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Tag: RBPs
Proteomic analysis of SARS-CoV-2 particles unveils a key role of G3BP proteins in viral assembly
Capturing proteins associated with SARS-CoV-2 virions To identify host cell proteins potentially present in extracellular SARS-CoV-2 virions, viral particles were produced from two lung epithelial cell models, A549 cells overexpressing ACE2 receptor (A549-ACE2) and Calu-3 cells that naturally express ACE2 receptor and TMPRSS2. Following infection with the D614G SARS-CoV-2 strain32,…
Their Roles and Interactome in Parkinson’s Disease Progression
Circular RNAs (circRNA) are products of alternative splicing that consist of a closed circular structure through a covalent 3′-5′ phosphodiester linkage. Their unique structure lends itself to a variety of physical properties and functions, including increased half-life within the cellular environment and the ability to sponge microRNA (miRNA) and RNA-binding…
“Regulation of mRNA and circRNA as a Cause and Consequence of Aging in” by Rebekah Napier-Jameson
Abstract A role for RNA binding proteins in regulating lifespan has emerged. We identified a pair of neuronal RBPs, exc-7 and mbl-1, which display synthetic lifespan defects. Such a strong synthetic phenotype represented an opportunity to use transcriptomics to search for potential causative targets that are synthetically regulated. We identified…
Carbohydrates and carbohydrate degradation gene abundance and transcription in Atlantic waters of the Arctic
Seawater samples were collected from surface waters (SRF) and the bottom of the surface mixed layer (BML) in the Eastern Fram Strait region to investigate the distribution of carbohydrates and their utilisation by microbial communities. The ten sites were grouped into three categories based on the underlying seafloor topography (above-slope,…
MD Anderson Research Highlights for November 15, 2023
Newswise — HOUSTON ― The University of Texas MD Anderson Cancer Center’s Research Highlights showcases the latest breakthroughs in cancer care, research and prevention. These advances are made possible through seamless collaboration between MD Anderson’s world-leading clinicians and scientists, bringing discoveries from the lab to the clinic and back. Recent…
Reviewing the Importance of circRNA
In recent years following the COVID-19 pandemic, RNA has gained attention for its successes and potential use in vaccines and therapeutics. One avenue of interest in RNA research is a non-coding class of RNA first identified almost 50 years ago, circular RNA (circRNA). In 1976, Sanger et al. first identified…
Meet circ2CBA: A Novel Deep Learning Model that Revolutionizes the Prediction of circRNA-RBP Binding Sites
In a recent development, a team of researchers from China have introduced a deep learning model, named circ2CBA, that promises to revolutionize the prediction of binding sites between circular RNAs (circRNAs) and RNA-binding proteins (RBPs). This development holds significant implications for understanding the intricate mechanisms underlying various diseases, particularly cancers….
Advancing circRNA-RBP Interaction Prediction: circ2CBA Deep Learning Model
TL;DR: Chinese researchers introduced circ2CBA, a deep learning model for predicting circRNA-RBP binding sites. CircRNAs play a crucial role in disease mechanisms, especially cancer, making their interaction with RBPs significant. circ2CBA stands out for its ability to predict binding sites using only circRNA sequence information, simplifying the process. The model…
Nascent ribosomal RNA act as surfactant that suppresses growth of fibrillar centers in nucleolus
Transcription and RNA processing The occupancy \({n}_{{{{{{\rm{ps}}}}}}}\) of the TSS of the active rDNA by Pol I follows the kinetic equation $$\frac{d}{{dt}}{n}_{{{{{{\rm{ps}}}}}}}={k}_{{{{{{\rm{on}}}}}}}\rho \left(1-{n}_{{{{{{\rm{ps}}}}}}}\right)-{k}_{{{{{{\rm{off}}}}}}}{n}_{{{{{{\rm{ps}}}}}}}-{k}_{{{{{{\rm{e}}}}}}}{n}_{{{{{{\rm{ps}}}}}}}.$$ (5) Equation (5) suggests that the occupancy \({n}_{{{{{{\rm{ps}}}}}}}\) changes due to the binding of Pol I from the FC (the first term), the unbinding of Pol I…
