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

RNA preprints: W4/2019

Extensive splicing across the Saccharomyces cerevisiae genome. Stephen Douglass, Calvin S Leung, Tracy L Johnson

Accurate detection of m6A RNA modifications in native RNA sequences. Huanle Liu, Oguzhan Begik, Morghan C Lucas, Christopher E Mason, Schraga Schwartz, John S Mattick, Martin A Smith, Eva Maria Novoa

Elucidating small RNA pathways in Arabidopsis thaliana egg cells. Stefanie Sprunck, Marc Urban, Nicholas Strieder, Maria Lindemeier, Andrea Bleckmann, Maurits Evers, Thomas Hackenberg, Christoph Moehle, Thomas Dresselhaus, Julia C. Engelmann

Whole Aegilops tauschii transcriptome investigation revealed nine novel miRNAs involved in stress response. Behnam Bakhshi, Ehsan Mohseni Fard

Broad antifungal resistance mediated by RNAi-dependent epimutation in the basal human fungal pathogen Mucor circinelloides. Zanetta Chang, R. Blake Billmyre, Soo Chan Lee, Joseph Heitman

Widespread selection for high and low secondary structure in coding sequences across all domains of life. Daniel Gebert, Julia Jehn, David Rosenkranz

The biofilm matrix scaffold of Pseudomonas species consists of non-canonically base paired extracellular DNA and RNA. Thomas W Seviour, Fernaldo Richtia Winnerdy, Wong Lan Li, Shi Xiangyan, Sudarsan Mugunthan, Gurjeet Singh Kohli, Heather M Shewan, Jason Stokes, Scott A Rice, Anh-Tuan Phan, Staffan Kjelleberg

Paternally-acting canonical RNA-directed DNA methylation pathway genes sensitize Arabidopsis endosperm to paternal dosage. Rajavasireddy P Satyaki, Mary Gehring

Splicing buffers suboptimal codon usage in human cells. Christine Mordstein, Rosina Savisaar, Robert S Young, Jeanne Bazile, Lana Talmane, Juliet Luft, Michael Liss, Martin S Taylor, Laurence D Hurst, Grzegorz Kudla

N6-methyladenosine dynamics during early vertebrate embryogenesis. Havard Aanes, Dominique Engelsen, Adeel Manaf, Endalkachew Ashenafi Alemu, Cathrine Broberg Vagbo, Leonardo Martin, Mads Lerdrup, Klaus Hansen, Sinnakaruppan Mathavan, Cecilia Winata, Robert B. Darnell, Peter Alestrom, Arne Klungland

Relevance of the iron-responsive element (IRE) pseudotriloop structure for IRP1/2 binding and validation of IRE-like structures using the yeast three-hybrid system. Shih-Cheng Chen, René C.L. Olsthoorn

Dynamic control of pathway expression with riboregulated switchable feedback promoters. Cameron J Glasscock, John T Lazar, Bradley W Biggs, Jack H Arnold, Min-Kyoung Kang, Danielle Tullman-Ercek, Keith E J Tyo, Julius B Lucks

Selective enrichment of A-to-I edited transcripts from cellular RNA using Endonuclease V. Steve D Knutson, Jennifer M Heemstra

Comparative identification of microRNAs in Apis cerana cerana workers’midguts responding to Nosema ceranae invasion. Rui Guo, Dafu Chen, Yu Du, Huazhi Chen, Haipeng Wang, Cuiling Xiong, Yanzhen Zheng, Chunsheng Hou, Qingyun Diao

Expression kinetics and innate immune response after electroporation and lipid nanoparticle mediated delivery of a self-amplifying mRNA in the skin of mice. Hanne Huysmans, Zifu Zhong, Joyca De Temmerman, Barbara L Mui, Ying K Tam, Sean Mc Cafferty, Arlieke Gitsels, Daisy Vanrompay, Niek Sanders

Comparative analysis of sfRNA in the genome of pre-epidemic and epidemic Zika viruses for host interacting proteins potentially related to the recent epidemic. Perumal Arumugam Desingu

