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N-6-methyladenosine RNA

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https://www.readbyqxmd.com/read/28433859/photoelectrochemical-immunosensor-for-methylated-rna-detection-based-on-g-c3n4-cds-quantum-dots-heterojunction-and-phos-tag-biotin
#1
Haiyan Wang, Qihai Zhang, Huanshun Yin, Minghui Wang, Wenjing Jiang, Shiyun Ai
N(6)-methyladenosine (m(6)A) is an enigmatic and abundant internal modification in eukaryotic messenger RNA (mRNA), which could affect various aspects of RNA metabolism and mRNA translation. Herein, a novel photoelectrochemical (PEC) immunosensor was constructed for m(6)A detection based on the inhibition of Cu(2+) to the photoactivity of g-C3N4/CdS quantum dots (g-C3N4/CdS) heterojunction, where g-C3N4/CdS heterojunction was used as photoactive material, anti-m(6)A antibody as recognition unit for m(6)A-containing RNA, Phos-tag-biotin as link unit and avidin functionalized CuO as PEC signal indicator...
April 12, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28399407/messenger-rna-methylation-regulates-glioblastoma-tumorigenesis
#2
Deobrat Dixit, Qi Xie, Jeremy N Rich, Jing Crystal Zhao
Messenger RNA (mRNA) modification provides an additional layer of gene regulation in cells. In this issue of Cancer Cell, Zhang et al. report that ALKBH5, a demethylase of the mRNA modification N(6)-methyladenosine, regulates proliferation and self-renewal of glioblastoma stem-like cells by modulating pre-mRNA stability and expression of the FOXM1 gene.
April 10, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28353398/a-fly-view-on-the-roles-and-mechanisms-of-the-m-6-a-mrna-modification-and-its-players
#3
Tina Lence, Matthias Soller, Jean-Yves Roignant
RNA modifications are an emerging layer of posttranscriptional gene regulation in eukaryotes. N(6)-methyladenosine (m(6)A) is amongst the most abundant modifications in messenger RNAs (mRNAs) that was shown to influence many physiological processes from yeast to mammals. Like DNA methylation, m(6)A in mRNA is dynamically regulated. A conserved methyltransferase complex catalyzes the deposition of the methyl group on adenosine, which can be removed by specific classes of demethylases. Furthermore, YTH-domain containing proteins can recognize this modification to mediate m(6)A-dependent activities...
March 29, 2017: RNA Biology
https://www.readbyqxmd.com/read/28349455/detection-and-quantification-of-n-6-methyladenosine-in-messenger-rna-by-tlc
#4
Zsuzsanna Bodi, Rupert G Fray
The base-modified nucleotide, N (6)-methyladenosine, is a relatively abundant modification found in the mRNA of most higher eukaryotes. Methylation levels can change dependent upon environmental conditions, cell differentiation state, or following knockdown of members of the methylase complex, and it is often useful to directly measure and compare N (6)-methyladenosine levels between samples. Two dimensional chromatography of radiolabeled nucleotides, following specific nuclease treatments, provides a robust, sensitive, and reproducible assay for this modification...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28349454/mapping-m-6-a-at-individual-nucleotide-resolution-using-crosslinking-and-immunoprecipitation-miclip
#5
Anya V Grozhik, Bastian Linder, Anthony O Olarerin-George, Samie R Jaffrey
N (6) -methyladenosine (m6A) is the most abundant modified base in eukaryotic mRNA and has been linked to diverse effects on mRNA fate. Current m6A mapping approaches localize m6A residues to 100-200 nt-long regions of transcripts. The precise position of m6A in mRNAs cannot be identified on a transcriptome-wide level because there are no chemical methods to distinguish between m6A and adenosine. Here, we describe a method for using anti-m6A antibodies to induce specific mutational signatures at m6A residues after ultraviolet light-induced antibody-RNA crosslinking and reverse transcription...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28349453/genome-wide-location-analyses-of-n6-methyladenosine-modifications-m-6-a-seq
#6
Benoit Molinie, Cosmas C Giallourakis
N(6)-methyladenosine-sequencing (m(6)A-seq) is a critical tool to obtain an unbiased genome-wide picture of m(6)A sites of modification at high resolution. It allows the study of the impact of various perturbations on m(6)A modification distribution and the study of m(6)A functions. Herein, we describe the m(6)A-seq protocol, which entails RNA immunoprecipitation (RIP) performed on fragmented poly(A) RNA utilizing anti-m(6)A antibodies. The captured/enriched m(6)A positive RNA fragments are subsequently sequenced by RNA-seq in parallel with background control non-immunoprecipitated input RNA fragments...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28349452/liquid-chromatography-mass-spectrometry-for-analysis-of-rna-adenosine-methylation
