scholarly journals SBSA: an online service for somatic binding sequence annotation

2021 ◽  
Author(s):  
Limin Jiang ◽  
Fei Guo ◽  
Jijun Tang ◽  
Hui Yu ◽  
Scott Ness ◽  
...  
Keyword(s):  
Somatic Mutation ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Human Subjects ◽  
Specific Factor ◽  
Single Nucleotide ◽  
Binding Motifs ◽  
Genomic Variants ◽  
Full Capacity ◽  
Binding Sequence

Abstract Efficient annotation of alterations in binding sequences of molecular regulators can help identify novel candidates for mechanisms study and offer original therapeutic hypotheses. In this work, we developed Somatic Binding Sequence Annotator (SBSA) as a full-capacity online tool to annotate altered binding motifs/sequences, addressing diverse types of genomic variants and molecular regulators. The genomic variants can be somatic mutation, single nucleotide polymorphism, RNA editing, etc. The binding motifs/sequences involve transcription factors (TFs), RNA-binding proteins, miRNA seeds, miRNA-mRNA 3′-UTR binding target, or can be any custom motifs/sequences. Compared to similar tools, SBSA is the first to support miRNA seeds and miRNA-mRNA 3′-UTR binding target, and it unprecedentedly implements a personalized genome approach that accommodates joint adjacent variants. SBSA is empowered to support an indefinite species, including preloaded reference genomes for SARS-Cov-2 and 25 other common organisms. We demonstrated SBSA by annotating multi-omics data from over 30,890 human subjects. Of the millions of somatic binding sequences identified, many are with known severe biological repercussions, such as the somatic mutation in TERT promoter region which causes a gained binding sequence for E26 transformation-specific factor (ETS1). We further validated the function of this TERT mutation using experimental data in cancer cells. Availability:http://innovebioinfo.com/Annotation/SBSA/SBSA.php.

scholarly journals SMDB: pivotal somatic sequence alterations reprogramming regulatory cascades

NAR Cancer ◽  
2020 ◽  
Vol 2 (4) ◽  
Author(s):  
Limin Jiang ◽  
Mingrui Duan ◽  
Fei Guo ◽  
Jijun Tang ◽  
Olufunmilola Oybamiji ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Translation Regulation ◽  
Single Nucleotide ◽  
Binding Motifs ◽  
Sequence Alteration ◽  
Regulatory Cascades ◽  
Gains And Losses

Abstract Binding motifs for transcription factors, RNA-binding proteins, microRNAs (miRNAs), etc. are vital for proper gene transcription and translation regulation. Sequence alteration mechanisms including single nucleotide mutations, insertion, deletion, RNA editing and single nucleotide polymorphism can lead to gains and losses of binding motifs; such consequentially emerged or vanished binding motifs are termed ‘somatic motifs’ by us. Somatic motifs have been studied sporadically but have never been curated into a comprehensive resource. By analyzing various types of sequence altering data from large consortiums, we successfully identified millions of somatic motifs, including those for important transcription factors, RNA-binding proteins, miRNA seeds and miRNA–mRNA 3′-UTR target motifs. While a few of these somatic motifs have been well studied, our results contain many novel somatic motifs that occur at high frequency and are thus likely to cause important biological repercussions. Genes targeted by these altered motifs are excellent candidates for further mechanism studies. Here, we present the first database that hosts millions of somatic motifs ascribed to a variety of sequence alteration mechanisms.

scholarly journals RNA–protein interactions: disorder, moonlighting and junk contribute to eukaryotic complexity

Open Biology ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 190096 ◽  
Author(s):  
Anna Balcerak ◽  
Alicja Trebinska-Stryjewska ◽  
Ryszard Konopinski ◽  
Maciej Wakula ◽  
Ewa Anna Grzybowska
Keyword(s):  
Protein Interactions ◽  
Regulatory Networks ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Protein Complexes ◽  
Binding Motifs ◽  
Coding Regions ◽  
Regulatory Circuits ◽  
Proteins Interactions