RNA interactions with CTCF are essential for its proper function. Ricardo Saldana-Meyer, Javier Rodriguez-Hernaez, Mayilaadumveettil Nishana, Karina Jacome-Lopez, Elphege P. Nora, Benoit G. Bruneau, Mayra Furlan-Magaril, Jane Skok, Danny Reinberg

RadiationGeneSigDB: A database of oxic and hypoxic radiation response gene signatures and their utility in identification of hypoxia-regulated MicroRNA. Venkata Manem, Andrew Dhawan

miRNA activity contributes to accurate RNA splicing in C. elegans intestine and body muscle tissues. Kasuen Kotagama, Anna L Schorr, Hannah S Steber, Marco Mangone

The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A)-translation. Andrea Hildebrandt, Mirko Brüggemann, Susan Boerner, Cornelia Rücklé, Jan Bernhard Heidelberger, Annabelle Dold, Anke Busch, Heike Hänel, Andrea Voigt, Stefanie Ebersberger, Ingo Ebersberger, Jean-Yves Roignant, Kathi Zarnack, Julian König, Petra Beli

Tracing the evolution of the plastome and mitogenome in the Chloropicophyceae uncovered convergent tRNA gene losses and a variant plastid genetic code. Monique Turmel, Adriana Lopes dos Santos, Christian Otis, Roxanne Sergerie, Claude Lemieux

DPAC: a tool for Differential Poly(A) Site usage from poly(A) targeted RNAseq data. Andrew Laurence Routh

Targeted Cleavage and Polyadenylation of RNA by CRISPR-Cas13. Kelly M Anderson, Pornthida Poosala, Sean R Lindley, Douglas M Anderson

RNA preprints: W3/2019

A single microRNA-Hox gene module controls complex movement in morphologically-distinct developmental forms of Drosophila. Raouf Issa, Joao Picao-Osorio, Nuno Rito, Maria Eugenia Chiappe, Claudio R. Alonso

3′UTR cleavage of transcripts localized in axons of sympathetic neurons. Catia Andreassi, Raphaelle Luisier, Hamish Crerar, Sasja Franke, Nicholas M. Luscombe, Giovanni Cuda, Marco Gaspari, Antonella Riccio

Pat1 promotes processing body assembly by enhancing the phase separation of the DEAD-box ATPase Dhh1 and RNA. Ruchika Sachdev, Maria Hondele, Miriam Linsenmeier, Pascal Vallotton, Christopher F Mugler, Paolo Arosio, Karsten Weis

Mature sperm small RNA profile in the sparrow: implications for transgenerational effects of age on fitness. Wayo Matsushima, Kristiana Brink, Julia Schroeder, Eric Alexander Miska, Katharina Gapp

RNA Polymerase II is involved in 18S and 25S ribosomal RNA transcription, in Candida albicans. Jacob Fleischmann, Miguel Angel Rocha, Peter V Hauser

Targeting of RBM10 to S1-1 Nuclear Bodies: Targeting Sequences and its Biological Significance. Ling-Yu Wang, Sheng-Jun Xiao, Hiroyuki Kunimoto, Kazuaki Tokunaga, Hirotada Kojima, Masatsugu Kimura, Takahiro Yamamoto, Naoki Yamamoto, Zhao Hong, Koji Nishio, Hideo Yamane, Tokio Tani, Koichi Nakajima, Hiroyoshi Iguchi, Akira Inoue

Termination of non-coding transcription in yeast relies on both a CTD-interaction domain and a CTD-mimic in Sen1. Zhong Han, Olga Jasnovidova, Agnieszka Tudek, Karel Kubicek, Domenico Libri, Richard Stefl, Odil Porrua

Divergence of piRNA pathway proteins affects piRNA biogenesis but not TE transcript level. Luyang Wang, Daniel Barbash, Erin Kelleher

No evidence of functional co-adaptation between clustered microRNAs. Antonio Marco

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

Targeted Long-Read RNA Sequencing Demonstrates Transcriptional Diversity Driven by Splice-Site Variation in MYBPC3. Alexandra Dainis, Elizabeth Tseng, Tyson A Clark, Ting Hon, Matthew Wheeler, Euan Ashley

Early genome activation in Drosophila is extensive with an initial tendency for aborted transcripts and retained introns. Jamie C Kwasnieski, Terry L Orr-Weaver, David P Bartel

