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A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package [PDF]
Methods, 2014 Despite the prevalent studies of DNA/Chromatin related epigenetics, such as, histone modifications and DNA methylation, RNA epigenetics has not drawn deserved attention until a new affinity-based sequencing approach MeRIP-Seq was developed and applied to survey the global mRNA N6-methyladenosine (m(6)A) in mammalian cells. As a marriage of ChIP-Seq and
Yufei Huang, Yidong Chen, Manjeet K Rao
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MeTDiff: A Novel Differential RNA Methylation Analysis for MeRIP-Seq Data
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018N6-Methyladenosine (m6A) transcriptome methylation is an exciting new research area that just captures the attention of research community. We present in this paper, MeTDiff, a novel computational tool for predicting differential m6A methylation sites from Methylated RNA immunoprecipitation sequencing (MeRIP-Seq) data.
Yufei Huang, Yidong Chen, Manjeet K Rao
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Modeling of replicates variances for detecting RNA methylation site in MERIP-SEQ data
2015 IEEE China Summit and International Conference on Signal and Information Processing (ChinaSIP), 2015The recent advent of the state-of-art high throughput sequencing technology, known as Methylated RNA immunoprecipitation (IP) sequencing (MeRIP-Seq), provided the biologists the first global view of epigenetic modifications on the transcriptome at a high resolution.
Yufei Huang, Xiadong Cui, Jia Meng
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Detecting differentially methylated mRNA from MeRIP-Seq with likelihood ratio test
2014 IEEE Global Conference on Signal and Information Processing (GlobalSIP), 2014The study of mRNA methylation is an emerging research field greatly fueled by recent advancement in high throughput sequencing technology. We propose here a binomial likelihood ratio test ("bltest") aiming at detecting differentially methylated mRNA with MeRIP-Seq data, "bltest" models the read counts of each RNA methylation site in IP and input ...
Yufei Huang, Yidong Chen, Xiadong Cui
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International Journal of Biological Macromolecules
Chinese hamster ovary (CHO) cells remain the primary host system for recombinant therapeutic protein production. Enhancing transgene expression efficiency while maintaining stable production persists as a key challenge in CHO cell engineering. While N6-methyladenosine (m6A) modification - the most abundant RNA methylation - regulates RNA stability and ...
JiangâTao Lu +2 more
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Chinese hamster ovary (CHO) cells remain the primary host system for recombinant therapeutic protein production. Enhancing transgene expression efficiency while maintaining stable production persists as a key challenge in CHO cell engineering. While N6-methyladenosine (m6A) modification - the most abundant RNA methylation - regulates RNA stability and ...
JiangâTao Lu +2 more
exaly +3 more sources
MeRIP-Seq for Identifying Stress-Responsive Transcriptome-Wide m6A Profiles in Plants
Recent advancements in detection and mapping methods have enabled researchers to uncover the biological importance of RNA chemical modifications, which play a vital role in post-transcriptional gene regulation. Although numerous types of RNA modifications have been identified in higher eukaryotes, only a few have been extensively studied for their ...Ganesan, Govindan, Ramanjulu, Sunkar
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Comparative Biochemistry and Physiology Part D: Genomics and Proteomics
As a widely epigenetic modification, m6A (N6-methyladenosine, m6A) can regulate the degradation, translation, and other biological functions of circRNAs through dynamic reversible processes. It plays an important role in regulating the life activities of biological organisms, particularly in cell differentiation, apoptosis, embryonic development ...
Ru, Zhang +9 more
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As a widely epigenetic modification, m6A (N6-methyladenosine, m6A) can regulate the degradation, translation, and other biological functions of circRNAs through dynamic reversible processes. It plays an important role in regulating the life activities of biological organisms, particularly in cell differentiation, apoptosis, embryonic development ...
Ru, Zhang +9 more
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Theoretical and Natural Science
N6-methyladenosine (m6A), recognized as the most prevalent post-transcriptional modification in organisms, has been substantiated to exert a significant influence on the genetic mechanisms underlying breast cancer. To delve deeper into the disparities in expression, modification, and interactions between mRNA and m6A in breast cancer (BC), we conducted
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N6-methyladenosine (m6A), recognized as the most prevalent post-transcriptional modification in organisms, has been substantiated to exert a significant influence on the genetic mechanisms underlying breast cancer. To delve deeper into the disparities in expression, modification, and interactions between mRNA and m6A in breast cancer (BC), we conducted
openaire +1 more source