Search results for "2′-O-methylation"

showing 2 items of 2 documents

Holistic Optimization of Bioinformatic Analysis Pipeline for Detection and Quantification of 2′-O-Methylations in RNA by RiboMethSeq

2020

International audience; A major trend in the epitranscriptomics field over the last 5 years has been the high-throughput analysis of RNA modifications by a combination of specific chemical treatment(s), followed by library preparation and deep sequencing. Multiple protocols have been described for several important RNA modifications, such as 5-methylcytosine (m5C), pseudouridine (ψ), 1-methyladenosine (m1A), and 2'-O-methylation (Nm). One commonly used method is the alkaline cleavage-based RiboMethSeq protocol, where positions of reads' 5'-ends are used to distinguish nucleotides protected by ribose methylation. This method was successfully applied to detect and quantify Nm residues in vari…

0301 basic medicinebioinformatic pipelinelcsh:QH426-470Computer scienceComputational biologyDeep sequencingPseudouridine03 medical and health scienceschemistry.chemical_compound0302 clinical medicine[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN]ribose methylationEpitranscriptomicsGeneticsGenetics (clinical)receiver operating characteristic2'-O-methylation2′-O-methylationhigh-throughput sequencingRNA[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry Molecular Biology/Molecular biologyBrief Research Reportlcsh:Genetics030104 developmental biologychemistry030220 oncology & carcinogenesisTransfer RNARNAMolecular MedicineSmall nuclear RNAReference genomeFrontiers in Genetics
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Next-Generation Sequencing-Based RiboMethSeq  Protocol for Analysis of tRNA 2'-O-Methylation.

2016

Analysis of RNA modifications by traditional physico-chemical approaches is labor  intensive,  requires  substantial  amounts  of  input  material  and  only  allows  site-by-site  measurements.  The  recent  development  of  qualitative  and  quantitative  approaches  based  on   next-generation sequencing (NGS) opens new perspectives for the analysis of various cellular RNA  species.  The  Illumina  sequencing-based  RiboMethSeq  protocol  was  initially  developed  and  successfully applied for mapping of ribosomal RNA (rRNA) 2'-O-methylations. This method also  gives excellent results in the quantitative analysis of rRNA modifications in different species and  under varying growth condi…

Sequence Analysis RNAComputational BiologyHigh-Throughput Nucleotide Sequencing2′-O-methylationhigh-throughput sequencingRNA FungalSaccharomyces cerevisiaeMethylationArticledeleted strainRNA BacterialRNA TransferTRM3Escherichia coliTrmHtRNARiboMethSeqBiomolecules
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