Results 1 to 10 of about 4,546 (178)

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

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
Raulas Krusnauskas, Rytis Stakaitis, Giedrius Steponaitis, Kristian Almstrup, Paulina Vaitkiene   +4 more
doaj   +4 more sources

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, Mark Eckert, Allen Zhu, Agnieszka Chryplewicz, Dario F. De Jesus, Decheng Ren, Rohit N. Kulkarni, Ernst Lengyel, Chuan He, Mengjie Chen   +10 more
doaj   +6 more sources

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
Yingjie Zhang, Wenjie Hua, Yini Dang, Yihui Cheng, Jiayue Wang, Xiu Zhang, Meiling Teng, Shenrui Wang, Min Zhang, Zihao Kong, Xiao Lu, Yu Zheng   +11 more
doaj   +5 more sources

m6A methylation profiling as a prognostic marker in nasopharyngeal carcinoma: insights from MeRIP-Seq and RNA-Seq [PDF]

Frontiers in Immunology
BackgroundNasopharyngeal carcinoma (NPC) is a type of malignant tumors commonly found in Southeast Asia and China, with insidious onset and clinical symptoms.
Xiaochuan Chen, Wenqian Xu, Junping Pan, Hanxuan Yang, Yi Li, Xin Chen, Yingming Sun, Qinying Liu, Sufang Qiu   +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 ...
Guo Z, Shafik AM, Jin P, Wu H.
europepmc   +3 more sources

Mapping the m1A, m5C, m6A and m7G methylation atlas in zebrafish brain under hypoxic conditions by MeRIP-seq. [PDF]

BMC Genomics, 2022
Abstract Background The epigenetic modifications play important regulatory roles in tissue development, maintenance of physiological functions and pathological process. RNA methylations, including newly identified m1A, m5C, m6A and m7G, are important epigenetic modifications.
Li W, Li X, Ma X, Xiao W, Zhang J.
europepmc   +5 more sources

A low-cost, low-input method establishment for m6A MeRIP-seq. [PDF]

Biosci Rep
Abstract N6-methyladenosine (m6A) is a highly prevalent modification found in mammal mRNA molecules that plays a crucial role in the regulation of cellular function. m6A RNA immunoprecipitation sequencing (MeRIP-seq) has been frequently used in transcriptomics research to identify the location of m6A.
Xia W, Guo L, Su H, Li J, Lu J, Li H, Huang B.   +6 more
europepmc   +3 more sources

A hierarchical model for clustering m(6)A 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.
Cui X, Meng J, Zhang S, Rao MK, Chen Y, Huang Y.   +5 more
europepmc   +4 more sources

m6ACali: machine learning-powered calibration for accurate m6A detection in MeRIP-Seq. [PDF]

Nucleic Acids Res
Abstract 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 ...
Ye H, Li T, Rigden DJ, Wei Z.
europepmc   +3 more sources