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Sensitive measurement of single-nucleotide polymorphism-induced changes of RNA conformation: application to disease studies

Raheleh Salari, Chava Kimchi-Sarfaty, Michael M. Gottesman, Teresa M. Przytycka
2012 Nucleic Acids Research  
Subsequently, we applied remuRNA to determine which of the disease-associated non-coding SNPs are potentially related to RNA structural changes.  ...  Changes in RNA secondary structure emerge as a possible explanation necessitating the development of methods to measure the impact of single-nucleotide variation on RNA structure.  ...  There are a number of studies indicating a key role of RNA structure changing SNPs in diseases.  ... 
doi:10.1093/nar/gks1009 pmid:23125360 pmcid:PMC3592397 fatcat:tzuucmawjfbbfktbv2f62q7qgm

Application of CRISPR/Cas9 to the study of brain development and neuropsychiatric disease

S.K. Powell, J. Gregory, S. Akbarian, K.J. Brennand
2017 Molecular and Cellular Neuroscience  
to directly probe the role of generegulatory and epigenetic pathways in order to examine their roles in basic biology and disease processes.  ...  Here we discuss these emerging CRISPR-based methodologies, with specific consideration of neurobiological applications using human induced pluripotent stem cell (hiPSC)based models.  ...  Applications of CRISPR/Cas9 Techniques to Human Induced Pluripotent Stem Cell Models In this section, we provide a brief overview of human induced pluripotent stem cell (hiPSC)based models and highlight  ... 
doi:10.1016/j.mcn.2017.05.007 pmid:28549865 pmcid:PMC5516945 fatcat:6644pkk5ezcxnfhlfgq7xlqpue

L-GIREMI uncovers RNA editing sites in long-read RNA-seq [article]

Zhiheng Liu, Giovanni Quinones-Valdez, Ting Fu, Mudra Choudhury, Fairlie Reese, Ali Mortazavi, Xinshu Xiao
2022 bioRxiv   pre-print
Here, we present the first study to detect and analyze RNA editing sites in long-read RNA-seq.  ...  L-GIREMI provides a valuable means to study RNA nucleotide variants in long-read RNA-seq.  ...  This work was supported in part by grants U01HG009417 and R01MH123177 to XX, and UM1HG009443 to AM.  ... 
doi:10.1101/2022.03.23.485515 fatcat:ctymsekatnhlnjkrqvtdqeqavy

Long Noncoding RNAs

Reinier A. Boon, Nicolas Jaé, Lesca Holdt, Stefanie Dimmeler
2016 Journal of the American College of Cardiology  
noncoding RNA in the INK4 locus (ANRIL).  ...  Moreover, alternative splicing can lead to the formation of circular RNAs.  ...  A potential application for lncRNAs lies in the use of circulating lncRNA levels as biomarkers for cardiovascular disease. Several pioneering studies have shown this to be feasible.  ... 
doi:10.1016/j.jacc.2015.12.051 pmid:26965544 fatcat:nuezgwdzt5gt3fptsyt276bije

RNA INTERFERENCE: APPLICATIONS AND CONFRONTATIONS

2019 International Journal of Biology Pharmacy and Allied Sciences  
which leads to particulate and effective degradation of complementary messenger (m RNA).  ...  Ribonucleic acid interference (RNAi) is one of modern techniques which involved in suppressing protein productions , this occurred via inserted of double stranded (ds) RNA into the cytoplasm in a cell  ...  ACKNOWLEDGMENT The authors would like to thank the Middle East University for their involvement in the  ... 
doi:10.31032/ijbpas/2019/8.10.4815 fatcat:fu5vquh3mvhk7gzjfiaioommzi

Role of m6A RNA methylation in cardiovascular disease (Review)