#7
Bi-Feng Yuan
Dynamic RNA modifications recently were considered to constitute another realm for biological regulation in the form of "RNA epigenetics". N (6)-methyladenosine (m(6)A), one of the most important modifications on RNA, plays a fundamental role in epigenetic regulation of the mammalian transcriptome. We recently established various liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS/MS)-based methods for the sensitive and accurate determination of modified nucleosides in both DNA and RNA...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28344040/m-6-a-demethylase-alkbh5-maintains-tumorigenicity-of-glioblastoma-stem-like-cells-by-sustaining-foxm1-expression-and-cell-proliferation-program
#8
Sicong Zhang, Boxuan Simen Zhao, Aidong Zhou, Kangyu Lin, Shaoping Zheng, Zhike Lu, Yaohui Chen, Erik P Sulman, Keping Xie, Oliver Bögler, Sadhan Majumder, Chuan He, Suyun Huang
The dynamic and reversible N(6)-methyladenosine (m(6)A) RNA modification installed and erased by N(6)-methyltransferases and demethylases regulates gene expression and cell fate. We show that the m(6)A demethylase ALKBH5 is highly expressed in glioblastoma stem-like cells (GSCs). Silencing ALKBH5 suppresses the proliferation of patient-derived GSCs. Integrated transcriptome and m(6)A-seq analyses revealed altered expression of certain ALKBH5 target genes, including the transcription factor FOXM1. ALKBH5 demethylates FOXM1 nascent transcripts, leading to enhanced FOXM1 expression...
April 10, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28297667/m-6-a-rna-methylation-regulates-the-self-renewal-and-tumorigenesis-of-glioblastoma-stem-cells
#9
Qi Cui, Hailing Shi, Peng Ye, Li Li, Qiuhao Qu, Guoqiang Sun, Guihua Sun, Zhike Lu, Yue Huang, Cai-Guang Yang, Arthur D Riggs, Chuan He, Yanhong Shi
RNA modifications play critical roles in important biological processes. However, the functions of N(6)-methyladenosine (m(6)A) mRNA modification in cancer biology and cancer stem cells remain largely unknown. Here, we show that m(6)A mRNA modification is critical for glioblastoma stem cell (GSC) self-renewal and tumorigenesis. Knockdown of METTL3 or METTL14, key components of the RNA methyltransferase complex, dramatically promotes human GSC growth, self-renewal, and tumorigenesis. In contrast, overexpression of METTL3 or inhibition of the RNA demethylase FTO suppresses GSC growth and self-renewal...
March 14, 2017: Cell Reports
https://www.readbyqxmd.com/read/28281539/extensive-translation-of-circular-rnas-driven-by-n-6-methyladenosine
#10
Yun Yang, Xiaojuan Fan, Miaowei Mao, Xiaowei Song, Ping Wu, Yang Zhang, Yongfeng Jin, Yi Yang, Lingling Chen, Yang Wang, Catherine Cl Wong, Xinshu Xiao, Zefeng Wang
Extensive pre-mRNA back-splicing generates numerous circular RNAs (circRNAs) in human transcriptome. However, the biological functions of these circRNAs remain largely unclear. Here we report that N(6)-methyladenosine (m(6)A), the most abundant base modification of RNA, promotes efficient initiation of protein translation from circRNAs in human cells. We discover that consensus m(6)A motifs are enriched in circRNAs and a single m(6)A site is sufficient to drive translation initiation. This m(6)A-driven translation requires initiation factor eIF4G2 and m(6)A reader YTHDF3, and is enhanced by methyltransferase METTL3/14, inhibited by demethylase FTO, and upregulated upon heat shock...
March 10, 2017: Cell Research
https://www.readbyqxmd.com/read/28256005/regulatory-role-of-n-6-methyladenosine-m-6-a-methylation-in-rna-processing-and-human-diseases
#11
Wenqiang Wei, Xinying Ji, Xiangqian Guo, Shaoping Ji
N(6) -methyladenosine (m(6) A) modification is an abundant and conservative RNA modification in bacterial and eukaryotic cells. m(6) A modification mainly occurs in the 3' untranslated regions (UTRs) and near the stop codons of mRNA. Diverse strategies have been developed for identifying m(6) A sites in single nucleotide resolution. Dynamic regulation of m(6) A is found in metabolism, embryogenesis and developmental processes, indicating a possible epigenetic regulation role along RNA processing and exerting biological functions...