RNA–protein interactions are crucial for most biological processes in all organisms. However, it appears that the complexity of RNA-based regulation increases with the complexity of the organism, creating additional regulatory circuits, the scope of which is only now being revealed. It is becoming apparent that previously unappreciated features, such as disordered structural regions in proteins or non-coding regions in DNA leading to higher plasticity and pliability in RNA–protein complexes, are in fact essential for complex, precise and fine-tuned regulation. This review addresses the issue of the role of RNA–protein interactions in generating eukaryotic complexity, focusing on the newly characterized disordered RNA-binding motifs, moonlighting of metabolic enzymes, RNA-binding proteins interactions with different RNA species and their participation in regulatory networks of higher order.

scholarly journals Role of RNA Motifs in RNA Interaction with Membrane Lipid Rafts: Implications for Therapeutic Applications of Exosomal RNAs

2021 ◽  
Vol 22 (17) ◽  
pp. 9416
Author(s):  
Rafał Mańka ◽  
Pawel Janas ◽  
Karolina Sapoń ◽  
Teresa Janas ◽  
Tadeusz Janas
Keyword(s):  
Lipid Rafts ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Membrane Lipid ◽  
Rna Aptamers ◽  
Target Cells ◽  
Rna Motifs ◽  
Binding Motifs ◽  
Rna Exosome ◽  
Rna Interaction

RNA motifs may promote interactions with exosomes (EXO-motifs) and lipid rafts (RAFT-motifs) that are enriched in exosomal membranes. These interactions can promote selective RNA loading into exosomes. We quantified the affinity between RNA aptamers containing various EXO- and RAFT-motifs and membrane lipid rafts in a liposome model of exosomes by determining the dissociation constants. Analysis of the secondary structure of RNA molecules provided data about the possible location of EXO- and RAFT-motifs within the RNA structure. The affinity of RNAs containing RAFT-motifs (UUGU, UCCC, CUCC, CCCU) and some EXO-motifs (CCCU, UCCU) to rafted liposomes is higher in comparison to aptamers without these motifs, suggesting direct RNA-exosome interaction. We have confirmed these results through the determination of the dissociation constant values of exosome-RNA aptamer complexes. RNAs containing EXO-motifs GGAG or UGAG have substantially lower affinity to lipid rafts, suggesting indirect RNA-exosome interaction via RNA binding proteins. Bioinformatics analysis revealed RNA aptamers containing both raft- and miRNA-binding motifs and involvement of raft-binding motifs UCCCU and CUCCC. A strategy is proposed for using functional RNA aptamers (fRNAa) containing both RAFT-motif and a therapeutic motif (e.g., miRNA inhibitor) to selectively introduce RNAs into exosomes for fRNAa delivery to target cells for personalized therapy.

scholarly journals A yeast RNA-binding protein shuttles between the nucleus and the cytoplasm.

1994 ◽  
Vol 14 (12) ◽  
pp. 8399-8407 ◽  
Author(s):  
J Flach ◽  
M Bossie ◽  
J Vogel ◽  
A Corbett ◽  
T Jinks ◽  
...  
Keyword(s):  
Nuclear Protein ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Rna Binding Protein ◽  
Wild Type ◽  
Yeast Saccharomyces Cerevisiae ◽  
Binding Motifs ◽  
C Terminus ◽  
N Terminus ◽  
Heterogeneous Nuclear Ribonucleoproteins

RNA-binding proteins have been suggested to move in association with RNA as it leaves the nucleus. The NPL3 gene of the yeast Saccharomyces cerevisiae encodes in nuclear protein with consensus RNA-binding motifs and similarity to heterogeneous nuclear ribonucleoproteins and members of the S/R protein family. We show that although Npl3 is located in the nucleus, it can shuttle between nuclei in yeast heterokaryons. In contrast, other nucleus-targeted proteins do not leave the nucleus under similar conditions. Mutants missing the RNA-binding motifs or the N terminus are still capable of shuttling in and out of the nucleus. Npl3 mutants missing the C terminus fail to localize to the nucleus. Overproduction of Npl3 in wild-type cells shows cell growth. This toxicity depends on the presence of series of unique repeats in the N terminus and localization to the nucleus. We suggest that the properties of Npl3 are consistent with it being involved in export of RNAs from the nucleus.

