The RNA Epistructurome: Uncovering RNA Function by Studying Structure and Post-Transcriptional Modifications.
暂无分享,去创建一个
[1] Zhike Lu,et al. m6A-dependent regulation of messenger RNA stability , 2013, Nature.
[2] J. Darnell,et al. The absolute frequency of labeled N-6-methyladenosine in HeLa cell messenger RNA decreases with label time. , 1978, Journal of molecular biology.
[3] C. Woese,et al. 5S RNA secondary structure , 1975, Nature.
[4] Christopher A. Lavender,et al. In-cell SHAPE reveals that free 30S ribosome subunits are in the inactive state , 2015, Proceedings of the National Academy of Sciences.
[5] K. Morris,et al. The rise of regulatory RNA , 2014, Nature Reviews Genetics.
[6] Cole Trapnell,et al. Multiplexed RNA structure characterization with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) , 2011, Proceedings of the National Academy of Sciences.
[7] Maxwell R. Mumbach,et al. Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA , 2014, Cell.
[8] O. Elemento,et al. Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons , 2012, Cell.
[9] Tao Pan,et al. RNA folding during transcription. , 2006, Annual review of biophysics and biomolecular structure.
[10] Irmtraud M. Meyer,et al. On the importance of cotranscriptional RNA structure formation , 2013, RNA.
[11] B. Maden,et al. Mapping 2'-O-methyl groups in ribosomal RNA. , 2001, Methods.
[12] Stuart Aitken,et al. Snapshots of pre-rRNA structural flexibility reveal eukaryotic 40S assembly dynamics at nucleotide resolution , 2014, Nucleic acids research.
[13] Y. Zhang,et al. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features , 2013, Nature.
[14] Jill P. Mesirov,et al. RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure , 2016, Cell.
[15] D. Turner,et al. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. , 1998, Biochemistry.
[16] Paul Ryvkin,et al. Global analysis of RNA secondary structure in two metazoans. , 2012, Cell reports.
[17] Kevin Y. Yip,et al. Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data , 2015, Nucleic acids research.
[18] J. Doudna,et al. Insights into RNA structure and function from genome-wide studies , 2014, Nature Reviews Genetics.
[19] S. Oliviero,et al. Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome , 2014, Genome Biology.
[20] M. Ares,et al. Use of dimethyl sulfate to probe RNA structure in vivo. , 2000, Methods in enzymology.
[21] D. Mathews,et al. Bridging the gap between in vitro and in vivo RNA folding , 2016, Quarterly Reviews of Biophysics.
[22] D. Turner,et al. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[23] Nikolay V. Dokholyan,et al. Single-molecule correlated chemical probing of RNA , 2014, Proceedings of the National Academy of Sciences.
[24] Tariq M Rana,et al. Target accessibility dictates the potency of human RISC , 2005, Nature Structural &Molecular Biology.
[25] R. Lease,et al. Hydroxyl radical footprinting in vivo: mapping macromolecular structures with synchrotron radiation , 2006, Nucleic acids research.
[26] E. Westhof,et al. Hierarchy and dynamics of RNA folding. , 1997, Annual review of biophysics and biomolecular structure.
[27] Yin Tang,et al. The RNA structurome: transcriptome-wide structure probing with next-generation sequencing. , 2015, Trends in biochemical sciences.
[28] Jernej Ule,et al. hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1 , 2015, Nature.
[29] Mark Helm,et al. Post-transcriptional nucleotide modification and alternative folding of RNA , 2006, Nucleic acids research.
[30] K. Weeks,et al. A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry. , 2007, Journal of the American Chemical Society.
[31] Yi Xing,et al. m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells. , 2014, Cell stem cell.
[32] Shiqing Ma,et al. Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome. , 2015, Nature chemical biology.
[33] P. Brown,et al. Transcriptome-Wide Mapping of Pseudouridines: Pseudouridine Synthases Modify Specific mRNAs in S. cerevisiae , 2014, PloS one.
[34] D. Engelke,et al. Probing RNA Structure with Chemical Reagents and Enzymes , 2000, Current protocols in nucleic acid chemistry.