March 3, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28192787/m-6-a-dependent-maternal-mrna-clearance-facilitates-zebrafish-maternal-to-zygotic-transition
#12
Boxuan Simen Zhao, Xiao Wang, Alana V Beadell, Zhike Lu, Hailing Shi, Adam Kuuspalu, Robert K Ho, Chuan He
The maternal-to-zygotic transition (MZT) is one of the most profound and tightly orchestrated processes during the early life of embryos, yet factors that shape the temporal pattern of vertebrate MZT are largely unknown. Here we show that over one-third of zebrafish maternal messenger RNAs (mRNAs) can be N(6)-methyladenosine (m(6)A) modified, and the clearance of these maternal mRNAs is facilitated by an m(6)A-binding protein, Ythdf2. Removal of Ythdf2 in zebrafish embryos decelerates the decay of m(6)A-modified maternal mRNAs and impedes zygotic genome activation...
February 23, 2017: Nature
https://www.readbyqxmd.com/read/28138061/pseudouridine-and-n-6-methyladenosine-modifications-weaken-puf-protein-rna-interactions
#13
Pavanapuresan P Vaidyanathan, Ishraq AlSadhan, Dawn K Merriman, Hashim Al-Hashimi, Daniel Herschlag
RNA modifications are ubiquitous in biology, with over 100 distinct modifications. While the vast majority were identified and characterized on abundant non-coding RNA such as tRNA and rRNA, the advent of sensitive sequencing-based approaches has led to the discovery of extensive and regulated modification of eukaryotic messenger RNAs as well. The two most abundant mRNA modifications -pseudouridine (Ψ) and N-6 methyladenosine (m6A)- affect diverse cellular processes including mRNA splicing, localization, translation, and decay and modulate RNA structure...
January 30, 2017: RNA
https://www.readbyqxmd.com/read/28121234/human-m-6-a-writers-two-subunits-2-roles
#14
Xiang Wang, Jinbo Huang, Tingting Zou, Ping Yin
Cellular RNAs with diverse chemical modifications have been observed, and N(6)-methyladenosine (m(6)A) is one of the most abundant internal modifications found on mRNA and non-coding RNAs, playing a vital role in diverse biologic processes. In humans, m(6)A modification is catalyzed by the METTL3-METTL14 methyltransferase complex, which is regulated by WTAP and another factor. Three groups have recently and independently reported the structure of this complex with or without cofactors. Here, we focus on the detailed mechanism of the m(6)A methyltransferase complex and the properties of each subunit...
March 4, 2017: RNA Biology
https://www.readbyqxmd.com/read/28106072/ythdf3-facilitates-translation-and-decay-of-n-6-methyladenosine-modified-rna
#15
Hailing Shi, Xiao Wang, Zhike Lu, Boxuan S Zhao, Honghui Ma, Phillip J Hsu, Chang Liu, Chuan He
N(6)-methyladenosine (m(6)A) is the most abundant internal modification in eukaryotic messenger RNAs (mRNAs), and plays important roles in cell differentiation and tissue development. It regulates multiple steps throughout the RNA life cycle including RNA processing, translation, and decay, via the recognition by selective binding proteins. In the cytoplasm, m(6)A binding protein YTHDF1 facilitates translation of m(6)A-modified mRNAs, and YTHDF2 accelerates the decay of m(6)A-modified transcripts. The biological function of YTHDF3, another cytoplasmic m(6)A binder of the YTH (YT521-B homology) domain family, remains unknown...
