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Yasuyuki Ito, Atsuko Honda, Michihiro Igarashi
Neuronal development is composed of the complex steps which involve many signaling proteins. On the other hand, there are many proteins highly expressed in the differentiated neurons at developmental stages, but of which physiological functions are not precisely known so far. Glycoprotein 6a (GPM6a) currently belongs to such proteins. This protein has four-transmembrane domains and is a member of proteolipid protein family. Recently, we demonstrated that GPM6a is highly concentrated in lipid rafts of the developing neuron with its palmitoylation, and that this molecule is involved in rapid determination of the neuronal polarity, in response to laminin, an extracellular matrix protein (Honda et al...
November 17, 2017: Neuroscience Research
Miki Imanishi, Shogo Tsuji, Akiyo Suda, Shiroh Futaki
We found that Escherichia coli MazF toxin, an ACA-sequence-specific endoribonuclease, was sensitive to N(6)-methyladenosine (m6A), representing the first m6A-sensitive RNA cleavage enzyme. The methyl-sensitivity of MazF allowed simple analyses of both m6A demethylase and methyltransferase activity. Furthermore, the approach could be used for inhibitor screening.
November 20, 2017: Chemical Communications: Chem Comm
Nathan C Boles, Sally Temple
Yoon et al. (2017) uncover a key role for the m6A RNA mark in regulating the timing of cerebral cortex development in mouse and human. This discovery opens new avenues of exploration into how the epitranscriptome helps orchestrate central nervous system formation.
November 15, 2017: Neuron
A Emilia Arguello, Amanda N DeLiberto, Ralph Kleiner
Epitranscriptomic RNA modifications can regulate mRNA function; however, there is a major gap in our understanding of the biochemical mechanisms mediating their effects. Here, we develop a chemical proteomics approach relying upon photo-crosslinking with synthetic diazirine-containing RNA probes and quantitative proteomics to profile RNA-protein interactions regulated by N6-methyladenosine (m6A), the most abundant internal modification in eukaryotic RNA. In addition to identifying YTH domain-containing proteins and ALKBH5, known interactors of this modification, we find that FMR1 and LRPPRC, two proteins associated with human disease, 'read' this modification...
November 15, 2017: Journal of the American Chemical Society
Zegang Wang, Kai Tang, Dayong Zhang, Yizhen Wan, Yan Wen, Quanyou Lu, Lei Wang
This study is the first to comprehensively characterize m6A patterns in the Arabidopsis chloroplast and mitochondria transcriptomes based on our open accessible data deposited in NCBI's Gene Expression Omnibus with GEO Series accession number of GSE72706. Over 86% of the transcripts were methylated by m6A in the two organelles. Over 550 and 350 m6A sites were mapped, with ~5.6 to ~5.8 and ~4.6 to ~4.9 m6A sites per transcript, to the chloroplast and mitochondria genome, respectively. The overall m6A methylation extent in the two organelles was greatly higher than that in the nucleus...
2017: PloS One
Hui Liu, Huaizhi Wang, Zhen Wei, Songyao Zhang, Gang Hua, Shao-Wu Zhang, Lin Zhang, Shou-Jiang Gao, Jia Meng, Xing Chen, Yufei Huang
Methyltranscriptome is an exciting new area that studies the mechanisms and functions of methylation in transcripts. A knowledge base with the systematic collection and curation of context specific transcriptome-wide methylations is critical for elucidating their biological functions as well as for developing bioinformatics tools. Since its inception in 2014, the Met-DB (Liu, H., Flores, M.A., Meng, J., Zhang, L., Zhao, X., Rao, M.K., Chen, Y. and Huang, Y. (2015) MeT-DB: a database of transcriptome methylation in mammalian cells...
November 8, 2017: Nucleic Acids Research
Xiao Shu, Qing Dai, Tong Wu, Ian R Bothwell, Yanan Yue, Zezhou Zhang, Jie Cao, Qili Fei, Minkui Luo, Chuan He, Jianzhao Liu
RNA labeling is crucial for the study of RNA structure and metabolism. Herein we report N(6)-allyladenosine (a(6)A) as a new small molecule for RNA labeling through both metabolic and enzyme-assisted manners. a(6)A behaves like A and can be metabolically incorporated into newly synthesized RNAs inside mammalian cells. We also show that human RNA N(6)-methyladenosine (m(6)A) methyltransferases METTL3/METTL14 can work with a synthetic cofactor, namely allyl-SAM (S-adenosyl methionine with methyl replaced by allyl) in order to site-specifically install an allyl group to the N(6)-position of A within specific sequence to generate a(6)A-labeled RNAs...