MicroRNA-222 regulates fluid shear stress-induced human nucleus pulposus cells degeneration through affecting c-Fos expression. Gaixiong Miao, Yicun Yao, Baoqing Ye, Libing Dai, Guowei Liang, Haixiong Miao , Yicun Yao , Baoqing Ye

Protein features for assembly of the RNA editing helicase 2 subcomplex (REH2C) in Trypanosome holo-editosomes. Vikas Kumar, Pawan K. Doharey, Shelly Gulati, Joshua Meehan, Mary Grace Martinez, Karissa Hughes, Blaine H.M. Mooers, Jorge Cruz-Reyes

Measuring amber initiator tRNA orthogonality in a genomically recoded organism. Russel M. Vincent, Bradley W. Wright, Paul R. Jaschke

RAI1 Regulates Activity-Dependent Nascent Transcription and Synaptic Scaling. Patricia M. Garay, Alex Chen, Takao Tsukahara, Rafi Kohen, J. Christian Althaus, Margarete A. Wallner, Roman J. Giger, Michael A. Sutton, Shigeki Iwase

AGO1 in association with NEAT1 lncRNA contributes to nuclear and 3D chromatin architecture in human cells. Muhammad Shuaib, Krishna Mohan Parsi, Hideya Kawaji, Manjula Thimma, Sabir Abdu Adroub, Alexandre Fort, Yanal Ghosheh, Tomohiro Yamazaki, Taro Mannen, Loqmane Seridi, Bodor Fallatah, Waad Albawardi, Timothy Ravasi, Piero Carninci, Tetsuro Hirose, Valerio Orlando

RNA preprints: W2/2019

Splicing inhibition enhances the antitumor immune response through increased tumor antigen presentation and altered MHC-I immunopeptidome. Alison Pierson, Romain Darrigrand, Marine Rouillon, Mathilde Boulpicante, Zafiarisoa Dolor Renko, Camille Garcia, Michael Ghosh, Marie-Charlotte Laiguillon, Camille Lobry, Mouad Alami, Sebastien Apcher

Inhibition of miR-22-3p reduces kidney disease associated with systemic lupus erythematosus. Danielle L Michell, Ashley Faust, Jared L Moore, Brenna D Appleton, Michelle Ormseth, Marisol Ramirez-Solano, Quanhu Sheng, Joseph F Solus, C. Michael Stein, Kasey C Vickers, Amy S Major

LncRNA Dnmt3aos regulates Dnmt3a expression leading to aberrant DNA methylation in macrophage polarization. Xueqin Li, Yingying Zhang, Mengying Zhang, Xiang Kong, Hui Yang, Min Zhong, Weiya Pei, Yang Xu, Xiaolong Zhu, Tianbing Chen, Jingjing Ye, Kun Lv

Hundreds of yeast mRNAs form a separately addressable, translation elongation-controlled regulon. Eleanna Kazana, Tobias von der Haar

Compartmentalized nonsense-mediated mRNA decay regulates synaptic plasticity and cognitive function via GluR1 signaling. Michael Notaras, Megan Allen, Francesco Longo, Nicole Volk, Miklos Toth, Noo Li Jeon, Eric Klann, Dilek Colak

Purification of Cross-linked RNA-Protein Complexes by Phenol-Toluol Extraction. Erika C Urdaneta, Carlos H Vieira-Vieira, Timon Hick, Hans-Herrmann Wessels, Davide Figini, Rebecca Moschall, Jan Medenbach, Uwe Ohler, Sander Granneman, Matthias Selbach, Benedikt M Beckmann

Tristetraprolin/ZFP36 regulates the turnover of autoimmune-associated HLA-DQ mRNAs. Laura Pisapia, Russell Hamilton, Federica FARINA, Vito D’Agostino, Pasquale Barba, Maria Strazzullo, Alessandro Provenzani, Carmela Gianfrani, Giovanna Del Pozzo

Interaction of modified oligonucleotides with nuclear proteins, formation of novel nuclear structures and sequence-independent effects on RNA processing. Loren L Flynn, Ruohan Li, May T Aung-Htut, Ianthe L Pitout, Jack A L Cooper, Alysia Hubbard, Lisa Griffiths, Charles Bond, Steve D Wilton, Archa H Fox, Sue Fletcher