A joint model for predicting circRNA-RBP binding sites based on deep learning
The flowchart of circ2CBA. Credit: Frontiers Journals The interaction between circRNAs and RBPs is related to many diseases, especially cancers. Understanding the mechanism of the interaction and predicting their binding sites is critical. New research published in Frontiers of Computer Science proposes a method to predict these binding sites using…
A joint model for predicting circRNA-RBP bind
image: The flowchart of circ2CBA view more Credit: Yajing GUO, Xiujuan LEI, Lian LIU, Yi PAN The interaction between circRNAs and RBPs is related to many diseases especially cancers. Understanding the mechanism of the interaction is critical and predicting the binding sites of them is helpful for this. Existing methods for…
Scientists train AI to illuminate drugs’ impact
An ideal medicine for one person may prove ineffective or harmful for someone else, and predicting who could benefit from a given drug has been difficult. Now, an international team led by neuroscientist Kirill Martemyanov, Ph.D., based at The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, is…
A Breakthrough in Predicting CircRNA-RBP Binding Sites using Deep Learning
New research published in Frontiers of Computer Science presents an innovative approach to predicting binding sites between circular RNAs (circRNAs) and RNA-binding proteins (RBPs). The study introduces a deep learning-based model named circ2CBA, which leverages sequence information of circRNAs to accurately predict their interaction with RBPs. Traditionally, understanding the complex…
Characteristics, Biogenesis and Functions of CircRNAs
Circular RNA (CircRNA), a single-stranded closed-loop RNA that lacks terminal 5′ caps and 3′ poly (A) tails, is more stable than linear RNA. CircRNA was first discovered in plant-infected viroids and was later observed in eukaryotes, although it was not produced via the back-splicing mechanism. 1. Characteristics Circular RNA (CircRNA),…
ncRNA | Free Full-Text | Novel Insights into Circular RNAs in Metastasis in Breast Cancer: An Update
Non-Coding RNA 2023, 9(5), 55; doi.org/10.3390/ncrna9050055 (registering DOI) Non-Coding RNA 2023, 9(5), 55; doi.org/10.3390/ncrna9050055 (registering DOI) Received: 23 July 2023 / Revised: 26 August 2023 / Accepted: 28 August 2023 / Published: 16 September 2023 Round 1 Reviewer 1 Report This manuscript by Zepeda-Enríquez et. al. sets out to review repertoire…
The important regulatory roles of circRNA-encoded proteins or peptides in cancer pathogenesis
1Institute for Translational Medicine, Qingdao University, China 2Qingdao University, China The final, formatted version of the article will be published soon. Notify me Receive an email when it is updated You just subscribed to receive the final version of the article …
UTR Full Form: Types, Importance, Evolutionary
Flanking Regions: UTRs are located at both ends of an mRNA molecule, surrounding the coding sequence. The 5′ UTR, which comes before the coding sequence, and the 3′ UTR, which comes after it, are the two primary forms of UTRs. Regulatory Functions: UTRs are involved in regulating various aspects of…
LncRNA FENDRR suppresses melanoma growth
Introduction Cutaneous melanoma is a kind of highly aggressive and metastatic cancer.1 It only occurs in 5% of all skin cancers but causes more than 75% of deaths.2,3 Melanoma can be cured by surgical removal at an early stage.4 However, when the disease progresses to an advanced stage (stage IV),…
Study Explores Role of Prostate Cancer Mutations in 3′ Untranslated Regions
NEW YORK— Researchers have unraveled the effects of mutations in the 3′ untranslated regions (UTR) of prostate cancer-related genes on disease progression, mRNA stability, and translation. In a study published in Cell Reports on Friday, the team, led by investigators at the Fred Hutchinson Cancer Center, studied somatic mutations in…
AMG-1/SLRP-1 is required for spermatogenesis
image: Graphical view of AMG-1 binding 12S rRNA to regulate mitochondrial gene translation (top), and amg-1 mutation results in reduced mitochondrial translation machinery (bottom). view more Credit: ©Science China Press This study is led by Prof. Long Miao (Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College…
