scholarly journals P2.03-32 Genome-Wide Analysis of m6A-Modified RNA Binding Proteins Associated with Lung Cancer Survival

2018 ◽  
Vol 13 (10) ◽  
pp. S728
Author(s):  
X. Shi ◽  
Y. Wang ◽  
D. Lu ◽  
X. Liu ◽  
X. Dong ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Binding Proteins ◽  
Cancer Survival ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Lung Cancer Survival

Replication of results of a genome-wide association study on lung cancer survival in a Korean population

2014 ◽  
Vol 207 (1-2) ◽  
pp. 35-39.e2 ◽  
Author(s):  
Seung Soo Yoo ◽  
Mi Jeong Hong ◽  
Hyo-Sung Jeon ◽  
Won Kee Lee ◽  
Shin Yup Lee ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Cancer Survival ◽  
Genome Wide Association ◽  
Korean Population ◽  
Genome Wide ◽  
A Genome ◽  
Lung Cancer Survival

Genome-wide survey of putative RNA-binding proteins encoded in the human proteome

2016 ◽  
Vol 12 (2) ◽  
pp. 532-540 ◽  
Author(s):  
Pritha Ghosh ◽  
R. Sowdhamini
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Human Proteome ◽  
Genome Wide ◽  
Genome Wide Survey

We have classified the existing RNA-binding protein (RBP) structures into different structural families. Here, we report ∼2600 proteins with RBP signatures in humans.

scholarly journals SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework

2019 ◽  
Author(s):  
Martin Lewinski ◽  
Yannik Bramkamp ◽  
Tino Köster ◽  
Dorothee Staiger
Keyword(s):  
Binding Sites ◽  
Binding Proteins ◽  
Target Genes ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Rna Seq ◽  
Web Based ◽  
Genome Wide ◽  
Functional Relevance ◽  
Nucleotide Resolution

AbstractBackgroundRNA-binding proteins interact with their target RNAs at specific sites. These binding sites can be determined genome-wide through individual nucleotide resolution crosslinking immunoprecipitation (iCLIP). Subsequently, the binding sites have to be visualized. So far, no visualization tool exists that is easily accessible but also supports restricted access so that data can be shared among collaborators.ResultsHere we present SEQing, a customizable interactive dashboard to visualize crosslink sites on target genes of RNA-binding proteins that have been obtained by iCLIP. Moreover, SEQing supports RNA-seq data that can be displayed in a diffrerent window tab. This allows, e.g. crossreferencing the iCLIP data with genes differentially expressed in mutants of the RBP and thus obtain some insights into a potential functional relevance of the binding sites. Additionally, detailed information on the target genes can be incorporated in another tab.ConclusionSEQing is written in Python3 and runs on Linux. The web-based access makes iCLIP data easily accessible, even with mobile devices. SEQing is customizable in many ways and has also the option to be secured by a password. The source code is available at https://github.com/malewins/SEQing.

scholarly journals Systematic discovery and functional interrogation of SARS-CoV-2 viral RNA-host protein interactions during infection

2020 ◽  
Author(s):  
Ryan A. Flynn ◽  
Julia A. Belk ◽  
Yanyan Qi ◽  
Yuki Yasumoto ◽  
Cameron O. Schmitz ◽  
...  
Keyword(s):  
Protein Interaction ◽  
Protein Interactions ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Viral Rna ◽  
Host Protein ◽  
List Type ◽  
Genome Wide ◽  
A Genome