RNA polymerase clamp movement aids dissociation from DNA but is not required for RNA release at intrinsic terminators. Michael J Bellecourt, Ananya Ray-Soni, Alex Harwig, Rachel Anne Mooney, Robert Landick

A novel rationale for targeting FXI: Insights from the hemostastic miRNA targetome for emerging anticoagulant strategies. Jamie Nourse, Sven Danckwardt

Polymerase recycling contributes to transcriptional noise. Massimo Cavallaro, Mark D. Walsh, Matt Jones, James Teahan, Simone Tiberi, Barbel Finkenstadt, Daniel Hebenstreit

MIR2052HG regulates ERα levels and aromatase inhibitor resistance through LMTK3 by recruiting EGR1. Junmei Cairns, James Ingle, Krishna Kalari, Lois E Shepherd, Michiaki Kubo, Matthew P Goetz, Richard M. Weinshilboum, Liewei Wang

Tau-mediated Disruption of the Spliceosome Triggers Cryptic RNA-splicing and Neurodegeneration in Alzheimer’s Disease. Yi-Chen Hsieh, Caiwei Guo, Hari K. Yalamanchili, Measho Abreha, Rami Al-Ouran, Yarong Li, Eric B. Dammer, James J. Lah, Allan I. Levey, David A. Bennett, Philip L. De Jager, Nicholas T. Seyfried, Zhandong Liu, Joshua M. Shulman

Interactions between dosage compensation complex components Msl-1, Msl-2 and NURF component NURF301 with long non-coding RNA gene hsrω. Deo Prakash Chaturvedi

The mir-35 family links maternal germline sex to embryonic viability in C. elegans. Lars Kristian Benner, Katherine Perkins Prothro, Katherine McJunkin

RBM10 variants and RBM5 involve in alternative splicing of RBM10v1 pre-mRNA: RBM10v1 includes its own exon 4, but RBM10v2 and RBM5 skip it. Koji Nishio

Deep neural networks for interpreting RNA binding protein target preferences. Mahsa Ghanbari, Uwe Ohler

Guanine content of microRNAs is associated with their tumor suppressive and oncogenic roles in lung and breast cancers. Amit Cohen, Mario Alberto Burgos-Aceves, Yoav Smith

DOT1L suppresses nuclear RNAi originating from enhancer elements in Caenorhabditis elegans. Ruben Esse, Ekaterina Gushchanskaia, Avery Lord, Alla Grishok

Modeling the dynamics of Let-7-coupled gene regulatory networks linking cell proliferation to malignant transformation. Claude Gerard, Frederic Lemaigre, Didier Gonze

RNA preprints: W1/2019

Dysregulation of splicing-related proteins in prostate cancer is controlled by FOXA1. John Gordon Foster, Rebecca Arkell, Marco Del Giudice, Chinedu Anene, Andrea Lauria, John Daniel Gerard Kelly, Nicholas Robert Lemoine, Salvatore Oliviero, Matteo Cereda, Prabhakar Rajan

PTBP1 mRNA isoforms and regulation of their translation. Luisa M Arake de Tacca, Mia C Pulos, Stephen N Floor, Jamie Cate

Detection of circulating extracellular mRNAs by modified small RNA-sequencing analysis. Kemal Marc Akat, Youngmin Anna Lee, Arlene Hurley, Pavel Morozov, Klaas E.A. Max, Miguel Brown, Kimberly Bogardus, Anuoluwapo Sopeyin, Kai Hildner, Thomas Diacovo, Markus F. Neurath, Martin Borggrefe, Thomas Tuschl

A widespread Xrn1-resistant RNA motif composed of two short hairpins. Ivar W Dilweg, Alexander P Gultyaev, Rene Olsthoorn

Secretion of an Argonaute protein by a parasitic nematode and the evolution of its siRNA guides. Franklin Wang-Ngai Chow, Georgios Koutsovoulos, Cesaré Ovando-Vázquez, Kyriaki Neophytou, Dominik R Laetsch, Jose R Bermúdez-Barrientos, Sujai Kumar, Elaine Robertson, Julie M Claycomb, Mark Blaxter, Cei Abreu-Goodger, Amy H Buck