Yuhan Qin, Linqing Li, Erfei Luo, Jiantong Hou, Gaoliang Yan, Dong Wang, Yong Qiao, Chengchun Tang
2020 International Journal of Molecular Medicine  
The aim of the present review article was to summarize the recent research progress on the role of m6A modification in CVD and give a brief perspective on its prospective applications in CVD.  ...  Recently, a number of studies have identified aberrant m6A methylation in cardiovascular diseases (CVDs), including cardiac hypertrophy, heart failure, arterial aneurysm, vascular calcification and pulmonary  ...  Acknowledgements Not applicable. Funding The present study was supported by the National Natural Science Foundation of china (grant nos. 81970237 and 81600227).  ... 
doi:10.3892/ijmm.2020.4746 pmid:33125109 pmcid:PMC7595665 fatcat:7lxvjyam4nefdetj72rd426dee

Which long noncoding RNAs and circular RNAs contribute to inflammatory bowel disease?

Lihui Lin, Gaoshi Zhou, Peng Chen, Ying Wang, Jing Han, Minhu Chen, Yao He, Shenghong Zhang
2020 Cell Death and Disease  
Studies have focused on the discovery of new therapeutic targets and application of precision medicine.  ...  The contributions of lncRNAs and circRNAs in IBD are less well-studied compared with those of miRNAs. However, lncRNAs and circRNAs are likely to drive personalized therapy for IBD.  ...  Publisher's note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.  ... 
doi:10.1038/s41419-020-2657-z pmid:32541691 pmcid:PMC7295799 fatcat:gzopf6puffeshklo7my3ltvhpq

Recent Applications of RNA Sequencing in Food and Agriculture [chapter]

Venkateswara R. Sripathi, Varsha C. Anche, Zachary B. Gossett, Lloyd T. Walker
2021 Applications of RNA-Seq in Biology and Medicine [Working Title]  
We began to witness the broader impacts of RNA-Seq in addressing complex biological questions in food and agriculture.  ...  The emergence and evolution of RNA-Seq chemistries have changed the landscape and the pace of transcriptome research in life sciences over a decade.  ...  Also, authors would like to thank anonymous reviewers and editor for their efforts in improving this book chapter.  ... 
doi:10.5772/intechopen.97500 fatcat:6u3ynas4kbfgteu6a3xtytdlne

MicroRNA-mediated regulation of gene expression is affected by disease-associated SNPs within the 3′-UTR via altered RNA structure

Ulrike Haas, Georg Sczakiel, Sandra Laufer
2012 RNA Biology  
Acknowledgements We wish to thank Winfried Wünsche for excellent technical assistance, Simon Dornseifer for initial help with the mfold analyses and Alessandra Mescalchin and Jeanette Erdmann for fruitful  ...  Indeed, RNA folding analyses of the polymorphic RNAs suggest SNP-induced changes in local structure supported by in vitro probing analyses showing differential cleavage patterns around this site as well  ...  However, some SNPs (e.g., AGTR1, MRAS) are related to clear changes in secondary structure.  ... 
doi:10.4161/rna.20497 pmid:22664914 pmcid:PMC3495750 fatcat:i64we7zkzraq3acmakohae3ahu

RNA Sequencing in Schizophrenia

Xin Li, Shaolei Teng
2015 Bioinformatics and Biology Insights  
This paper provides an overview on the genetics of SCZ, the advantages of RNA-Seq for transcriptome analysis, the accomplishments of RNA-Seq in SCZ cohorts, and the applications of induced pluripotent  ...  The underlying genetic mechanism of SCZ remains unknown, but studies indicate that the disease is associated with a global gene expression disturbance across many genes.  ...  Genome-wide association studies (GWASs) have been widely used to identify the common single-nucleotide polymorphisms (SNPs) at novel loci implicated in SCZ.  ... 
doi:10.4137/bbi.s28992 pmid:27053919 pmcid:PMC4818022 fatcat:efs3gachajbblaiwfeww7jud2a

m6A RNA Methylation in Systemic Autoimmune Diseases—A New Target for Epigenetic-Based Therapy?