November 15, 2017: Journal of the American Chemical Society
Andreas Marx, Joos Aschenbrenner, Stephan Werner, Virginie Marchand, Martina Adam, Yuri Motorin, Mark Helm
Methodologies for the detection of RNA modifications are of fundamental importance for advancing epitranscriptomics. N6-methyladenosine (m6A) is the most abundant RNA modification in mammalian mRNA and involved in regulation of gene expression. Current detection techniques are laborious and rely on antibody based enrichment of m6A containing RNA prior to sequencing, as m6A modifications are generally "erased" during reverse transcription (RT). To overcome the drawbacks associated with indirect detection, we aimed to generate novel DNA polymerase variants for direct m6A sequencing...
November 8, 2017: Angewandte Chemie
Atsuko Honda, Hiroshi Usui, Kenji Sakimura, Michihiro Igarashi
RUN and FYVE domain-containing 3 (Rufy3) is an adapter protein for small GTPase proteins and is bound to activated Rap2, a Ras family protein in the developing neuron. Previously, we reported the presence of a rapid cell polarity determination mechanism involving Rufy3, which is likely required for in vivo neuronal development. However, the molecular details of this mechanism are unclear. To this end, here we produced Rufy3 knockout (Rufy3-KO) mice to study the role of Rufy3 in more detail. Examining Rufy3-KO neurons, we found that Rufy3 is recruited via glycoprotein M6A (GPM6a) to detergent-resistant membrane domains, which are biochemically similar to lipid rafts...
October 31, 2017: Journal of Biological Chemistry
Nidarshana Chaturvedi Parashar, Gaurav Parashar, Harsh Nayyar, Rajat Sandhir
N(6)-methyl-2'-deoxyadenosine (m6dA) is a well characterized DNA modification in prokaryotes. Its existence in eukaryotic DNA remained doubtful until recently. Evidence suggests that the m6dA levels decrease with the increasing complexity of eukaryotic genomes. Analysis of m6dA levels in genome of lower eukaryotes reveals its role in gene regulation, nucleosome positioning and early development. In higher eukaryotes m6dA is enriched in nongenic region compared to genic region, preferentially in chromosome X and 13 suggesting a chromosome bias...
October 23, 2017: Biochimie
Jia-Jia Xuan, Wen-Ju Sun, Peng-Hui Lin, Ke-Ren Zhou, Shun Liu, Ling-Ling Zheng, Liang-Hu Qu, Jian-Hua Yang
More than 100 distinct chemical modifications to RNA have been characterized so far. However, the prevalence, mechanisms and functions of various RNA modifications remain largely unknown. To provide transcriptome-wide landscapes of RNA modifications, we developed the RMBase v2.0 (, which is a comprehensive database that integrates epitranscriptome sequencing data for the exploration of post-transcriptional modifications of RNAs and their relationships with miRNA binding events, disease-related single-nucleotide polymorphisms (SNPs) and RNA-binding proteins (RBPs)...
October 10, 2017: Nucleic Acids Research
Yueyuan Zheng, Peng Nie, Di Peng, Zhihao He, Mengni Liu, Yubin Xie, Yanyan Miao, Zhixiang Zuo, Jian Ren
Identifying disease-causing variants among a large number of single nucleotide variants (SNVs) is still a major challenge. Recently, N6-methyladenosine (m6A) has become a research hotspot because of its critical roles in many fundamental biological processes and a variety of diseases. Therefore, it is important to evaluate the effect of variants on m6A modification, in order to gain a better understanding of them. Here, we report m6AVar (, a comprehensive database of m6A-associated variants that potentially influence m6A modification, which will help to interpret variants by m6A function...
October 3, 2017: Nucleic Acids Research
A Visvanathan, V Patil, A Arora, A S Hegde, A Arivazhagan, V Santosh, K Somasundaram
Despite advances in biology and therapeutic modalities, existence of highly tumorigenic glioma stem-like cells (GSCs) makes glioblastomas (GBMs) invincible. N6-methyl adenosine (m(6)A), one of the abundant mRNA modifications catalyzed by methyltransferase-like 3 and 14 (METTL3/14), influences various events in RNA metabolism. Here, we report the crucial role of METTL3-mediated m(6)A modification in GSC (neurosphere) maintenance and dedifferentiation of glioma cells. METTL3 expression is elevated in GSC and attenuated during differentiation...