Unlocking the power of mRNA technology
By Yochi Slonim, CEO and co-founder of Anima Biotech mRNA technology has gained widespread recognition due to its role in the development of vaccines, such as those used against COVID-19; however, the scope of mRNA extends far beyond vaccines, offering a range of possibilities for addressing different conditions. Vaccines represent…
Single-cell quantification of ribosome occupancy in early mouse development
PDMS chip fabrication Moulds were 3D-printed by Proto Labs with WaterShed XC 11122 at high resolution (Supplementary Fig. 1). Reusable moulds were assembled by taping 3D-printed molds to glass slides (5″ × 4″; Ted Pella). Sylgard 184 PDMS monomer and curing agent (4019862, Ellsworth Adhesives) were mixed at a 10:1…
Cumulative effects of weakly repressive regulatory regions in the 3’ UTR maintain PD-1 expression homeostasis in mammals
The PD-1 3’ UTR repressed reporter gene expression by promoting mRNA decay The human PD-1 3’ UTR is made up of 1,174 nucleotides, longer than its coding region (867 nts). To explore the revolutionary relationship of PD-1 3’ UTRs of species, we systematically analyzed the sequence conservation of 21,050 protein-coding…
CRISPR-Cas13 guide RNA predictor for transcript depletion
Cite As: Krohannon A, Srivastava M, Rauch S, Srivastava R, Dickinson BC, Janga SC. CASowary: CRISPR-Cas13 guide RNA predictor for transcript depletion. BMC Genomics. 2022;23(1):172. Published 2022 Mar 2. doi:10.1186/s12864-022-08366-2 Abstract: Background: Recent discovery of the gene editing system – CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats) associated proteins (Cas),…
Locanabio Presents Preclinical Data from its Vectorized snRNA Exon Skipping Program for DMD and Cas13d Multi-targeting Program for C9orf72 ALS at the American Society of Gene and Cell Therapy (ASGCT) 26th Annual Meeting
Locanabio, Inc. LBIO-115 demonstrates robust exon 51 skipping resulting in high levels of dystrophin restoration in patient-derived muscle cells and an in vivo DMD disease model Cas13d Multi-targeting efficiently knocks down both sense and antisense toxic RNAs and decreases dipeptide repeats in C9orf72 ALS patient fibroblasts and an in vivo…
CircRNAs: versatile players and new targets in organ fibrosis | Cell Communication and Signaling
Organ fibrosis is the final common pathological pathway of many chronic diseases and is characterized by various injuries and insults with maladaptive tissue repair, followed by excessive collagen deposition into the extracellular matrix (ECM). Structural alterations lead to tissue stiffness, vascular rarefaction, hypoxia, proliferation, differentiation and activation of fibroblasts and…
A map to study exRNA, a novel form of cell-to-cell communication
Ribonucleic acid or RNA, one type of genetic material that is present inside all living cells, is mostly known to act as a messenger carrying instructions encoded in the DNA for the synthesis of proteins. However, in recent years research has shown that RNA not only exists inside cells, but…
Establishing the basis for mammalian intracellular computing with mRNA switches
Credit: Kyoto University Professor Hirohide Saito and his research team have developed a new approach to control mRNA translation using Cas proteins, thus expanding the variety of mRNA switches and making it easier to build synthetic gene circuits in mammalian cells. The results of this research were published in Nature…
BIO 344 Exam 2-8 – tRNA and rRNA Processing – Inosine base pairs with cytosine (acts like guanine)
– Inosine base pairs with cytosine (acts like guanine) – CIG =CGG= codon for arginine – Recent studies suggest there are over 23,000 editing sites in human genome – Another RNA editing enzyme used by human cells is cytidine deaminase: converts cytosine to uracil through deamination – Cytidine deaminases regulate…
Researchers develop a new powerful resource to study extracellular RNA
An international team led by researchers at Baylor College of Medicine with the National Institutes of Health Extracellular RNA Communication Consortium and the Bogdan Mateescu laboratory at the ETH Zürich and University of Zürich has developed a new powerful resource to study extracellular RNA (exRNA), a novel form of cell-to-cell…
