RNA preprints: W9/2019

BIQ: A method for searching circular RNAs in transcriptome databases by indexing backsplice junctions. Peter Menzel, Irmtraud M Meyer

Coding Triplets in the Transfer RNA Arm and Their Role in Present and Past tRNA Recognition. Ilana Agmon, Itay Fayerverker, Tal Mor

Classification of RNA backbone conformation into rotamers using 13C’ chemical shifts: How far we can go? Alejandro Ariel Icazatti, Juan Martín Loyola, Igal Szleifer, Jorge Alberto Vila, Osvaldo A Martin

Bacterial Cyclopropane Fatty Acid Synthase mRNA is targeted by activating and repressing small RNAs. Colleen M. Bianco, Kathrin Froehlich, Carin K. Vanderpool

Interaction of Sox2 with RNA binding proteins in mouse embryonic stem cells. Samudyata S, Paulo Amaral, Par G Engstrom, Samuel C Robson, Michael L Nielsen, Tony Kouzarides, Goncalo Castelo-Branco

Empowering the annotation and discovery of structured RNAs with scalable and accessible integrative clustering. Milad Miladi, Eteri Sokhoyan, Torsten Houwaart, Steffen Heyne, Fabrizio Costa, Bjoern Gruening, Rolf Backofen

A splice donor variant in CCDC189 is associated with asthenospermia in Nordic Red dairy cattle. Terhi Iso-Touru, Christine Wurmser, Heli Venhoranta, Maya Hiltpold, Tujia Savolainen, Anu Sironen, Konrad Fischer, Krzysztof Flisikowski, Ruedi Fries, Alejandro Vicente-Carrillo, Manuel Alvarez-Rodriguez, Szabolcs Nagy, Mervi Mutikainen, Jaana Peippo, Juhani Taponen, Goutam Sahana, Bernt Guldbrandtsen, Henri Simonen, Heriberto Rodriguez-Martinez, Magnus Andersson, Hubert Pausch

A new pathway of pre-tRNA surveillance in yeast. Matthew J Payea, Thareendra C De Zoysa, Eric M Phizicky

RumimiR: a detailed microRNA database focused on ruminant species.Celine Bourdon, Philippe Bardou, Etienne Aujean, Sandrine Le Guillou, Gwenola Tosser-Klopp, FABIENNE LE PROVOST

Identification of RBPMS as a smooth muscle master splicing regulator via proximity of its gene with super-enhancers. Erick E Nakagaki-Silva, Clare Gooding, Miriam Llorian, Aishwarya G Jacob, Frederick Richards, Adrian Buckroyd, Sanjay Sinha, Christopher WJ Smith

Quantitative modelling predicts the impact of DNA methylation on RNA polymerase II traffic. Justyna Cholewa-Waclaw, Ruth Shah, Shaun Webb, Kashyap Chhatbar, Barnard Ramsahoye, Oliver Pusch, Miao Yu, Philip Greulich, Bartlomiej Waclaw, Adrian Bird

Crosstalk between RNA Pol II C-Terminal Domain Acetylation and Phosphorylation via RPRD Proteins. Ibraheem Ali, Diego Garrido-Ruiz, Zuyao Ni, Jeffrey R Johnson, Heng Zhang, Pao-Chen Li, Mir Mubashir Khalid, Ryan J Conrad, Xinghua Guo, Jinrong Min, Jack Greenblatt, Matthew Jacobson, Nevan J Krogan, Melanie Ott

Dinucleoside polyphosphates act as 5′-RNA caps in Escherichia coli. Oldrich Hudecek, Roberto Benoni, Martin Culka, Martin Hubalek, Lubomir Rulisek, Josef Cvacka, Hana Cahova

Fragment-based discovery of a new class of inhibitors targeting mycobacterial tRNA modification. Sherine E. Thomas, Andrew J. Whitehouse, Karen Brown, Juan M. Belardinelli, Ramanuj Lahiri, M. Daben J. Libardo, Pooja Gupta, Sony Malhotra, Helena I. M. Boshoff, Mary Jackson, Chris Abell, Anthony G. Coyne, Tom L. Blundell, R. Andres Floto, Vitor Mendes

siRNA containing a unique 5-nucleotide motif acts as a quencher of IFI16-mediated innate immune response. Hongyan Sui, Jun Yang, Xiaojun Hu, Tomozumi Imamichi, Qian Chen

Nanotubes effectively deliver siRNA to intact plant cells and protect siRNA against nuclease degradation. Gozde S Demirer, Huan Zhang, Natalie S Goh, Roger Chang, Markita P Landry

Active role of free RNA during the early phase of proteostasis stress. Marion Alriquet, Adrian Martinez-Limon, Gerd Hanspach, Martin Hengesbach, Gian G. Tartaglia, Giulia Calloni, R. Martin Vabulas

Exon-mediated activation of transcription starts. Ana Fiszbein, Keegan S. Krick, Christopher B. Burge

Binding specificities of human RNA binding proteins towards structured and linear RNA sequences. Arttu Jolma, Jilin Zhang, Estefania Mondragón, Teemu Kivioja, Yimeng Yin, Fangjie Zhu, Quaid Morris, Timothy R. Hughes, L. James Maher III, Jussi Taipale

Scans of the MYC mRNA reveal multiple stable secondary structures—including a 3′ UTR motif, conserved across vertebrates, that can affect gene expression. Collin O’Leary, Ryan Andrews, Van Tompkins, Jonathan Chen, Jessica Childs-Disney, Matthew Disney, Walter N Moss

Splice junction centric approach to identify translated noncanonical isoforms in the human proteome. Edward Lau, Yu Han, Maggie Pui Yu Lam

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