[35] Tao Pan,et al. Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures , 2007, Proceedings of the National Academy of Sciences.
[36] Zhao Su,et al. Genome-Wide Analysis of RNA Secondary Structure. , 2016, Annual review of genetics.
[37] D. Herschlag. RNA Chaperones and the RNA Folding Problem (*) , 1995, The Journal of Biological Chemistry.
[38] M. Kupiec,et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq , 2012, Nature.
[39] D. Mathews. Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. , 2004, RNA.
[40] Howard Y. Chang,et al. RNA SHAPE analysis in living cells. , 2013, Nature chemical biology.
[41] Gianmarc Grazioli,et al. m1A and m1G Potently Disrupt A-RNA Structure Due to the Intrinsic Instability of Hoogsteen Base Pairs , 2016, Nature Structural &Molecular Biology.
[42] B. Blencowe,et al. Global Mapping of Human RNA-RNA Interactions. , 2016, Molecular cell.
[43] Howard Y. Chang,et al. Genome-wide measurement of RNA secondary structure in yeast , 2010, Nature.
[44] Erez Y. Levanon,et al. m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation , 2015, Science.
[45] Rhiju Das,et al. Consistent global structures of complex RNA states through multidimensional chemical mapping , 2015, eLife.
[46] Howard Y. Chang,et al. Structure and thermodynamics of N6-methyladenosine in RNA: a spring-loaded base modification. , 2015, Journal of the American Chemical Society.
[47] Y. Pilpel,et al. Determinants of translation efficiency and accuracy , 2011, Molecular systems biology.
[48] Olivier Elemento,et al. 5′ UTR m6A Promotes Cap-Independent Translation , 2015, Cell.
[49] Isabelle Behm-Ansmant,et al. Use of Specific Chemical Reagents for Detection of Modified Nucleotides in RNA , 2011, Journal of nucleic acids.
[50] D. Mathews,et al. Improved RNA secondary structure prediction by maximizing expected pair accuracy. , 2009, RNA.
[51] Gideon Rechavi,et al. The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA , 2016, Nature.
[52] D. Crothers,et al. In vivo structural analysis of spliced leader RNAs in Trypanosoma brucei and Leptomonas collosoma: a flexible structure that is independent of cap4 methylations. , 1995, RNA.
[53] S. Butcher,et al. The molecular interactions that stabilize RNA tertiary structure: RNA motifs, patterns, and networks. , 2011, Accounts of chemical research.
[54] Schraga Schwartz,et al. Transcriptome-Wide Mapping of 5-methylcytidine RNA Modifications in Bacteria, Archaea, and Yeast Reveals m5C within Archaeal mRNAs , 2013, PLoS genetics.
[55] Jan Gorodkin,et al. Profiling of ribose methylations in RNA by high-throughput sequencing. , 2014, Angewandte Chemie.
[56] W. Gilbert,et al. Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells , 2014, Nature.
[57] P. Agris,et al. The importance of being modified: roles of modified nucleosides and Mg2+ in RNA structure and function. , 1996, Progress in nucleic acid research and molecular biology.
[58] Chengqi Yi,et al. Transcriptome-wide mapping reveals reversible and dynamic N(1)-methyladenosine methylome. , 2016, Nature chemical biology.
[59] Niranjan Nagarajan,et al. In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation. , 2016, Molecular cell.
[60] Lukasz Jan Kielpinski,et al. Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility , 2014, Nucleic acids research.
[61] Gideon Rechavi,et al. Gene expression regulation mediated through reversible m6A RNA methylation , 2014, Nature Reviews Genetics.
[62] Rhiju Das,et al. Massively parallel RNA chemical mapping with a reduced bias MAP-seq protocol. , 2013, Methods in molecular biology.
[63] Nadav S. Bar,et al. Landscape of transcription in human cells , 2012, Nature.
[64] K. Weeks,et al. Detection of RNA-Protein Interactions in Living Cells with SHAPE. , 2015, Biochemistry.
[65] Steven Busan,et al. RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP) , 2014, Nature Methods.
[66] Howard Y. Chang,et al. Structural imprints in vivo decode RNA regulatory mechanisms , 2015, Nature.
