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Sensitive measurement of single-nucleotide polymorphism-induced changes of RNA conformation: application to disease studies
2012
Nucleic Acids Research
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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
2017
Molecular and Cellular Neuroscience
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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]
2022
bioRxiv
pre-print
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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
2016
Journal of the American College of Cardiology
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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
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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)
2020
International Journal of Molecular Medicine
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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?
2020
Cell Death and Disease
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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]
2021
Applications of RNA-Seq in Biology and Medicine [Working Title]
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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
2012
RNA Biology
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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
2015
Bioinformatics and Biology Insights
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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?
2021
Pharmaceuticals
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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
2020
RNA: A publication of the RNA Society
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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
2012
European Journal of Human Genetics
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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
2013
Human Mutation
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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
2022
Frontiers in Cardiovascular Medicine
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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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