RNA preprints: W6/2019

Evolution of the nonsense-mediated decay (NMD) pathway is associated with decreased cytolytic immune infiltration. Justin R Pritchard, Boyang Zhao

Targeted, High-Resolution RNA Sequencing Of Non-Coding Genomic Regions Associated With Neuropsychiatric Functions. Simon A Hardwick, Samuel D Bassett, Dominik Kaczorowski, James Blackburn, Kirston Barton, Nenad Bartonicek, Shaun L Carswell, Hagen U Tilgner, Clement Loy, Glenda Halliday, Tim R Mercer, Martin A Smith, John S Mattick

Ecdysone signaling promotes expression of multifunctional RNA binding proteins essential for ovarian germline stem cell self-renewal in Drosophila. Danielle S Finger, Vivian V Holt, Elizabeth T Ables

FUS controls the processing of snoRNAs into smaller RNA fragments that can regulate gene expression. Patrycja Plewka, Michal Szczesniak, Agata Stepien, Marek Zywicki, Andrzej Pacak, Martino Colombo, Izabela Makalowska, Marc-David Ruepp, Katarzyna Dorota Raczynska

Dynamics of microRNA expression during mouse prenatal development. Sorena Rahmanian, Rabi Murad, Alessandra Breschi, Weihua Zeng, Brian A Williams, Mark Mackiewicz, Brian Roberts, Sarah Meadows, Dianne Moore, Carrie Davis, Diane Trout, Chris Zaleski, Alexander Dobin, Lei-Hoon Sei, Jorg Drenkow, Alex Scavelli, Thomas R Gingeras, Barbara Wold, Richard M. Myers, Roderic Guigo, Ali Mortazavi

Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods. Carrie Wright, Anandita Rajpurohit, Emily E. Burke, Courtney Williams, Leonardo Collado-Torres, Martha Kimos, Nicholas J. Brandon, Alan J. Cross, Andrew E. Jaffe, Daniel R. Weinberger, Joo Heon Shin

Control of ϕC31 integrase-mediated site-specific recombination by protein trans splicing. Femi J Olorunniji, Makeba Lawson-Williams, Arlene L McPherson, Jane E Paget, Marshall Stark, Susan J Rosser

The genetic determinants of the relative expression of alternative 3’UTR isoforms in human. Elisa Mariella, Federico Marotta, Elena Grassi, Stefano Gilotto, Paolo Provero

The landscape of the alternatively spliced transcriptome remains stable during aging across different species and tissues. Patricia Sieber, Emanuel Barth, Manja Marz

Musashi expression in intestinal stem cells attenuates radiation-induced decline in intestinal homeostasis and survival in Drosophila. Amit Sharma, Kazutaka Akagi, Pankaj Kapahi, Blaine Pattavina, Kenneth A Wilson, Christopher Nelson, Mark Watson, Elie Maksoud, Mauricio Ortega, Rachel Brem

Brain-enriched coding and long non-coding RNA genes are overrepresented in recurrent autism spectrum disorder CNVs. Hamid Alinejad-Rokny, Julian Heng, Alistair Forrest

HMGB1 as a rheostat of chromatin topology and RNA homeostasis on the path to senescence. Konstantinos Sofiadis, Milos Nikolic, Anne Zirkel, Yulia Kargapolova, Natasa Josipovic, Antonis Papadakis, Eduardo Gusmao, Athanasia Mizi, Theodore Georgomanolis, Mirjam Koker, Roland Ullrich, Janine Altmueller, Peter Nuernberg, Andreas Beyer, Argyris Papantonis

The structure of a highly conserved picocyanobacterial protein reveals a Tudor domain with a novel tRNA binding function. Katherine M Bauer, Rose Dicovitsky, Maria Pellegrini, Olga Zhaxybayeva, Michael J Ragusa

Trypanosoma brucei ribonuclease H2A is an essential enzyme that resolves R-loops associated with transcription initiation and antigenic variation. Emma M Briggs, Kathryn Crouch, Leandro Lemgruber, Graham Hamilton, Craig Lapsley, Richard McCulloch

Global increase in circRNA levels in myotonic dystrophy. Karol Czubak, Katarzyna Taylor, Agnieszka Piasecka, Krzysztof Sobczak, Katarzyna Kozlowska, Anna Philips, Saam Sedehizadeh, John David Brook, Marzena Wojciechowska, Piotr Kozlowski

OPTIMIR, a novel algorithm for integrating available genome-wide genotype data into miRNA sequence alignment analysis. Florian Thibord, Claire Perret, Maguelonne Roux, Pierre Suchon, Marine Germain, Jean-Francois Deleuze, Pierre-Emmanuel Morange, David-Alexandre Tregouet

Borrelia burgdorferi 297 bmpA encode the mRNA that contains ORF for a leader peptide that regulates bmpA gene expression. Lidiya Dubytska

An RNA-binding protein secreted by Listeria monocytogenes activates RIG-I signaling. Alessandro Pagliuso, To Nam Tham, Eric Allemand, Stevens Robertin, Bruno Dupuy, Quentin Bertrand, Christophe Bécavin, Mikael Koutero, Valérie Najburg, Marie-Anne Nahori, Fabrizia Stavru, Andréa Dessen, Christian Muchard, Alice Lebreton, Anastassia V Komarova, Pascale Cossart

Loss of function of the RNA export factor, Nxt1, in Drosophila causes muscle degeneration and reduced expression of genes with long introns. Kevin van der Graaf, Helen White-Cooper