Genetic interactions of histone acetyl-transferase enzymes encoding genes Gcn5 and Mof with hsrω lncRNA gene. Deo Prakash Chaturvedi

Disentangling sRNA-Seq data to study RNA communication between species. Jose Roberto Bermudez-Barrientos, Obed Ramirez-Sanchez, Franklin WN Chow, Amy H Buck, Cei Abreu-Goodger

Detecting Circular RNA from High-throughput Sequence Data with de Bruijn Graph. Xin Li, Yufeng Wu

SpliceV: Analysis and publication quality printing of linear and circular RNA splicing, expression and regulation. Nathan A Ungerleider, Erik K Flemington

Trapping a somatic endogenous retrovirus into a germline piRNA cluster immunizes the germline against further invasion. Celine Duc, Marianne Yoth, Nolwenn Mouniee, Silke Jensen, Chantal Vaury, Emilie Brasset

In vitro analysis of RNA polymerase II elongation complex dynamics. Yoo Jin Joo, Scott B. Ficarro, Yujin Chun, Jarrod A. Marto, Stephen Buratowski

Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features. Lisa Barros De Andrade e Sousa, Iris Jonkers, Laurene Syx, Julie Chaumell, Christel Picard, Benjamin Foret, Chong-Jian Chen, John T. Lis, Edith Heard, Edda G. Schulz, Annalisa Marsico

Overexpression of long noncoding RNA GAS5 suppresses tumorigenesis and development of gastric cancer by sponging miR-106a-5p through the Akt/mToR pathway. Shuaijun Dong, Xiefu Zhang, Dechun Liu

Systematic identification and characterization of Aedes aegypti long noncoding RNAs. Azali Azlan, Sattam M. Obeidat, Muhammad Amir Yunus, Ghows Azzam

Role of MPK4 in pathogen-associated molecular pattern-triggered alternative splicing in Arabidopsis. Bazin Jeremie, Kiruthiga Gayathri Mariappan, Thomas Blein, Ronny Volz, Martin Crespi, Heribert Hirt

Tombusvirus p19 captures RNase III-cleaved double-stranded RNAs formed by overlapping sense and antisense transcripts in E. coli. Linfeng Huang, Padraig Deighan, Jingmin Jin, Yingxue Li, Elaine Lee, Shirley S. Mo, Heather Hoover, Sahar Abubucker, Nancy Finkel, Larry McReynolds, Ann Hochschild, Judy Lieberman

Quantitative proteomics reveals key roles for post-transcriptional gene regulation in the molecular pathology of FSHD. Sujatha Jagannathan, Yuko Ogata, Philip Gafken, Stephen J Tapscott, Robert K Bradley

Evolutionary implications of the microRNA- and piRNA complement of Lepidodermella squamata (Gastrotricha). Bastian Fromm, Juan Pablo Tosar, Felipe Aguilera, Marc Riemer Friedlander, Lutz Bachmann, Andreas Hejnol

RNA preprints: W52/2018

A systems view of spliceosomal assembly and branchpoints with iCLIP. Michael Briese, Nejc Haberman, Christopher Sibley, Anob Chakrabarti, Zhen Wang, Julian Konig, David Perera, Vihandha Wickramasinghe, Ashok Venkitaraman, Nicholas Luscombe, Christopher Smith, Tomaz Curk, Jernej Ule

RNA Polymerase II Independent Recruitment of SPT6 at Transcription Start Sites in Arabidopsis. Chen Chen, Jie Shu, Chenlong Li, Raj K. Thapa, Vi Nguyen, Kangfu Yu, Zechun Yuan, Susanne E. Kohalmi, Jun Liu, Frederic Marsolais, Shangzhi Huang, Yuhai Cui

Structures of the Human Spliceosomes Before and After Release of the Ligated Exon. Xiaofeng Zhang, Xiechao Zhan, Chuangye Yan, Wenyu Zhang, Dongliang Liu, Jianlin Lei, Yigong Shi

Multiplexed detection of RNA using MERFISH and branched DNA amplification. Chenglong Xia, Hazen P Babcock, Jeffrey R Moffitt, Xiaowei Zhuang

