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Shunian Xiang, Ke Liu, Zhangming Yan, Yaou Zhang, Zhirong Sun
N6-Methyladenosine (m6A) is the most common mRNA modification; it occurs in a wide range of taxon and is associated with many key biological processes. High-throughput experiments have identified m6A-peaks and sites across the transcriptome, but studies of m6A sites at the transcriptome-wide scale are limited to a few species and tissue types. Therefore, the computational prediction of mRNA m6A sites has become an important strategy. In this study, we integrated multiple features of mRNA (flanking sequences, local secondary structure information, and relative position information) and trained a SVM classifier to predict m6A sites in mammalian mRNA sequences...
2016: PloS One
Ann Fiegen Durbin, Chen Wang, Joseph Marcotrigiano, Lee Gehrke
UNLABELLED: Invading pathogen nucleic acids are recognized and bound by cytoplasmic (retinoic acid-inducible gene I [RIG-I]-like) and membrane-bound (Toll-like) pattern recognition receptors to activate innate immune signaling. Modified nucleotides, when present in RNA molecules, diminish the magnitude of these signaling responses. However, mechanisms explaining the blunted signaling have not been elucidated. In this study, we used several independent biological assays, including inhibition of virus replication, RIG-I:RNA binding assays, and limited trypsin digestion of RIG-I:RNA complexes, to begin to understand how RNAs containing modified nucleotides avoid or suppress innate immune signaling...
2016: MBio
Chyi-Ying A Chen, Ann-Bin Shyu
mRNA is the molecule that conveys genetic information from DNA to the translation apparatus. mRNAs in all organisms display a wide range of stability, and mechanisms have evolved to selectively and differentially regulate individual mRNA stability in response to intracellular and extracellular cues. In recent years, three seemingly distinct aspects of RNA biology-mRNA N(6)-methyladenosine (m6A) modification, alternative 3' end processing and polyadenylation (APA), and mRNA codon usage-have been linked to mRNA turnover, and all three aspects function to regulate global mRNA stability in cis...
September 16, 2016: Trends in Biochemical Sciences
Shu-Tao Qi, Jun-Yu Ma, Zhen-Bo Wang, Lei Guo, Yi Hou, Qing-Yuan Sun
During the oogenesis of Xenopus laevis, oocytes accumulate maternal materials for early embryo development. As the transcription activity of oocyte is silenced at the fully-grown stage and the global genome is reactivated only by the mid-blastula embryo stage, the translation of maternal mRNAs accumulated during oocyte growth should be accurately regulated. Previous evidence has illustrated that the poly(A) tail length and RNA binding elements mediate RNA translation regulation in oocyte. Recently, RNA methylation is found to exist in various systems...
September 9, 2016: Journal of Biological Chemistry
Chuanzhao Zhang, Wanqing Iris Zhi, Haiquan Lu, Debangshu Samanta, Ivan Chen, Edward Gabrielson, Gregg L Semenza
Exposure of breast cancer cells to hypoxia increases the percentage of breast cancer stem cells (BCSCs), which are required for tumor initiation and metastasis, and this response is dependent on the activity of hypoxia-inducible factors (HIFs). We previously reported that exposure of breast cancer cells to hypoxia induces the ALKBH5-mediated demethylation of N6-methyladenosine (m6A) in NANOG mRNA leading to increased expression of NANOG, which is a pluripotency factor that promotes BCSC specification. Here we report that exposure of breast cancer cells to hypoxia also induces ZNF217-dependent inhibition of m6A methylation of mRNAs encoding NANOG and KLF4, which is another pluripotency factor that mediates BCSC specification...
August 31, 2016: Oncotarget
Richard D Morgan, Yvette A Luyten, Samuel A Johnson, Emily M Clough, Tyson A Clark, Richard J Roberts
We identify a new subgroup of Type I Restriction-Modification enzymes that modify cytosine in one DNA strand and adenine in the opposite strand for host protection. Recognition specificity has been determined for ten systems using SMRT sequencing and each recognizes a novel DNA sequence motif. Previously characterized Type I systems use two identical copies of a single methyltransferase (MTase) subunit, with one bound at each half site of the specificity (S) subunit to form the MTase. The new m4C-producing Type I systems we describe have two separate yet highly similar MTase subunits that form a heterodimeric M1M2S MTase...
August 31, 2016: Nucleic Acids Research
G E Saraceno, L G Caceres, L R Guelman, R Castilla, L D Udovin, M H Ellisman, M A Brocco, F Capani
Perinatal asphyxia (PA) is one of the most frequent risk factors for several neurodevelopmental disorders (NDDs) of presumed multifactorial etiology. Dysfunction of neuronal connectivity is thought to play a central role in the pathophysiology of NDDs. Because underlying causes of some NDDs begin before/during birth, we asked whether this clinical condition might affect accurate establishment of neural circuits in the hippocampus as a consequence of disturbed brain plasticity. We used a murine model that mimics the pathophysiological processes of perinatal asphyxia...
