A census of human RNA-binding proteins.
TL;DR: This work presents a census of 1,542 manually curated RBPs that are analysed for their interactions with different classes of RNA, their evolutionary conservation, their abundance and their tissue-specific expression, a critical step towards the comprehensive characterization of proteins involved in human RNA metabolism.
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Abstract: Post-transcriptional gene regulation (PTGR) concerns processes involved in the maturation, transport, stability and translation of coding and non-coding RNAs. RNA-binding proteins (RBPs) and ribonucleoproteins coordinate RNA processing and PTGR. The introduction of large-scale quantitative methods, such as next-generation sequencing and modern protein mass spectrometry, has renewed interest in the investigation of PTGR and the protein factors involved at a systems-biology level. Here, we present a census of 1,542 manually curated RBPs that we have analysed for their interactions with different classes of RNA, their evolutionary conservation, their abundance and their tissue-specific expression. Our analysis is a critical step towards the comprehensive characterization of proteins involved in human RNA metabolism.
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omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data.
TL;DR: A probabilistic model called omniCLIP is presented that can detect regulatory elements in RNAs from data of all CLIP-seq assays, and jointly models data across replicates and can integrate background information.
Circadian mRNA expression: insights from modeling and transcriptomics
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TL;DR: The charting of circadian output rhythms in mRNA expression, focusing on mammals, is reviewed, emphasizing the challenges in statistics, interpretation, and quantitative descriptions that such investigations have faced and continue to face, and outline remaining outstanding questions.
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RNA-binding proteins and their role in kidney disease
TL;DR: In this article, the authors discuss current knowledge of RNA-binding proteins and their interactions with RNAs and proteins, their roles in kidney diseases, and their potential as novel therapeutic targets for kidney diseases.
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A non-radioactive, improved PAR-CLIP and small RNA cDNA library preparation protocol.
Dimitrios G. Anastasakis,Alexis Jacob,Parthena Konstantinidou,Kazuyuki Meguro,Duncan Claypool,Pavol Cekan,Astrid D. Haase,Markus Hafner +7 more
TL;DR: Fluorescence-based PAR-CLIP (fPARCLIP) as mentioned in this paper was proposed to eliminate the need to use radioactivity by direct ligation of a fluorescently labeled adapter to the 3'end of crosslinked RNA on immobilized ribonucleoproteins, followed by isolation of the adapter-ligated RNA and efficient conversion into cDNA without the previously needed size fractionation.
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The role of RNA conformation in RNA-protein recognition.
TL;DR: This study suggests an additional way by which the RRM domain recognizes its RNA target, involving a conformational readout, which enables the recognition of a wide variety of different RNA sequences and shapes.
32
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