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a pandemic with growing global mortality. There is an urgent need to understand the molecular pathways required for host infection and anti-viral immunity. Using comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS), we identified 309 host proteins that bind the SARS-CoV-2 RNA during active infection. Integration of this data with viral ChIRP-MS data from three other positive-sense RNA viruses defined pan-viral and SARS-CoV-2-specific host interactions. Functional interrogation of these factors with a genome-wide CRISPR screen revealed that the vast majority of viral RNA-binding proteins protect the host from virus-induced cell death, and we identified known and novel anti-viral proteins that regulate SARS-CoV-2 pathogenicity. Finally, our RNA-centric approach demonstrated a physical connection between SARS-CoV-2 RNA and host mitochondria, which we validated with functional and electron microscopy data, providing new insights into a more general virus-specific protein logic for mitochondrial interactions. Altogether, these data provide a comprehensive catalogue of SARS-CoV-2 RNA-host protein interactions, which may inform future studies to understand the mechanisms of viral pathogenesis, as well as nominate host pathways that could be targeted for therapeutic benefit.Highlights· ChIRP-MS of SARS-CoV-2 RNA identifies a comprehensive viral RNA-host protein interaction network during infection across two species· Comparison to RNA-protein interaction networks with Zika virus, dengue virus, and rhinovirus identify SARS-CoV-2-specific and pan-viral RNA protein complexes and highlights distinct intracellular trafficking pathways· Intersection of ChIRP-MS and genome-wide CRISPR screens identify novel SARS-CoV-2-binding proteins with pro- and anti-viral function· Viral RNA-RNA and RNA-protein interactions reveal specific SARS-CoV-2-mediated mitochondrial dysfunction during infection

scholarly journals Genetic polymorphisms in RNA binding proteins contribute to breast cancer survival

2012 ◽  
Vol 132 (3) ◽  
pp. E128-E138 ◽  
Author(s):  
Rohit Upadhyay ◽  
Sandhya Sanduja ◽  
Vimala Kaza ◽  
Dan A. Dixon
Keyword(s):  
Breast Cancer ◽  
Genetic Polymorphisms ◽  
Binding Proteins ◽  
Cancer Survival ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Breast Cancer Survival

scholarly journals Identification and Validation of an RNA Binding Proteins-Associated Prognostic Signature for Non-Small Cell Lung Cancer

2020 ◽  
Author(s):  
Ti-wei Miao ◽  
Fang-ying Chen ◽  
Wei Xiao ◽  
Long-yi Du ◽  
Bing Mao ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Small Cell ◽  
Functional Enrichment ◽  
Prognostic Signature ◽  
Small Cell Lung

Abstract Background: Non-small cell lung cancer (NSCLC) is a malignancy with relatively high incidence and poor prognosis. RNA-binding proteins (RBPs) were reported to be dysregulated in multiple cancers and were closely associated with tumor initiation and progression. However, the functions of RBPs in NSCLC remain unclear. Method: The RNA sequencing data and corresponding clinical information of NSCLC was downloaded from The Cancer Genome Atlas (TCGA) database. We identified aberrantly expressed RBPs between tumor and control tissue, and systemically investigated the expression and prognostic value of these RBPs by a series of bioinformatics analysis.Results: A total of 459 aberrantly expressed RBPs (291 up-regulated and 168 down-regulated RBPs) were identified. Functional enrichment analysis indicated that the differentially expressed RBPs were mainly associated with RNA splicing, ncRNA metabolic process, regulation of translation, mRNA surveillance pathway, RNA degradation, and RNA transport. Thirteen RBPs (ZC3H12C, ZC3H12D, BOP1, CASC3, DDX24, IGF2BP1, KHDC1, FASTKD3, TARBP1, INTS7, NOL12, SNRPB, PABPC1L) were identified as prognostic RBPs by multivariate Cox regression analysis, and were used to construct a prognostic signature. Further analysis demonstrated that high-risk group were significantly related to poor overall survival in training and testing cohort. The area under receiver operator characteristic curve of the prognostic signature was 0.703 in training cohort and 0.636 in testing cohort. In addition, the prognostic signature was further validated in differently clinical subgroup (>=65, <65, female, male, stage I-II, III- IV, T1-2, T3-4, N0, N1-3, M0 and M1). The risk score was an independent prognostic factor of NSCLC. A nomogram based on thirteen RBPs was constructed to predict the survival of patients.Conclusion: Our results provide novel insights into the pathogenesis of NSCLC. The RBPs-associated prognostic signature showed predictive value for NSCLC prognosis, with potential applications in clinical decision-making and individualized treatment.

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