Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome

[1]  S. Oliviero,et al.  Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome , 2014, Genome Biology.

[2]  A. Křepelová,et al.  High-throughput single nucleotide variant discovery in E14 mouse embryonic stem cells provides a new reference genome assembly. , 2014, Genomics.

[3]  Qiangfeng Cliff Zhang,et al.  Landscape and variation of RNA secondary structure across the human transcriptome , 2014, Nature.

[4]  Yiliang Ding,et al.  Determination of in vivo RNA structure in low-abundance transcripts , 2013, Nature Communications.

[5]  Manolis Kellis,et al.  Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo , 2013, Nature.

[6]  Y. Zhang,et al.  In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features , 2013, Nature.

[7]  H. Stunnenberg,et al.  Dnmt3L Antagonizes DNA Methylation at Bivalent Promoters and Favors DNA Methylation at Gene Bodies in ESCs , 2013, Cell.

[8]  P. Becker,et al.  ATP-dependent roX RNA remodeling by the helicase maleless enables specific association of MSL proteins. , 2013, Molecular cell.

[9]  Rolf Backofen,et al.  Tandem stem-loops in roX RNAs act together to mediate X chromosome dosage compensation in Drosophila. , 2013, Molecular cell.

[10]  Nicholas T. Ingolia,et al.  Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins , 2013, Cell.

[11]  D. Mathews,et al.  Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots , 2013, Proceedings of the National Academy of Sciences.

[12]  Yoosik Kim,et al.  LIN28A Is a Suppressor of ER-Associated Translation in Embryonic Stem Cells , 2012, Cell.

[13]  Robert Tibshirani,et al.  Genome-wide measurement of RNA folding energies. , 2012, Molecular cell.

[14]  David G. Knowles,et al.  The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression , 2012, Genome research.

[15]  Nadav S. Bar,et al.  Landscape of transcription in human cells , 2012, Nature.

[16]  James B. Brown,et al.  Long noncoding RNAs are rarely translated in two human cell lines , 2012, Genome research.

[17]  Raymond K. Auerbach,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[18]  Paul Ryvkin,et al.  Global analysis of RNA secondary structure in two metazoans. , 2012, Cell reports.

[19]  P. Stadler,et al.  ViennaRNA Package 2.0 , 2011, Algorithms for Molecular Biology : AMB.

[20]  Eugene Bolotin,et al.  The noncoding RNA Mistral activates Hoxa6 and Hoxa7 expression and stem cell differentiation by recruiting MLL1 to chromatin. , 2011, Molecular cell.

[21]  Cole Trapnell,et al.  Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. , 2011, Genes & development.

[22]  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.

[23]  Alan M. Zahler,et al.  The conformation of microRNA seed regions in native microRNPs is prearranged for presentation to mRNA targets , 2011, Nucleic acids research.

[24]  D. Haussler,et al.  FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing , 2010, Nature Methods.

[25]  C. Waldsich,et al.  RNA folding in living cells , 2010, RNA biology.

[26]  Howard Y. Chang,et al.  Genome-wide measurement of RNA secondary structure in yeast , 2010, Nature.

[27]  Howard Y. Chang,et al.  Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes , 2010, Science.

[28]  C. Oubridge,et al.  Structure of spliceosomal ribonucleoproteins , 2010, F1000 biology reports.

[29]  David H. Mathews,et al.  RNAstructure: software for RNA secondary structure prediction and analysis , 2010, BMC Bioinformatics.

[30]  Yann Ponty,et al.  VARNA: Interactive drawing and editing of the RNA secondary structure , 2009, Bioinform..

[31]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[32]  Lan Jin,et al.  Biological basis for restriction of microRNA targets to the 3' untranslated region in mammalian mRNAs. , 2009, Nature structural & molecular biology.

[33]  D. Mathews,et al.  Accurate SHAPE-directed RNA structure determination , 2009, Proceedings of the National Academy of Sciences.

[34]  A. Laederach,et al.  Energy barriers, pathways, and dynamics during folding of large, multidomain RNAs. , 2008, Current opinion in chemical biology.

[35]  Shulan Tian,et al.  Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells , 2007, Science.

[36]  J. Puglisi,et al.  Probing the conformation of human tRNA3 Lys in solution by NMR , 2007, FEBS letters.

[37]  Michael Kertesz,et al.  The role of site accessibility in microRNA target recognition , 2007, Nature Genetics.

[38]  Tao Pan,et al.  RNA folding during transcription. , 2006, Annual review of biophysics and biomolecular structure.

[39]  Aleksey Y. Ogurtsov,et al.  A periodic pattern of mRNA secondary structure created by the genetic code , 2006, Nucleic acids research.

[40]  P. Clote,et al.  Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency. , 2005, RNA.

[41]  Tariq M Rana,et al.  Target accessibility dictates the potency of human RISC , 2005, Nature Structural &Molecular Biology.

[42]  O. Nygård,et al.  Secondary structure of two regions in expansion segments ES3 and ES6 with the potential of forming a tertiary interaction in eukaryotic 40S ribosomal subunits. , 2004, RNA.

[43]  D. Fabris,et al.  Direct probing of RNA structures and RNA-protein interactions in the HIV-1 packaging signal by chemical modification and electrospray ionization fourier transform mass spectrometry. , 2003, Journal of molecular biology.

