RNA-binding proteins (RBPs) are important regulators of eukaryotic gene expression. Genomes typically encode dozens to hundreds of proteins containing RNA-binding domains, which collectively recognize diverse RNA sequences and structures. Recent advances in high-throughput methods for assaying the targets of RBPs in vitro and in vivo allow large-scale derivation of RNA-binding motifs as well as determination of RNA-protein interactions in living cells. In parallel, many computational methods have been developed to analyze and interpret these data. The interplay between RNA secondary structure and RBP binding has also been a growing theme. Integrating RNA-protein interaction data with observations of post-transcriptional regulation will enhance our understanding of the roles of these important proteins.
Different complexes are formed on the 3' end of histone mRNA with nuclear and polyribosomal proteins
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
mRNA polyadenylate-binding protein: gene isolation and sequencing and identification of a ribonucleoprotein consensus sequence
Comparative mutational analysis of the double-stranded RNA binding domains of Xenopus laevis RNA-binding protein A.
The stem-loop binding protein forms a highly stable and specific complex with the 3' stem-loop of histone mRNAs
RNA-binding proteins to assess gene expression states of co-cultivated cells in response to tumor cells
Evidence for reassociation of RNA-binding proteins after cell lysis: implications for the interpretation of immunoprecipitation analyses
The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression
Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster
Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes
Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities
RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins
The solution structure of the ADAR2 dsRBM-RNA complex reveals a sequence-specific readout of the minor groove
CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins
Quantitative profiling of in vivo-assembled RNA-protein complexes using a novel integrated proteomic approach.
Specific and modular binding code for cytosine recognition in Pumilio/FBF (PUF) RNA-binding domains.
Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability
SeqFold: genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data
Measurements of the impact of 3' end sequences on gene expression reveal wide range and sequence dependent effects
Quantitative proteomic analysis reveals concurrent RNA-protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae
RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins
Genome-wide analysis of Staufen-associated mRNAs identifies secondary structures that confer target specificity
Modeling the binding specificity of the RNA-binding protein GLD-1 suggests a function of coding region-located sites in translational repression
starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data
RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome
RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins
De novo prediction of PTBP1 binding and splicing targets reveals unexpected features of its RNA recognition and function
Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes
Biochemical Methods To Investigate lncRNA and the Influence of lncRNA:Protein Complexes on Chromatin
Identification of novel proteins binding the AU-rich element of α-prothymosin mRNA through the selection of open reading frames (RIDome)
IPMiner: hidden ncRNA-protein interaction sequential pattern mining with stacked autoencoder for accurate computational prediction
Analysis of the RNA Binding Specificity Landscape of C5 Protein Reveals Structure and Sequence Preferences that Direct RNase P Specificity
Non-Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non-Invasive Diagnostic Tools
In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors
Comprehensive review and empirical analysis of hallmarks of DNA-, RNA- and protein-binding residues in protein chains
Long Noncoding RNA Signatures Induced by Toll-Like Receptor 7 and Type I Interferon Signaling in Activated Human Plasmacytoid Dendritic Cells
SCRIBER: accurate and partner type-specific prediction of protein-binding residues from proteins sequences
Localization elements and zip codes in the intracellular transport and localization of messenger RNAs in Saccharomyces cerevisiae
Chromatin Landscape Distinguishes the Genomic Loci of Hundreds of Androgen-Receptor-Associated LincRNAs From the Loci of Non-associated LincRNAs
Upstream analysis of alternative splicing: a review of computational approaches to predict context-dependent splicing factors
Rules of RNA specificity of hnRNP A1 revealed by global and quantitative analysis of its affinity distribution
The contribution of the C5 protein subunit of Escherichia coli ribonuclease P to specificity for precursor tRNA is modulated by proximal 5' leader sequences
Accurate prediction of protein-lncRNA interactions by diffusion and HeteSim features across heterogeneous network
Relative Information Gain: Shannon entropy-based measure of the relative structural conservation in RNA alignments.
Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.
Alzheimer's Disease: MS4A
Variants within the membrane-spanning 4-domains subfamily A (MS4A) gene cluster have recently been implicated in Alzheimer's disease in genome-wide association studies. Here is the latest research on Alzheimer's disease and MS4A.
Pediculosis pubis is a disease caused by a parasitic insect known as Pthirus pubis, which infests human pubic hair, as well as other areas with hair including eye lashes. Here is the latest research.
Rh isoimmunization is a potentially preventable condition that occasionally is associated with significant perinatal morbidity or mortality. Discover the latest research on Rh Isoimmunization here.
Genetic Screens in iPSC-derived Brain Cells
Genetic screening is a critical tool that can be employed to define and understand gene function and interaction. This feed focuses on genetic screens conducted using induced pluripotent stem cell (iPSC)-derived brain cells. It also follows CRISPR-Cas9 approaches to generating genetic mutants as a means of understanding the effect of genetics on phenotype.
This feed focuses on molecular models of enzyme evolution and new approaches (such as adaptive laboratory evolution) to metabolic engineering of microorganisms. Here is the latest research.
Chronic Fatigue Syndrome
Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.
Pharmacology of Proteinopathies
This feed focuses on the pharmacology of proteinopathies - diseases in which proteins abnormally aggregate (i.e. Alzheimer’s, Parkinson’s, etc.). Discover the latest research in this field with this feed.
Alignment-free Sequence Analysis Tools
Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. Here is the latest research.