August 27, 2016: Experimental Neurology
Guang-Qing Li, Zi Liu, Hong-Bin Shen, Dong-Jun Yu
As one of the most ubiquitous post-transcriptional modifications of RNA, N6-methyladenosine (m6A) plays an essential role in many vital biological processes. The identification of m6A sites in RNAs is significantly important for both basic biomedical research and practical drug development. In this study, we designed a computational-based method, called TargetM6A, to rapidly and accurately target m6A sites solely from the primary RNA sequences. Two new features, i.e., position-specific nucleotide / dinucleotide propensities (PSNP / PSDP), are introduced and combined with the traditional nucleotide composition (NC) feature to formulate RNA sequences...
August 10, 2016: IEEE Transactions on Nanobioscience
Xiaodong Cui, Jia Meng, Shaowu Zhang, Yidong Chen, Yufei Huang
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 profiling of m(6)A. We previously developed a peak calling algorithm called exomePeak. However, exomePeak over-simplifies data characteristics and ignores the reads' variances among replicates or reads dependency across a site region...
June 15, 2016: Bioinformatics
Ming Zhang, Jia-Wei Sun, Zi Liu, Ming-Wu Ren, Hong-Bin Shen, Dong-Jun Yu
N(6)-methyladenosine (m(6)A) is one of the most common and abundant post-transcriptional RNA modifications found in viruses and most eukaryotes. m(6)A plays an essential role in many vital biological processes to regulate gene expression. Because of its widespread distribution across the genomes, the identification of m(6)A sites from RNA sequences is of significant importance for better understanding the regulatory mechanism of m(6)A. Although progress has been achieved in m(6)A site prediction, challenges remain...
September 1, 2016: Analytical Biochemistry
Chelsea M Hull, Philip C Bevilacqua
Pathogens are recognized by the innate immune system in part via their unique and complex RNA signatures. A key sensor in human innate immunity is the RNA-activated protein kinase, protein kinase R (PKR), which has two double-stranded RNA (dsRNA) binding motifs (dsRBMs) at its N-terminus. Early studies described PKR as being activated potently by long stretches of perfect dsRNA, a signature typical of viruses. More recently, we and others have found that PKR is also activated by RNAs having structural defects such as bulges and internal loops...
June 21, 2016: Accounts of Chemical Research
Guangchao Cao, Hua-Bing Li, Zhinan Yin, Richard A Flavell
The identification of m(6)A demethylases and high-throughput sequencing analysis of methylated transcriptome corroborated m(6)A RNA epigenetic modification as a dynamic regulation process, and reignited its investigation in the past few years. Many basic concepts of cytogenetics have been revolutionized by the growing understanding of the fundamental role of m(6)A in RNA splicing, degradation and translation. In this review, we summarize typical features of methylated transcriptome in mammals, and highlight the 'writers', 'erasers' and 'readers' of m(6)A RNA modification...
April 2016: Open Biology
Yunshu Wu, Shiwen Zhang, Quan Yuan
The discovery of mammalian N(6)-methyladenosine (m(6)A) methyltransferases and demethylases has enriched our knowledge of the dynamic regulation of the most prevalent posttranscriptional RNA modification, m(6)A methylation. This reversible methylation process of adding and removing m(6)A marks on RNA has been shown to have broad biological functions in fine tuning cellular processes and gene expression. Recent studies have revealed a critical role for the currently known m(6)A methyltransferases and demethylases in regulating the pluripotency and differentiation of stem cells...
July 15, 2016: Stem Cells and Development
Zhangming Yan, Ke Liu, Shunian Xiang, Zhirong Sun
Since the development of new technologies such as RIP-Seq and m6A-seq, peak calling has become an important step in transcriptomic sequencing data analysis. However, many of the reported genomic coordinates of transcriptomic peaks are incorrect owing to negligence of the introns. There is currently a lack of a convenient tool to address this problem. Here, we present txCoords, a novel and easy-to-use web application for transcriptomic peak re-mapping. txCoords can be used to correct the incorrectly reported transcriptomic peaks and retrieve the true sequences...