Anna Wardowska
2021 Pharmaceuticals  
Moreover, only selected autoimmune diseases have been studied in respect of m6A role in their pathogenesis.  ...  Even though m6A is confirmed as an essential player in immune response, little is known about its role in autoimmunity. Only few data have been published up to date in the field of RNA methylome.  ...  They either modulate the structure of the methylated transcript to prevent/induce protein-RNA interaction or induce subsequent reactions through direct recognition by m6A binding protein [44] .  ... 
doi:10.3390/ph14030218 pmid:33807762 fatcat:4sh44fkmhvahxodo3tkjzve4im

Impact of virus subtype and host IFNL4 genotype on large-scale RNA structure formation in the genome of hepatitis C virus

Peter Simmonds, Lize Kuypers, Will L Irving, John McLauchlan, Graham S. Cooke, Ellie Barnes, M Azim Ansari
2020 RNA: A publication of the RNA Society  
Mechanisms underlying the ability of hepatitis C virus (HCV) to establish persistent infections and induce progressive liver disease remain poorly understood.  ...  Structurally conserved RNA secondary structure in coding regions of HCV localised exclusively to polyprotein ends (core, NS5B).  ...  (D) Application of contour plotting to an alignment of HCV sequences in the core/E1 region in three-and two-dimensional representations.  ... 
doi:10.1261/rna.075465.120 pmid:32747607 pmcid:PMC7566573 fatcat:b4cs5wthnfajzao7v5m6ef3qxu

RNA-Seq and human complex diseases: recent accomplishments and future perspectives

Valerio Costa, Marianna Aprile, Roberta Esposito, Alfredo Ciccodicola
2012 European Journal of Human Genetics  
ACKNOWLEDGEMENTS This work was supported by COST Action BM1006: Next Generation Sequencing Data Analysis Network (SEQAHEAD), from European Cooperation in the field of Scientific and Technical Research,  ...  expression, as well as the detection of expressed SNPs in RNA samples.  ...  studies (RNA-Seq and other NGS applications) are needed.  ... 
doi:10.1038/ejhg.2012.129 pmid:22739340 pmcid:PMC3548270 fatcat:voyba2bavfb2pl3gzut6vbjqli

RNAsnp: Efficient Detection of Local RNA Secondary Structure Changes Induced by SNPs

Radhakrishnan Sabarinathan, Hakim Tafer, Stefan E. Seemann, Ivo L. Hofacker, Peter F. Stadler, Jan Gorodkin
2013 Human Mutation  
On a data set comprising 501 SNPs associated with human-inherited diseases, we predict 54 to have significant local structural effect in the untranslated region of mRNAs.  ...  SNPs may disrupt these structures, interfere with their molecular function, and hence cause a phenotypic effect. RNA folding algorithms can provide detailed insights into structural effects of SNPs.  ...  The options "Mode 1" and "Mode 2" help to detect the SNP induced local structural changes in a Accession ids: NS5B -AJ238799.1, p53 -NM_001126114.2, Nef -K02013.1, AARS -D32050.1. c Position of the local  ... 
doi:10.1002/humu.22273 pmid:23315997 pmcid:PMC3708107 fatcat:3rgfahxdkbeobl2cgphsboxkri

N6-Methyladenosine RNA Methylation in Cardiovascular Diseases

Chi Liu, Lei Gu, Wenjuan Deng, Qianchao Meng, Nan Li, Guifeng Dai, Suli Yu, Hong Fang
2022 Frontiers in Cardiovascular Medicine  
Recent studies have suggested that m6A modification of RNA may contribute to the pathogenesis of CVDs, providing a novel research insight for CVDs.  ...  Substantial evidence has shown that m6A RNA modification can exert important functions in physiological and pathological processes.  ...  AUTHOR CONTRIBUTIONS CL, LG, WD, QM, NL, and GD contributed to collection of references and manuscript writing. SY and HF contributed to determining the subject and manuscript revisions.  ... 
doi:10.3389/fcvm.2022.887838 pmid:35571209 pmcid:PMC9098837 fatcat:pcgoglck3zcrzmscnwi7jxjdmy
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