Identification and comparison of m6A modifications in glioblastoma non-coding RNAs with MeRIP-seq and Nanopore dRNA-seq [PDF]
Epigenetics, 2023 The most prominent RNA modification – N6-methyladenosine (m6A) – affects gene regulation and cancer progression. The extent and effect of m6A on long non-coding RNAs (lncRNAs) is, however, still not clear. The most established method for m6A detection is
Rytis Stakaitis +2 more
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RADAR: differential analysis of MeRIP-seq data with a random effect model [PDF]
Genome Biology, 2019 Epitranscriptome profiling using MeRIP-seq is a powerful technique for in vivo functional studies of reversible RNA modifications. We develop RADAR, a comprehensive analytical tool for detecting differentially methylated loci in MeRIP-seq data.
Zijie Zhang, Qi Zhan, Allen C Zhu
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Validated Impacts of N6-Methyladenosine Methylated mRNAs on Apoptosis and Angiogenesis in Myocardial Infarction Based on MeRIP-Seq Analysis [PDF]
Frontiers in Molecular Biosciences, 2022 Objectives: N6-methyladenosine (m6A) is hypothesized to play a role in the regulation of pathogenesis of myocardial infarction (MI). This study was designed to compare m6A-tagged transcript profiles to identify mRNA-specific changes on pathophysiological
Yini Dang, Zhang Xiu
exaly +7 more sources
A hierarchical model for clustering m6A methylation peaks in MeRIP-seq data [PDF]
BMC Genomics, 2016 The recent advent of the state-of-art high throughput sequencing technology, known as Methylated RNA Immunoprecipitation combined with RNA sequencing (MeRIP-seq) revolutionizes the area of mRNA epigenetics and enables the biologists and biomedical researchers to have a global view of N (6)-Methyladenosine (m(6)A) on transcriptome.
Xiaodong Cui, Jia Meng, Manjeet K Rao
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MoAIMS: efficient software for detection of enriched regions of MeRIP-Seq [PDF]
BMC Bioinformatics, 2020 Background Methylated RNA immunoprecipitation sequencing (MeRIP-Seq) is a popular sequencing method for studying RNA modifications and, in particular, for N6-methyladenosine (m6A), the most abundant RNA methylation modification found in various species ...
Yiqian Zhang, Michiaki Hamada
doaj +5 more sources
m6ACali: machine learning-powered calibration for accurate m6A detection in MeRIP-Seq [PDF]
Nucleic Acids ResearchAbstract We present m6ACali, a novel machine-learning framework aimed at enhancing the accuracy of N6-methyladenosine (m6A) epitranscriptome profiling by reducing the impact of non-specific antibody enrichment in MeRIP-Seq. The calibration model serves as a genomic feature-based classifier that refines the identification of m6A sites ...
Tenglong Li, Daniel J Rigden, Zhen Wei
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A novel algorithm for calling mRNA m 6 A peaks by modeling biological variances in MeRIP-seq data [PDF]
Bioinformatics, 2016 Abstract Motivation: N 6 -methyl-adenosine (m 6 A) is the most prevalent mRNA methylation but precise prediction of its mRNA location is important for understanding its function. A recent sequencing technology, known as Methylated RNA Immunoprecipitation Sequencing technology (MeRIP-seq), has been developed for transcriptome-wide ...
Xiaodong Cui, Jia Meng, Yidong Chen
exaly +6 more sources
m6A methylation profiling as a prognostic marker in nasopharyngeal carcinoma: insights from MeRIP-Seq and RNA-Seq [PDF]
Frontiers in ImmunologyBackgroundNasopharyngeal carcinoma (NPC) is a type of malignant tumors commonly found in Southeast Asia and China, with insidious onset and clinical symptoms.
Xiaochuan Chen +8 more
doaj +4 more sources
Differential RNA methylation analysis for MeRIP-seq data under general experimental design [PDF]
Bioinformatics, 2022 AbstractMotivationRNA epigenetics is an emerging field to study the post-transcriptional gene regulation. The dynamics of RNA epigenetic modification have been reported to associate with many human diseases. Recently developed high-throughput technology named Methylated RNA Immunoprecipitation Sequencing (MeRIP-seq) enables the transcriptome-wide ...
Peng Jin +2 more
exaly +4 more sources
Statistical modeling of immunoprecipitation efficiency of MeRIP-seq data enabled accurate detection and quantification of epitranscriptome [PDF]
Computational and Structural Biotechnology JournalAbstract Background Recent advancements in epitranscriptomics highlight reversible RNA modifications as crucial regulators, with N6-methyladenosine (m 6 A) being abundant in eukaryotic mRNAs.
Kunqi Chen, Zhen Wei, Bowen Song
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