Arenaviridae exoribonuclease presents genomic RNA edition capacity. Elsie Yekwa, Chutima Aphibanthammakit, Xavier Carnec, Bruno Coutard, Caroline Picard, Bruno Canard, Sylvain Baize, François Ferron

Non-canonical Features of Pentatricopeptide Repeat Protein-Facilitated RNA Editing in Arabidopsis Chloroplasts. Yueming Kelly Sun, Bernard Gutmann, Ian Small

Amyloid conformers of the FXR1 protein prevent mRNA degradation in cortical neurons. Julia Sopova, Elena Koshel, Tatyana Belashova, Sergey Zadorsky, Aleksandra Sergeeva, Vera Siniukova, Aleksandr Shenfeld, Marya Velizhanina, Kirill Volkov, Anton Nizhnikov, Elena Gaginskaya, Alexey Galkin

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RNA preprints: W5/2019

RNA-antimicrobial peptide LL-37 complexes activate a self-sustaining TLR- and NET-mediated cycle of neutrophil activation. Franziska Herster, Zsofia Bittner, Sabine Dickhoefer, David Eisel, Tatjana Eigenbrod, Thomas Knorpp, Nicole Schneiderhan-Marra, Markus W Loeffler, Hubert Kalbacher, Dominik Hartl, Lukas Freund, Knut Schaekel, Martin Heiser, Kamran Ghoreschi, Alexander N. R. Weber

Tubulin mRNA stability is sensitive to change in microtubule dynamics caused by multiple physiological and toxic cues. Ivana Gasic, Sarah A. Boswell, Timothy J. Mitchison

G4-iM Grinder: DNA and RNA G-Quadruplex, i-Motif and higher order structure search and analyser tool. Efres Belmonte Reche, Juan Carlos Morales

Stool-derived eukaryotic RNA biomarkers for detection of high-risk adenomas. Erica K. Barnell, Yiming Kang, Andrew R. Barnell, Katie M. Campbell, Kimberly R. Kruse, Elizabeth M. Wurtzler, Malachi Griffith, Aadel A. Chaudhuri, Obi L. Griffith

A novel plasmid-transcribed regulatory sRNA, QfsR, controls chromosomal polycistronic mRNAs in Agrobacterium tumefaciens. Benjamin Diel, Magali Dequivre, Florence Wisniewski-Dyé, Ludovic Vial, Florence Hommais

The SUMO ligase Su(var)2-10 links piRNA-guided target recognition to chromatin silencing. Maria Ninova, Yung-Chia Ariel Chen, Baira Godneeva, Alicia K Rogers, Yicheng Luo, Alexei A Aravin, Katalin Fejes Tóth

lncRNA Neat1 drives neuronal histone methylation and age-related memory impairments. Anderson A Butler, Daniel R Johnston, Simranjit Kaur, Farah D Lubin

Argonaute bypasses cellular obstacles without hindrance during target search. Tao Ju Cui, Misha Klein, Jorrit Hegge, Stanley D Chandradoss, John van der Oost, Martin Depken, Chirlmin Joo

DypFISH: Dynamic Patterned FISH to Interrogate RNA and Protein Spatial and Temporal Subcellular Distribution. Anca F. Savulescu, Robyn Brackin, Emmanuel Bouilhol, Benjamin Dartigues, Jonathan H. Warrell, Mafalda R. Pimentel, Stephane Dallongeville, Jan Schmoranzer, Jean-Christophe Olivo-Marin, Edgar R. Gomes, Macha Nikolski, Musa M. Mhlanga

Regulation of CHD2 expression by the Chaserr long noncoding RNA is essential for viability. Aviv Rom, Liliya Melamed, Micah Jonathan Goldrich, Rotem Kadir, Matan Golan, Inbal Biton, Rotem Ben-Tov Perry, Igor Ulitsky

Impact of population structure in the design of RNA-based diagnostics for antibiotic resistance in Neisseria gonorrhoeae. Crista B. Wadsworth, Mohamad R.A. Sater, Roby P. Bhattacharyya, Yonatan H. Grad

Using pan RNA-seq analysis to reveal the ubiquitous existence of 5′ and 3′ end small RNAs. Xiaofeng Xu, Haishuo Ji, Zhi Cheng, Xiufeng Jin, Xue Yao, Yanqiang Liu, Qiang Zhao, Tao Zhang, Jishou Ruan, Wenjun Bu, Ze Chen, Gao Shan

Staufen2 mediated RNA recognition and localization requires combinatorial action of multiple domains. Simone Heber, Imre Gaspar, Jan-Niklas Tants, Johannes Günther, Sandra M Fernández Moya, Robert Janowski, Anne Ephrussi, Michael Sattler, Dierk Niessing

Testing models of mRNA localization reveals robustness regulated by reducing transport between cells. Jonathan U Harrison, Richard M Parton, Ilan Davis, Ruth E Baker

Differential gene expression and the importance of regulatory ncRNAs in acidophilic microorganisms. Daniela S Aliaga Goltsman, Loren Hauser, Mauna Dasari, Brian C Thomas, Jillian F Banfield

Comprehensive Evaluation of Deep Learning Architectures for Prediction of DNA/RNA Sequence Binding Specificities. Ameni Trabelsi, Mohamed Chaabane, Asa Ben Hur

A note on some conjectures about combinatorial models for RNA secondary structures. Adam Zsolt Wagner