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.
Yufei Huang, Yidong Chen, Manjeet K Rao
exaly +6 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 ...
Zhen Wei, Tenglong Li, Daniel J. Rigden
exaly +5 more sources
A novel algorithm for calling mRNA m6A 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 ...
Yufei Huang, Yidong Chen, Xiadong Cui
exaly +6 more sources
Integrative MeRIP-Seq and RNA-Seq Analyses Reveal Innate Immune and Infection-Related Transcriptomic Changes upon METTL3 Knockout. [PDF]
Genes (Basel)Background: As a major regulator, methyltransferase-like 3 (METTL3) catalyzes N6-methyladenosine (m6A) modification in mRNA. The m6A modifications mediated by METTL3 influence RNA splicing, nucleocytoplasmic distribution, stability, and other functions, thereby playing a vital and indispensable role in genetic regulatory network.
Tang Q +7 more
europepmc +3 more sources
Construction of RNA m6A profiles in liver tissue of mice in sepsis-induced liver injury based on m6A MeRIP-seq and RNA-seq [PDF]
European Journal of Medical ResearchAbstract Sepsis-induced liver injury (SILI) indicates liver functional or structural impairment occurring during sepsis and is one of the common complications of sepsis. N6-methyladenosine (m6A) modification plays a significant role in the pathological processes of SILI, but its specific mechanisms remain unclear and require further ...
Lijie Qin, Yitao Fan, Yingru Liu
exaly +5 more sources
Refined RIP-seq protocol for epitranscriptome analysis with low input materials. [PDF]
PLoS Biology, 2018 N6-Methyladenosine (m6A) accounts for approximately 0.2% to 0.6% of all adenosine in mammalian mRNA, representing the most abundant internal mRNA modifications.
Yong Zeng +11 more
doaj +2 more sources
Additional file 1 of MoAIMS: efficient software for detection of enriched regions of MeRIP-Seq
, 2020 Additional file 1 Supplementary materials for "MoAIMS: efficient software for detection of enriched regions of MeRIP-Seq".
Zhang, Yiqian, Hamada, Michiaki
openaire +2 more sources
Epigenetic Effects and Potential Contributions of m<sup>6</sup>A Modification to Mammary Gland Development and Lactation of Dairy Goats Explored via MeRIP-seq. [PDF]
Animals (Basel)To date, more than 170 chemical modifications have been identified in RNA. m6A (N6-methyladenine) RNA methylation is the most abundant form of mRNA modification in eukaryotes, playing an important role in RNA post-transcriptional processes. To investigate the function of m6A methylation modification in the development and lactation of dairy goat ...
Zhang L, Ji Z, Zhao M, Fu J, Meng X.
europepmc +4 more sources
MOESM1 of RADAR: differential analysis of MeRIP-seq data with a random effect model
, 2019 Additional file 1: Figure S1. Scatter plot of read count. Figure S2. Read count distribution of INPUT data. Figure S3. Sequencing depth distribution of m6A-seq in published literatures. Figure S4. Variability distribution comparing RNA-seq and m6A-seq (MeRIP-seq). Figure S5. Evaluating performances of benchmarked methods on simulated data using sliding
Zhang, Zijie +10 more
openaire +2 more sources
, 2022 Additional file 3. Supplemental Figure 1. Distribution of differential methylation peaks of m1A, m5C, m6A and m7G in the transcriptome. . The fold enrichment of transcript methylation modification peaks analyzed by MACS2 software is displayed in 5 quantiles (boxplot), and the bottom of the box plot shows the number of methylation modification peaks in ...
Li, Wei +4 more
openaire +2 more sources