October 9, 2017: Oncogene
Micaela D Garcia, Karina Formoso, Gabriela I Aparicio, Alberto C C Frasch, Camila Scorticati
Single point mutations or variations in the expression of the gene encoding the neuronal glycoprotein M6a have been associated with psychiatric disorders such as Alzheimer's disease, depression and schizophrenia. In cultured neurons, M6a positively contributes to neurite extension, axon guidance, filopodia/spine outgrowth, and synapse formation. The endocytic processes of neuronal membrane proteins are linked to the differentiation, growth, signaling and plasticity of neurons. However, the roles of M6a and the precise mechanisms through which M6a internalizes and recycles back to the neuronal membrane are unknown...
2017: Frontiers in Molecular Neuroscience
Marek Bartosovic, Helena Covelo Molares, Pavlina Gregorova, Dominika Hrossova, Grzegorz Kudla, Stepanka Vanacova
N6-methyladenosine (m6A) is the most abundant base modification found in messenger RNAs (mRNAs). The discovery of FTO as the first m6A mRNA demethylase established the concept of reversible RNA modification. Here, we present a comprehensive transcriptome-wide analysis of RNA demethylation and uncover FTO as a potent regulator of nuclear mRNA processing events such as alternative splicing and 3' end mRNA processing. We show that FTO binds preferentially to pre-mRNAs in intronic regions, in the proximity of alternatively spliced (AS) exons and poly(A) sites...
August 30, 2017: Nucleic Acids Research
Zijun Zhang, Yi Xing
Crosslinking or RNA immunoprecipitation followed by sequencing (CLIP-seq or RIP-seq) allows transcriptome-wide discovery of RNA regulatory sites. As CLIP-seq/RIP-seq reads are short, existing computational tools focus on uniquely mapped reads, while reads mapped to multiple loci are discarded. We present CLAM (CLIP-seq Analysis of Multi-mapped reads). CLAM uses an expectation-maximization algorithm to assign multi-mapped reads and calls peaks combining uniquely and multi-mapped reads. To demonstrate the utility of CLAM, we applied it to a wide range of public CLIP-seq/RIP-seq datasets involving numerous splicing factors, microRNAs and m6A RNA methylation...
September 19, 2017: Nucleic Acids Research
Michèle Brocard, Alessia Ruggieri, Nicolas Locker
The role of m6A methylation of RNA has remained elusive for decades, but recent technological advances are now allowing the mapping of the m6A methylation landscape at nucleotide level. This has spurred an explosion in our understanding of the role played by RNA epigenetics in RNA biology. m6A modifications have been tied to almost every aspect of the mRNA life cycle and it is now clear that RNA virus genomes are subject to m6A methylation. These modifications play various roles in the viral replication cycle...
September 2017: Journal of General Virology
Chan Zhou, Benoit Molinie, Kaveh Daneshvar, Joshua V Pondick, Jinkai Wang, Nicholas Van Wittenberghe, Yi Xing, Cosmas C Giallourakis, Alan C Mullen
N(6)-methyladenosine (m(6)A) is the most abundant internal modification of mRNAs and is implicated in all aspects of post-transcriptional RNA metabolism. However, little is known about m(6)A modifications to circular (circ) RNAs. We developed a computational pipeline (AutoCirc) that, together with depletion of ribosomal RNA and m(6)A immunoprecipitation, defined thousands of m(6)A circRNAs with cell-type-specific expression. The presence of m(6)A circRNAs is corroborated by interaction between circRNAs and YTHDF1/YTHDF2, proteins that read m(6)A sites in mRNAs, and by reduced m(6)A levels upon depletion of METTL3, the m(6)A writer...
August 29, 2017: Cell Reports
Melisa C Monteleone, Silvia C Billi, Marcela A Brocco, Alberto C Frasch
Membrane neuronal glycoprotein M6a is highly expressed in the brain and contributes to neural plasticity promoting neurite growth and spine and synapse formation. We have previously showed that chronic stressors alter hippocampal M6a mRNA levels in rodents and tree shrews. We now show that M6a glycoprotein can be detected in mouse blood. M6a is a transmembrane glycoprotein and, as such, unlikely to be free in blood. Here we demonstrate that, in blood, M6a is transported in extracellular vesicles (EVs). It is also shown that M6a-containing EVs are delivered from cultured primary neurons as well as from M6a-transfected COS-7 cells...
August 29, 2017: Scientific Reports
N Cervera, N Carbuccia, M-J Mozziconacci, J Adélaïde, S Garnier, A Guille, A Murati, M Chaffanet, N Vey, D Birnbaum, V Gelsi-Boyer
No abstract text is available yet for this article.
August 25, 2017: Blood Cancer Journal
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