scholarly journals Prediction of RNA-protein sequence and structure binding preferences using deep convolutional and recurrent neural networks

2017 ◽  
Author(s):  
Xiaoyong Pan ◽  
Peter Rijnbeek ◽  
Junchi Yan ◽  
Hong-Bin Shen
Keyword(s):  
Neural Networks ◽  
Binding Sites ◽  
Large Scale ◽  
Rna Binding ◽  
Short Term Memory ◽  
Rna Binding Proteins ◽  
Point Of View ◽  
Rna Sequences ◽  
Close Relationship ◽  
Binding Sequence

AbstractRNA regulation is significantly dependent on its binding protein partner, which is known as the RNA-binding proteins (RBPs). Unfortunately, the binding preferences for most RBPs are still not well characterized, especially on the structure point of view. Informative signals hiding and interdependencies between sequence and structure specificities are two challenging problems for both predicting RBP binding sites and accurate sequence and structure motifs mining.In this study, we propose a deep learning-based method, iDeepS, to simultaneously identify the binding sequence and structure motifs from RNA sequences using convolutional neural networks (CNNs) and a bidirectional long short term memory network (BLSTM). We first perform one-hot encoding for both the sequence and predicted secondary structure, which are appropriate for subsequent convolution operations. To reveal the hidden binding knowledge from the observations, the CNNs are applied to learn the abstract motif features. Considering the close relationship between sequences and predicted structures, we use the BLSTM to capture the long range dependencies between binding sequence and structure motifs identified by the CNNs. Finally, the learned weighted representations are fed into a classification layer to predict the RBP binding sites. We evaluated iDeepS on verified RBP binding sites derived from large-scale representative CLIP-seq datasets, and the results demonstrate that iDeepS can reliably predict the RBP binding sites on RNAs, and outperforms the state-of-the-art methods. An important advantage is that iDeepS is able to automatically extract both binding sequence and structure motifs, which will improve our transparent understanding of the mechanisms of binding specificities of RBPs. iDeepS is available at https://github.com/xypan1232/iDeepS.

scholarly journals Before It Gets Started: Regulating Translation at the 5′ UTR

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Patricia R. Araujo ◽  
Kihoon Yoon ◽  
Daijin Ko ◽  
Andrew D. Smith ◽  
Mei Qiao ◽  
...  
Keyword(s):  
Rna Binding ◽  
Rna Binding Proteins ◽  
Regulatory Elements ◽  
Open Reading Frame ◽  
Upstream Open Reading Frame ◽  
Translation Regulation ◽  
Binding Motifs ◽  
Reading Frame ◽  
Physiological Conditions ◽  
The Impact

Translation regulation plays important roles in both normal physiological conditions and diseases states. This regulation requires cis-regulatory elements located mostly in 5′ and 3′ UTRs and trans-regulatory factors (e.g., RNA binding proteins (RBPs)) which recognize specific RNA features and interact with the translation machinery to modulate its activity. In this paper, we discuss important aspects of 5′ UTR-mediated regulation by providing an overview of the characteristics and the function of the main elements present in this region, like uORF (upstream open reading frame), secondary structures, and RBPs binding motifs and different mechanisms of translation regulation and the impact they have on gene expression and human health when deregulated.

scholarly journals A yeast RNA-binding protein shuttles between the nucleus and the cytoplasm

1994 ◽  
Vol 14 (12) ◽  
pp. 8399-8407
Author(s):  
J Flach ◽  
M Bossie ◽  
J Vogel ◽  
A Corbett ◽  
T Jinks ◽  
...  
Keyword(s):  
Nuclear Protein ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Rna Binding Protein ◽  
Wild Type ◽  
Yeast Saccharomyces Cerevisiae ◽  
Binding Motifs ◽  
C Terminus ◽  
N Terminus ◽  
Heterogeneous Nuclear Ribonucleoproteins

