RNA preprints: W10/2018

Bacteriophage cooperation suppresses CRISPR-Cas3 and Cas9 immunity. Adair L Borges, Jenny Y Zhang, MaryClare Rollins, Beatriz A Osuna, Blake Wiedenheft, Joseph Bondy-Denomy

A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain. Benjamin Kleaveland, Charlie Y Shi, Joanna Stefano, David P Bartel

An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys. Marilyn Parra, Ben W. Booth, Richard Weiszmann, Brian A. Yee, Gene W. Yeo, James B. Brown, Susan E. Celniker, John G. Conboy

Efficient computation of co-transcriptional RNA-ligand interaction dynamics. Michael T Wolfinger, Christoph Flamm, Ivo L Hofacker

Structure of the 30S ribosomal decoding complex at ambient temperature. E. Han Dao, Frederic Poitevin, Raymond G. Sierra, Cornelius Gati, Yashas Rao, Halil Ibrahim Ciftci, Fulya Akşit, Alex McGurk, Trevor Obrinski, Paul Mgbam, Brandon Hayes, Casper de Lichtenberg, Fatima Pardo-Avila, Nicholas Corsepius, Lindsey Zhang, Matt Seaberg, Mark S. Hunter, Mengling Liang, Jason E. Koglin, Soichi Wakatsuki, Hasan DeMirci

Selection removes Shine-Dalgarno-like sequences from within protein coding genes. Adam J Hockenberry, Luis AN Amaral, Michael C Jewett, Claus O Wilke

OMCD: OncoMir Cancer Database. Aaron Sarver, Anne Sarver, Ce Yuan, Subbaya Subramanian

Anti-CRISPR phages cooperate to overcome CRISPR-Cas immunity. Mariann Landsberger, Sylvain Gandon, Sean Meaden, Hélène Chabas, Angus Buckling, Edze R. Westra, Stineke van Houte

Conserved Methyltransferase Spb1 Targets mRNAs for Regulated Modification with 2′-O-Methyl Ribose. Kristen M Bartoli, Cassandra Schaening, Thomas Carlile, Wendy V Gilbert

RNA-directed activation of cytoplasmic dynein-1 in reconstituted transport RNPs. Mark A McClintock, Carly I Dix, Christopher M Johnson, Stephen H McLaughlin, Rory J Maizels, Ha Thi Hoang, Simon L Bullock

The RNA polymerase clamp interconverts dynamically among three states and is stabilized in a partly closed state by ppGpp. Diego Duchi, Abhishek Mazumder, Anssi M Malinen, Richard Ebright, Achillefs Kapanidis

Higher-Order Organization Principles of Pre-translational mRNPs. Mihir Metkar, Hakan Ozadam, Bryan R. Lajoie, Maxim Imakaev, Leonid A. Mirny, Job Dekker, Melissa J. Moore

Comprehensive catalog of dendritically localized mRNA isoforms from sub-cellular sequencing of single mouse neurons. Sarah A Middleton, James Eberwine, Junhyong Kim

EukRef: phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution. Javier del Campo, Martin Kolisko, Vittorio Boscaro, Luciana F. Santoferrara, Ramon Massana, Laure Guillou, Alastair Simpson, Cedric Berney, Colomban de Vargas, Matt Brown, Patrick Keeling, Laura Wegener Parfrey

Comprehensive analysis of small RNA profile by massive parallel sequencing in HTLV-1 asymptomatic subjects with monoclonal and polyclonal rearrangement of the T-cell antigen receptor γ-chain. Daniela Raguer Valadão de Souza, Rodrigo Pessôa, Youko Nukui, Juliana Pereira, Jorge Casseb, Augusto César Penalva de Oliveira, Patricia Bianca Clissa, Sabri Saeed Sanabani

Formation of tRNA wobble inosine in humans is perturbed by a millennia-old mutation linked to intellectual disability. Jillian Ramos, Lu Han, Yan Li, Fowzan S Alkuraya, Eric M Phizicky, Dragony Fu

mRNA structure determines specificity of a polyQ-driven phase separation. Erin M Langdon, Yupeng Qiu, Amirhossein Ghanbari Niaki, Grace McLaughlin, Chase Weidmann, Therese Gerbich, Jean A Smith, John M Crutchley, Christina M Termini, Kevin M Weeks, Sua Myong, Amy Gladfelter

A dual sRNA in Staphylococcus aureus induces a metabolic switch responding to glucose consumption. Delphine Bronesky, Emma Desgranges, Anna Corvaglia, Patrice François, Carlos J Caballero, Laura Prado, Alejandro Toledo-Arana, Inigo Lasa, Karen Moreau, François Vandenesch, Stefano Marzi, Pascale Romby, Isabelle Caldelari

A learning-based framework for miRNA-disease association prediction using neural networks. Jiajie Peng, Weiwei Hui, Qianqian Li, Bolin Chen, Zhongyu Wei, Xuequn Shang

miR-21-5p and miR-30a-5p are identical in human and bovine, have similar isomiR distribution, and cannot be used to identify xenomiR uptake from cow milk. Bastian Fromm, Juan Pablo Tosar, Lin Yu, Marc K Halushka, Kenneth W Witwer

Analysis of P granules in vivo and ex vivo. Jarrett Smith, Geraldine Seydoux

Long-read sequencing of nascent RNA reveals coupling among RNA processing events. Lydia Herzel, Korinna Straube, Karla M. Neugebauer

Transgenerational sterility of small RNA genome silencing mutants in response to germ granule dysfunction. Katherine Kretovich Billmyre, Bree Heestand, Maya Spichal, Shawn Ahmed

Ferrous iron folds rRNA and mediates translation. Marcus S Bray, Timothy K Lenz, Jessica C Bowman, Anton S Petrov, Amit R Reddi, Nicholas V Hud, Loren D Williams, Jennifer B Glass

A method for simultaneous targeted mutagenesis of all nuclear rDNA repeats in Saccharomyces cerevisiae using CRISPR-Cas9. Lilly Chiou, Daniele Armaleo

Single nucleotide polymorphisms that modulate microRNA regulation of gene expression in tumors. Gary Wilk, Rosemary Braun

SentRNA: Improving computational RNA design by incorporating a prior of human design strategies. Jade Shi (EteRNA players), Rhiju Das, Vijay S. Pande

Global analysis of A-to-I RNA editing reveals association with common disease variants. Oscar Franzén, Raili Ermel, Katyayani Sukhavasi, Rajeev Jain, Anamika Jain, Christer Betsholtz, Chiara Giannarelli, Jason C. Kovacic, Arno Ruusalepp, Josefin Skogsberg, Ke Hao, Eric E. Schadt, Johan L.M. Björkegren

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