocitosis de la albúmina en astrocitos de rata en cultivo primario. Material y Métodos: Se utilizaron neonatos (1 día de vida) de ratas Wistar para obtener astrocitos en cultivo primario. Los astrocitos se incubaron con albúmina al 2% o albúmina-FITC al 0,5%, durante 20 minutos, a 4ºC para los estudios de unión y durante 20 minutos a 4ºC, seguido de 10 minutos a 37ºC, para los estudios de internalización. Para los experimentos de pérdida de función, los astrocitos se transfectaron con 50nM de siRNA específico para el silenciamiento de la proteína diana durante 72 h. El ácido oleico presente en el medio de cultivo de astrocitos incubados con albúmina al 2% durante una hora se cuantifico por HPLC. Resultados: la megalina y la caveolina-1, pero no la clatrina, colocalizan con la albúmina en la membrana plasmática. El silenciamiento de la megalina y de la caveolina-1 reduce la capacidad de la albúmina para unirse a la membrana e internalizarse y reduce la capacidad de los astrocitos para sintetizar el factor neurotrófico ácido oleico. El silenciamiento de la clatrina no modifica la internalización de la albúmina ni la síntesis del ácido oleico. Conclusiones: la albúmina se internaliza mediante endocitosis dependiente de caveolas vía megalina en los astrocitos y que este proceso se requiere para la síntesis del factor neurotrófico ácido oleico (AU)

Aim: Study of the endocytic pathway of albumin in rat astrocytes from primary culture. Material y Methods: One day postnatal Wistar rats were used to obtain astrocytes form primary culture. Astrocytes were incubated with 2% albumin or 0.5% FITC-albumin during 20 minutes at 4ºC for binding experiments or during 20 minutes at 4ºC followed by 10 minutes at 37ºC for internalization experiments. For lossof- function experiments, astrocytes were transfected during 72h with 50 nM of siRNA specific for target protein, followed by the binding and internalization experiments. Oleic acid present in the culture medium of astrocytes incubated with 2% albumin during one hour was quantified by HPLC. Results: We observed that megalin and caveolin-1, but not clathrin, co-localize with albumin in the membrane. Megalin and caveolin-1 silencing by siRNA reduces albumin binding and internalization, as well as oleic acid synthesis in astrocytes. Nonetheless, clathrin silencing do not modify albumin internalization or oleic acid synthesis in astrocytes Conclusions: albumin is internalized in a caveola-dependent mechanism via megalin and that this event is required for the synthesis of the neurotrophic factor oleic acid (AU)

Interactive proteomics: what lies ahead?

Interactive proteomics addresses the physical associations among proteins and establishes global, disease-, and pathway-specific protein interaction networks. The inherent chemical and structural diversity of proteins, their different expression levels, and their distinct subcellular localizations pose unique challenges for the exploration of these networks, necessitating the use of a variety of innovative and ingenious approaches. Consequently, recent years have seen exciting developments in protein interaction mapping and the establishment of very large interaction networks, especially in model organisms. In the near future, attention will shift to the establishment of interaction networks in humans and their application in drug discovery and understanding of diseases. In this review, we present an impressive toolbox of different technologies that we expect to be crucial for interactive proteomics in the coming years.

Advances in RIP-chip analysis : RNA-binding protein immunoprecipitation-microarray profiling.

In eukaryotic organisms, gene regulatory networks require an additional level of coordination that links transcriptional and post-transcriptional processes. Messenger RNAs have traditionally been viewed as passive molecules in the pathway from transcription to translation. However, it is now clear that RNA-binding proteins (RBPs) play a major role in regulating multiple mRNAs to facilitate gene expression patterns. On this basis, post-transcriptional and transcriptional gene expression networks appear to be very analogous. Our previous research focused on targeting RBPs to develop a better understanding of post-transcriptional gene-expression processing and the regulation of mRNA networks. We developed technologies for purifying endogenously formed RBP-mRNA complexes from cellular extracts and identifying the associated messages using genome-scale, microarray technology, a method called ribonomics or RNA-binding protein immunoprecipitation-microarray (Chip) profiling or RIP-Chip. The use of the RIP-Chip methods has provided great insight into the infrastructure of coordinated eukaryotic post-transcriptional gene expression, insights which could not have been obtained using traditional RNA expression profiling approaches (1). This chapter describes the most current RIP-Chip techniques as we presently practice them. We also discuss some of the informatic aspects that are unique to analyzing RIP-Chip data.

Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK).

Present screening methods for protein-protein interactions (PPIs) rely on the overexpression of artificial fusion proteins, making it difficult to assess in vivo relevance. Here we combine stable isotope labeling with amino acids in cell culture (SILAC), RNA interference (RNAi), coimmunoprecipitation and quantitative mass-spectrometry analysis to detect cellular interaction partners of endogenous proteins in mammalian cells with very high confidence. We used this screen to identify interaction partners of beta-catenin and Cbl.

RNA immunoprecipitation for determining RNA-protein associations in vivo.

Similar to chromatin immunoprecipitation (ChIP), RNA immunoprecipitation (RIP) can be used to detect the association of individual proteins with specific nucleic acid regions, in this case on RNA. Live cells are treated with formaldehyde to generate protein-RNA cross-links between molecules that are in close proximity in vivo. RNA sequences that cross-link with a given protein are isolated by immunoprecipitation of the protein, and reversal of the formaldehyde cross-linking permits recovery and quantitative analysis of the immunoprecipitated RNA by reverse transcription PCR. The basics of RIP are very similar to those of ChIP, but with some important caveats. This unit describes the RIP procedure for Saccharomyces cerevisiae. Although the corresponding steps for metazoan cells have not yet been worked out, it is likely that the yeast procedure can easily be adapted for use in other organisms.