[44]  S. Woodson,et al.  Effect of transcription on folding of the Tetrahymena ribozyme. , 2003, RNA.

[45]  G. Pruijn,et al.  The hU3-55K Protein Requires 15.5K Binding to the Box B/C Motif as Well as Flanking RNA Elements for Its Association with the U3 Small Nucleolar RNA in Vitro * , 2002, The Journal of Biological Chemistry.

[46]  E. Le Cam,et al.  G-quartets assembly within a G-rich DNA flap. A possible event at the center of the HIV-1 genome. , 2002, Nucleic acids research.

[47]  Christina Waldsich,et al.  RNA folding in vivo. , 2002, Current opinion in structural biology.

[48]  R. Lührmann,et al.  Direct probing of RNA structure and RNA-protein interactions in purified HeLa cell's and yeast spliceosomal U4/U6.U5 tri-snRNP particles. , 2002, Journal of molecular biology.

[49]  Tamás Kiss,et al.  Analysis of the structure of human telomerase RNA in vivo. , 2002, Nucleic acids research.

[50]  S. Dorner,et al.  A conformational change in the ribosomal peptidyl transferase center upon active/inactive transition , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[51]  D. K. Treiber,et al.  Beyond kinetic traps in RNA folding. , 2001, Current opinion in structural biology.

[52]  Yutaka Muto,et al.  Structure and Assembly of the Spliceosomal snRNPs , 2001 .

[53]  H. Pluk,et al.  Interaction of the U3-55k protein with U3 snoRNA is mediated by the box B/C motif of U3 and the WD repeats of U3-55k. , 2000, Nucleic acids research.

[54]  C. Donahue,et al.  The kinetic mechanism of the hairpin ribozyme in vivo: influence of RNA helix stability on intracellular cleavage kinetics. , 2000, Journal of molecular biology.

[55]  D. K. Treiber,et al.  Exposing the kinetic traps in RNA folding. , 1999, Current opinion in structural biology.

[56]  C. Will,et al.  Conserved Loop I of U5 Small Nuclear RNA Is Dispensable for Both Catalytic Steps of Pre-mRNA Splicing in HeLa Nuclear Extracts , 1999, Molecular and Cellular Biology.

[57]  E. Cartocci,et al.  The Dystrophin Promoter Is Negatively Regulated by YY1 in Undifferentiated Muscle Cells* , 1998, The Journal of Biological Chemistry.

[58]  T. Pan,et al.  Intermediates and kinetic traps in the folding of a large ribozyme revealed by circular dichroism and UV absorbance spectroscopies and catalytic activity , 1997, Nature Structural Biology.

[59]  C. Donahue,et al.  Kinetics of hairpin ribozyme cleavage in yeast. , 1997, RNA.

[60]  K. Weeks.  Protein-facilitated RNA folding. , 1997, Current opinion in structural biology.

[61]  O. Nygård,et al.  Structure of 18 S Ribosomal RNA in Native 40 S Ribosomal Subunits* , 1997, The Journal of Biological Chemistry.

[62]  D. Herschlag.  RNA Chaperones and the RNA Folding Problem (*) , 1995, The Journal of Biological Chemistry.

[63]  O. Nygård,et al.  Probing the structure of mouse Ehrlich ascites cell 5.8S, 18S and 28S ribosomal RNA in situ. , 1994, Nucleic acids research.

[64]  B. Hingerty,et al.  Further refinement of the structure of yeast tRNAPhe. , 1978, Journal of molecular biology.

[65]  N. Ho,et al.  Reaction of pseudouridine and inosine with N-cyclohexyl-N'-beta-(4-methylmorpholinium)ethylcarbodiimide. , 1971, Biochemistry.

[66]  D. Metz,et al.  The investigation of nucleic acid secondary structure by means of chemical modification with a carbodiimide reagent. II. The reaction between N-cyclohexyl-N'-beta-(4-methylmorpholinium)ethylcarbodiimide and transfer ribonucleic acid. , 1969, Biochemistry.

[67]  Howard Y. Chang,et al.  RNA SHAPE analysis in living cells. , 2013, Nature chemical biology.

[68]  Ira M. Hall,et al.  BEDTools: a flexible suite of utilities for comparing genomic features , 2010, Bioinform..

[69]  R. Russell.  RNA misfolding and the action of chaperones. , 2008, Frontiers in bioscience : a journal and virtual library.

[70]  R. Russell,et al.  DMS footprinting of structured RNAs and RNA–protein complexes , 2007, Nature Protocols.

[71]  J. Darlix,et al.  The ubiquitous nature of RNA chaperone proteins. , 2002, Progress in nucleic acid research and molecular biology.

[72]  M. Ares,et al.  Use of dimethyl sulfate to probe RNA structure in vivo. , 2000, Methods in enzymology.

[73]  D. Metz,et al.  The investigation of nucleic acid secondary structure by means of chemical modification with a carbodiimide reagent. I. The reaction between N-cyclohexyl-N'-beta-(4-methylmorpholinium)ethylcarbodiimide and model nucleotides. , 1969, Biochemistry.

[74]  J. Rinn,et al.  NIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author Manuscript NIH Public Access Author Manuscript Nature. Author manuscript; available in PMC 2012 March 15. , 2022 .