May 16, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Marina Radoul, Limor Lewin, Batya Cohen, Roni Oren, Stanislav Popov, Geula Davidov, Moriel H Vandsburger, Alon Harmelin, Ronit Bitton, Jean-Marc Greneche, Michal Neeman, Raz Zarivach
Ferritin has gained significant attention as a potential reporter gene for in vivo imaging by magnetic resonance imaging (MRI). However, due to the ferritin ferrihydrite core, the relaxivity and sensitivity for detection of native ferritin is relatively low. We report here on a novel chimeric magneto-ferritin reporter gene - ferritin-M6A - in which the magnetite binding peptide from the magnetotactic bacteria magnetosome-associated Mms6 protein was fused to the C-terminal of murine h-ferritin. Biophysical experiments showed that purified ferritin-M6A assembled into a stable protein cage with the M6A protruding into the cage core, enabling magnetite biomineralisation...
2016: Scientific Reports
Shui Zou, Joel D W Toh, Kendra H Q Wong, Yong-Gui Gao, Wanjin Hong, Esther C Y Woon
N(6)-Methyladenosine (m6A) is currently one of the most intensively studied post-transcriptional modifications in RNA. Due to its critical role in epigenetics and physiological links to several human diseases, it is also of tremendous biological and medical interest. The m6A mark is dynamically reversed by human demethylases FTO and ALKBH5, however the mechanism by which these enzymes selectively recognise their target transcripts remains unclear. Here, we report combined biophysical and biochemical studies on the specificity determinants of m6A demethylases, which led to the identification of an m6A-mediated substrate discrimination mechanism...
2016: Scientific Reports
Daniel Wibberg, Andreas Bremges, Tanja Dammann-Kalinowski, Irena Maus, M Isabel Igeño, Ralph Vogelsang, Christoph König, Víctor M Luque-Almagro, M Dolores Roldán, Alexander Sczyrba, Conrado Moreno-Vivián, Rafael Blasco, Alfred Pühler, Andreas Schlüter
Pseudomonas pseudoalcaligenes CECT5344 tolerates cyanide and is also able to utilize cyanide and cyano-derivatives as a nitrogen source under alkaline conditions. The strain is considered as candidate for bioremediation of habitats contaminated with cyanide-containing liquid wastes. Information on the genome sequence of the strain CECT5344 became available previously. The P. pseudoalcaligenes CECT5344 genome was now resequenced by applying the single molecule, real-time (SMRT(®)) sequencing technique developed by Pacific Biosciences...
August 20, 2016: Journal of Biotechnology
Chuanzhao Zhang, Debangshu Samanta, Haiquan Lu, John W Bullen, Huimin Zhang, Ivan Chen, Xiaoshun He, Gregg L Semenza
N(6)-methyladenosine (m(6)A) modification of mRNA plays a role in regulating embryonic stem cell pluripotency. However, the physiological signals that determine the balance between methylation and demethylation have not been described, nor have studies addressed the role of m(6)A in cancer stem cells. We report that exposure of breast cancer cells to hypoxia stimulated hypoxia-inducible factor (HIF)-1α- and HIF-2α-dependent expression of AlkB homolog 5 (ALKBH5), an m(6)A demethylase, which demethylated NANOG mRNA, which encodes a pluripotency factor, at an m(6)A residue in the 3'-UTR...
April 5, 2016: Proceedings of the National Academy of Sciences of the United States of America
Jian Yu, Eric Solon, Helen Shen, Nishit B Modi, Aravind Mittur
1. This study examined the pharmacokinetics, distribution, metabolism, and excretion of [(14)C] nefopam in rats after a single oral administration. Blood, plasma, and excreta were analyzed for total radioactivity, nefopam, and metabolites. Metabolites were profiled and identified. Radioactivity distribution was determined by quantitative whole-body autoradiography. 2. The pharmacokinetic profiles of total radioactivity and nefopam were similar in male and female rats. Radioactivity partitioned approximately equally between plasma and red blood cells...
November 2016: Xenobiotica; the Fate of Foreign Compounds in Biological Systems
Yan Qiao, Bin Zhou, Meizi Zhang, Weijia Liu, Zhifu Han, Chuanjun Song, Wenquan Yu, Qinghua Yang, Ruiyong Wang, Shaomin Wang, Shuai Shi, Renbin Zhao, Jijie Chai, Junbiao Chang
Fe(II) and α-ketoglutarate-dependent fat mass and obesity associated protein (FTO)-dependent demethylation of m⁶A is important for regulation of mRNA splicing and adipogenesis. Developing FTO-specific inhibitors can help probe the biology of FTO and unravel novel therapeutic targets for treatment of obesity or obesity-associated diseases. In the present paper, we have identified that 4-chloro-6-(6'-chloro-7'-hydroxy-2',4',4'-trimethyl-chroman-2'-yl)benzene-1,3-diol (CHTB) is an inhibitor of FTO. The crystal structure of CHTB complexed with human FTO reveals that the novel small molecule binds to FTO in a specific manner...
March 15, 2016: Biochemistry
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