March 2017: Cell Research
https://www.readbyqxmd.com/read/28079126/detecting-n-6-methyladenosine-sites-from-rna-transcriptomes-using-ensemble-support-vector-machines
#16
Wei Chen, Pengwei Xing, Quan Zou
As one of the most abundant RNA post-transcriptional modifications, N(6)-methyladenosine (m(6)A) involves in a broad spectrum of biological and physiological processes ranging from mRNA splicing and stability to cell differentiation and reprogramming. However, experimental identification of m(6)A sites is expensive and laborious. Therefore, it is urgent to develop computational methods for reliable prediction of m(6)A sites from primary RNA sequences. In the current study, a new method called RAM-ESVM was developed for detecting m(6)A sites from Saccharomyces cerevisiae transcriptome, which employed ensemble support vector machine classifiers and novel sequence features...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28060253/a-method-for-measuring-rna-n-6-methyladenosine-modifications-in-cells-and-tissues
#17
Chao-Yung Wang, Mei-Hsiu Lin, Hui-Ting Su
N(6)-Methyladenosine (m(6)A) modifications of RNA are diverse and ubiquitous amongst eukaryotes. They occur in mRNA, rRNA, tRNA, and microRNA. Recent studies have revealed that these reversible RNA modifications affect RNA splicing, translation, degradation, and localization. Multiple physiological processes, like circadian rhythms, stem cell pluripotency, fibrosis, triglyceride metabolism, and obesity are also controlled by m(6)A modifications. Immunoprecipitation/sequencing, mass spectrometry, and modified northern blotting are some of the methods commonly employed to measure m(6)A modifications...
December 5, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28017614/fto-plays-an-oncogenic-role-in-acute-myeloid-leukemia-as-a-n-6-methyladenosine-rna-demethylase
#18
Zejuan Li, Hengyou Weng, Rui Su, Xiaocheng Weng, Zhixiang Zuo, Chenying Li, Huilin Huang, Sigrid Nachtergaele, Lei Dong, Chao Hu, Xi Qin, Lichun Tang, Yungui Wang, Gia-Ming Hong, Hao Huang, Xiao Wang, Ping Chen, Sandeep Gurbuxani, Stephen Arnovitz, Yuanyuan Li, Shenglai Li, Jennifer Strong, Mary Beth Neilly, Richard A Larson, Xi Jiang, Pumin Zhang, Jie Jin, Chuan He, Jianjun Chen
N(6)-Methyladenosine (m(6)A) represents the most prevalent internal modification in mammalian mRNAs. Despite its functional importance in various fundamental bioprocesses, the studies of m(6)A in cancer have been limited. Here we show that FTO, as an m(6)A demethylase, plays a critical oncogenic role in acute myeloid leukemia (AML). FTO is highly expressed in AMLs with t(11q23)/MLL rearrangements, t(15;17)/PML-RARA, FLT3-ITD, and/or NPM1 mutations. FTO enhances leukemic oncogene-mediated cell transformation and leukemogenesis, and inhibits all-trans-retinoic acid (ATRA)-induced AML cell differentiation, through regulating expression of targets such as ASB2 and RARA by reducing m(6)A levels in these mRNA transcripts...
January 9, 2017: Cancer Cell
https://www.readbyqxmd.com/read/27919081/m-6-a-potentiates-sxl-alternative-pre-mrna-splicing-for-robust-drosophila-sex-determination
#19
Irmgard U Haussmann, Zsuzsanna Bodi, Eugenio Sanchez-Moran, Nigel P Mongan, Nathan Archer, Rupert G Fray, Matthias Soller
N(6)-methyladenosine (m(6)A) is the most common internal modification of eukaryotic messenger RNA (mRNA) and is decoded by YTH domain proteins. The mammalian mRNA m(6)A methylosome is a complex of nuclear proteins that includes METTL3 (methyltransferase-like 3), METTL14, WTAP (Wilms tumour 1-associated protein) and KIAA1429. Drosophila has corresponding homologues named Ime4 and KAR4 (Inducer of meiosis 4 and Karyogamy protein 4), and Female-lethal (2)d (Fl(2)d) and Virilizer (Vir). In Drosophila, fl(2)d and vir are required for sex-dependent regulation of alternative splicing of the sex determination factor Sex lethal (Sxl)...
December 8, 2016: Nature
https://www.readbyqxmd.com/read/27919077/m-6-a-modulates-neuronal-functions-and-sex-determination-in-drosophila
#20
Tina Lence, Junaid Akhtar, Marc Bayer, Katharina Schmid, Laura Spindler, Cheuk Hei Ho, Nastasja Kreim, Miguel A Andrade-Navarro, Burkhard Poeck, Mark Helm, Jean-Yves Roignant
N(6)-methyladenosine RNA (m(6)A) is a prevalent messenger RNA modification in vertebrates. Although its functions in the regulation of post-transcriptional gene expression are beginning to be unveiled, the precise roles of m(6)A during development of complex organisms remain unclear. Here we carry out a comprehensive molecular and physiological characterization of the individual components of the methyltransferase complex, as well as of the YTH domain-containing nuclear reader protein in Drosophila melanogaster...
December 8, 2016: Nature
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