KEGG T01001: 10137
Entry 10137 CDS T01001 Symbol RBM12, HRIHFB2091, SCZD19, SWAN Name (RefSeq) RNA binding motif protein 12 KO K24526 RNA-binding protein 12 Organism hsa Homo sapiens (human) Disease H01649 Schizophrenia Brite KEGG Orthology (KO) [BR:hsa00001] 09180 Brite Hierarchies 09182 Protein families: genetic information processing 03041 Spliceosome [BR:hsa03041] 10137 (RBM12)Spliceosome [BR:hsa03041] Other splicing related proteins Spliceosome associated proteins (SAPs) RNA binding proteins…
Understanding the roles and regulation patterns of circRNA on its host gene in tumorigenesis and tumor progression
Circular RNAs (circRNAs) are a novel type of endogenous non-coding RNAs, which are covalently closed loop structures formed by precursor mRNAs (pre-mRNAs) through back-splicing. CircRNAs are abnormally expressed in many tumors, and play critical roles in a variety of tumors as oncogenes or tumor suppressor genes by sponging miRNAs, regulating…
An in vivo CRISPR screen identifies that SNRPC promotes triple-negative breast cancer progression | Cancer Research
Dysregulation of RNA-binding proteins (RBPs) is one of the characteristics of cancer. Investigating the biological functions and molecular mechanisms of abnormal RBPs can help uncover new cancer biomarkers and treatment strategies. To identify oncogenic RBPs in triple-negative breast cancer (TNBC), we employed an in vivo CRISPR screen and a TNBC…
fRNC: Uncovering the dynamic and condition-specific RBP-ncRNA circuits from multi-omics data
Comput Struct Biotechnol J. 2023; 21: 2276–2285. ,a,1 ,a,1 ,a ,b,c and a,b,⁎ Leiming Jiang aComputational Systems Biology Laboratory, Department of Bioinformatics, Shantou University Medical College (SUMC), 515041 Shantou, China Shijia Hao aComputational Systems Biology Laboratory, Department of Bioinformatics, Shantou University Medical College (SUMC), 515041 Shantou, China Lirui Lin aComputational…
ncRNA | Free Full-Text | CircRNAs and RNA-Binding Proteins Involved in the Pathogenesis of Cancers or Central Nervous System Disorders
1. Introduction Many studies have identified some non-coding RNAs (ncRNAs) with abnormal expressions in several diseases and/or disorders [1]. Among them, circular RNAs (circRNAs) are a special type of endogenous ncRNAs, probably formed by back-splicing events, which have attracted more and more interest nowadays. CircRNAs are closed loop structures [2],…
Advance on engineering of bacteriophages
Introduction Bacteriophage (phage) is a class of widespread viruses exclusively infecting bacteria, playing a key role in ecosystems.1–3 Since phages were discovered over a hundred years ago, many techniques and reagents, such as DNA polymerase, restriction endonuclease, ligase, and CRISPR/Cas system, have been developed from phages, which have together accelerated…
RIP Sequencing Q&A – CD Genomics
General Questions What information should I know before I do the RIP-Seq? Before doing a RIP-SEQ you generally need to specify • The type of sample to be done • What RBPs are of interest • Whether IP-level antibodies are available for these RBPs • The type…
Roles of circRNAs | CMAR
Introduction Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer, with an increasing global incidence, and a leading cause of cancer-related mortality.1 Although hepatitis B and C virus infections, cirrhosis, alcohol intake, and non-alcoholic fatty liver disease (NAFLD) are the main risk factors contributing to HCC.1,2 Approximately…
SAWRPI: A Stacking Ensemble Framework With Adaptive Weight for Predicting ncRNA-Protein Interactions Using Sequence Information
doi: 10.3389/fgene.2022.839540. eCollection 2022. Affiliations Expand Affiliations 1 School of Information Engineering, Xijing University, Xi’an, China. 2 School of Computer Science, Northwestern Polytechnical University, Xi’an, China. Item in Clipboard Zhong-Hao Ren et al. Front Genet. 2022. Show details Display options Display options Format AbstractPubMedPMID doi: 10.3389/fgene.2022.839540. eCollection 2022. Affiliations 1 School…