[67] Ligang Wu,et al. YTHDF2 destabilizes m6A-containing RNA through direct recruitment of the CCR4–NOT deadenylase complex , 2016, Nature Communications.
[68] Qiangfeng Cliff Zhang,et al. Landscape and variation of RNA secondary structure across the human transcriptome , 2014, Nature.
[69] Jernej Ule,et al. NSun2-Mediated Cytosine-5 Methylation of Vault Noncoding RNA Determines Its Processing into Regulatory Small RNAs , 2013, Cell reports.
[70] Douglas H. Turner,et al. The contribution of pseudouridine to stabilities and structure of RNAs , 2013, Nucleic acids research.
[71] J. Shendure,et al. High-throughput determination of RNA structure by proximity ligation , 2015, Nature Biotechnology.
[72] D. K. Treiber,et al. Exposing the kinetic traps in RNA folding. , 1999, Current opinion in structural biology.
[73] David E Draper,et al. A guide to ions and RNA structure. , 2004, RNA.
[74] Yuri Motorin,et al. Illumina-based RiboMethSeq approach for mapping of 2′-O-Me residues in RNA , 2016, Nucleic acids research.
[75] J. Ofengand,et al. Mapping pseudouridines in RNA molecules. , 2001, Methods.
[76] D. Haussler,et al. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing , 2010, Nature Methods.
[77] Aleksey Y. Ogurtsov,et al. A periodic pattern of mRNA secondary structure created by the genetic code , 2006, Nucleic acids research.
[78] David Sankoff,et al. RNA secondary structures and their prediction , 1984 .
[79] Thomas Preiss,et al. Mapping and significance of the mRNA methylome , 2013, Wiley interdisciplinary reviews. RNA.
[80] Anton Nekrutenko,et al. StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo , 2015, Bioinform..
[81] Bradley R. Cairns,et al. Identification of direct targets and modified bases of RNA cytosine methyltransferases , 2013, Nature Biotechnology.
[82] Data production leads,et al. An integrated encyclopedia of DNA elements in the human genome , 2012 .
[83] Robert Tibshirani,et al. Genome-wide measurement of RNA folding energies. , 2012, Molecular cell.
[84] D. Davis. Stabilization of RNA stacking by pseudouridine. , 1995, Nucleic acids research.
[85] Kang Zhang,et al. Mapping RNA–RNA interactome and RNA structure in vivo by MARIO , 2016, Nature Communications.
[86] S. Oliviero,et al. RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data , 2016, Bioinform..
[87] K. Weeks,et al. Fingerprinting noncanonical and tertiary RNA structures by differential SHAPE reactivity. , 2012, Journal of the American Chemical Society.
[88] Unique structural and stabilizing roles for the individual pseudouridine residues in the 1920 region of Escherichia coli 23S rRNA. , 2000, Nucleic acids research.
[89] Christopher E. Mason,et al. Single-nucleotide resolution mapping of m6A and m6Am throughout the transcriptome , 2015, Nature Methods.
[90] Howard Y. Chang,et al. Understanding the transcriptome through RNA structure , 2011, Nature Reviews Genetics.
[91] Fei Wang,et al. Transcriptome-wide distribution and function of RNA hydroxymethylcytosine , 2016, Science.
[92] M. Esteller. Non-coding RNAs in human disease , 2011, Nature Reviews Genetics.
[93] Shu-Bing Qian,et al. Dynamic m6A mRNA methylation directs translational control of heat shock response , 2015, Nature.
[94] Michael Kertesz,et al. The role of site accessibility in microRNA target recognition , 2007, Nature Genetics.
[95] Biophysics of RNA Folding , 2013, Biophysics for the Life Sciences.
[96] T. Preiss,et al. Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA , 2012, Nucleic acids research.
[97] Manolis Kellis,et al. Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo , 2013, Nature.
[98] Francesco Neri,et al. High-throughput single-base resolution mapping of RNA 2΄-O-methylated residues , 2016, Nucleic acids research.
[99] Andrea Barta,et al. Strategies for RNA folding and assembly , 2004, Nature Reviews Molecular Cell Biology.