RNA-binding proteins have been suggested to move in association with RNA as it leaves the nucleus. The NPL3 gene of the yeast Saccharomyces cerevisiae encodes in nuclear protein with consensus RNA-binding motifs and similarity to heterogeneous nuclear ribonucleoproteins and members of the S/R protein family. We show that although Npl3 is located in the nucleus, it can shuttle between nuclei in yeast heterokaryons. In contrast, other nucleus-targeted proteins do not leave the nucleus under similar conditions. Mutants missing the RNA-binding motifs or the N terminus are still capable of shuttling in and out of the nucleus. Npl3 mutants missing the C terminus fail to localize to the nucleus. Overproduction of Npl3 in wild-type cells shows cell growth. This toxicity depends on the presence of series of unique repeats in the N terminus and localization to the nucleus. We suggest that the properties of Npl3 are consistent with it being involved in export of RNAs from the nucleus.

scholarly journals Profiling the binding sites of RNA-binding protein by LACE-seq

2021 ◽  
Author(s):  
Ruibao Su ◽  
Di Wang ◽  
Changchang Cao ◽  
Yuanchao Xue
Keyword(s):  
Binding Sites ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Transcription Termination ◽  
Early Embryo ◽  
Linear Amplification ◽  
Single Nucleotide ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution

Abstract RNA-binding proteins (RBPs) directly interact with various RNAs in living cells to regulate their processing, translation, and stability. Identifying the precise binding sites of RBPs is critical for appreciating their physiological or pathological roles in germline and early embryo development. Current methods typically need millions of cells to map RBP binding positions, which prevents us from appreciating the crucial role of RBPs in early development. Here, we present the LACE-seq method for unbiased mapping of RBP-binding sites at single-nucleotide resolution in fewer cells or even single oocytes. LACE-seq depends on RBP-mediated reverse transcription termination, and linear amplification of the cDNA ends for deep sequencing. To further promote its application, we describe a step-by-step protocol about how to construct a successful LACE-seq library.

scholarly journals The Mitochondrial Message-specific mRNA Protectors Cbp1 and Pet309 Are Associated in a High-Molecular Weight Complex

2004 ◽  
Vol 15 (6) ◽  
pp. 2674-2683 ◽  
Author(s):  
Kirsten Krause ◽  
Renata Lopes de Souza ◽  
Douglas G.W. Roberts ◽  
Carol L. Dieckmann
Keyword(s):  
Rna Binding ◽  
Hydrophobic Interactions ◽  
Rna Binding Proteins ◽  
Gel Filtration ◽  
Specific Factor ◽  
Mitochondrial Cytochrome ◽  
Native Page ◽  
High Molecular Weight Complex ◽  
C Terminus ◽  
Mitochondrial Cytochrome B

In Saccharomyces cerevisiae, the nuclear-encoded protein Cbp1 promotes stability and translation of mitochondrial cytochrome b transcripts through interaction with the 5′ untranslated region. Fusion of a biotin binding peptide tag to the C terminus of Cbp1 has now allowed detection in mitochondrial extracts by using peroxidase-coupled avidin. Cbp1 is associated with the mitochondrial membranes when high ionic strength extraction conditions are used. However, the protein is easily solubilized by omitting salt from the extraction buffer, which suggests Cbp1 is loosely associated with the membrane through weak hydrophobic interactions. Gel filtration analysis and blue native PAGE showed that Cbp1 is part of a single 900,000-Da complex. The complex was purified using the biotin tag and a sequence-specific protease cleavage site. In addition to Cbp1, the complex contains several polypeptides of molecular weights between 113 and 40 kDa. Among these, we identified another message-specific factor, Pet309, which promotes the stability and translation of mitochondrial cytochrome oxidase subunit I mRNA. A hypothesis is presented in which the Cbp1–Pet309 complex contains several message-specific RNA binding proteins and links transcription to translation of the mRNAs at the membrane.

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