RNA sequencing identifies dysregulated circular RNAs in early-stage breast cancer. Vittal Rangan Arvinden, Deva Magendhra Rao Arinagiri Kuha, Meenakumari Balaiah, Priya Ramanathan, Shirley Sundersingh, Sridevi Velusami, Rajkumar Thangarajan, Zdenko Herceg, Samson Mani

A Regulatory Loop between the Retinoid-Related Orphan Nuclear Receptor NHR-23 and let-7 family microRNAs Modulates the C. elegans Molting Cycle. Ruhi Patel, Alison R Frand

Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API. Thomas Desvignes, Phillipe Loher, Karen Eilbeck, Jeffery Ma, Gianvito Urgese, Bastian Fromm, Jason Sydes, Ernesto Aparicio-Puerta, Victor Barrera, Roderic Espin, Eric Londin, Aristeidis G Telonis, Elisa Ficarra, Marc R Friedlander, John H Postlethwait, Isidore Rigoutsos, Michael Hackenberg, Ioannis S Vlachos, Marc K. Halushka, Lorena Pantano

Transgenic Mice and Pluripotent Stem Cells Express EGFP under the Control of miR-302 Promoter. Karim Rahimi, Sara Parsa, Mehrnoush Nikzaban, Seyed Javad Mowla, Fardin Fathi

The miR-338-3p involve in response to acute radiation syndrome by targeting DYRK2 in Tibet minipig. Wang Yujue, Yue Min, Guo Kai, Wu Shaojie, Tian Yuguang

miRNAs, target genes expression and morphological analysis on the heart in gestational protein-restricted offspring. José A.R. Gontijo, Heloisa Balan Assalin, Patrícia Aline Boer

A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs. Alexandra L McCorkindale, Philipp Wahle, Sascha Werner, Irwin Jungreis, Peter Menzel, Chinmay J Shukla, Ruben Lopes Pereira Abreu, Rafael Irizarry, Irmtraud Meyer, Manolis Kellis, Robert P Zinzen

Differential expression of microRNAs in Alzheimer’s disease brain, blood and cerebrospinal fluid: a systematic review and meta-analysis. Petros Takousis, Angélique Sadlon, Jessica Schulz, Inken Wohlers, Valerija Dobricic, Lefkos Middleton, Christina M. Lill, Robert Perneczky, Lars Bertram

A machine-learning classifier trained with microRNA ratios to distinguish melanomas from nevi. Rodrigo Torres, Ursula E Lang, Miroslav Hejna, Samuel J Shelton, Nancy M Joseph, Alan Hunter Shain, Iwei Yeh, Maria L Wei, Michael C. Oldham, Boris C Bastian, Robert L Judson-Torres

A tRNA modification balances carbon and nitrogen metabolism by regulating phosphate homeostasis, to couple metabolism to cell cycle progression. Ritu Gupta, Adhish Walvekar, Shun Liang, Zeenat Rashida, Premal Shah, Sunil Laxman

Detection of a novel mutation G511T in the 530 loop in 16S rRNA in multi drugs resistant Mycobacterium tuberculosis isolated from Sudanese patients. Yousif Mohammed Alfatih, Abeer Babiker Idris, Hadeel Gassim Hassan, Eman O M Nour, Nihad M A Elhaj, Salah-Eldin El-Zaki, Muataz M Eldirdery, Rahma H Ali, Nuha Y Ibrahim, Asrar M Elegail, Mohamed Ahmed Salih

miRsponge: an R/Bioconductor package for the identification and analysis of miRNA sponge interaction networks and modules. Junpeng Zhang, Lin Liu, Taosheng Xu, Yong Xie, Chunwen Zhao, Jiuyong Li, Thuc Duy Le

Biophysical characterizations of the recognition of the AAUAAA polyadenylation signal. Keith Hamilton, Yadong Sun, Liang Tong

Proteasome inhibitor-induced modulation reveals the spliceosome as a specific therapeutic vulnerability in multiple myeloma. Hector Han-Li Huang, Ian D. Ferguson, Alexis M. Thornton, Christine Y. T. Lam, Yu-Hsiu Tony Lin, Prabhakar Bastola, Margarette C. Mariano, Makeba D. Marcoulis, Julia Malato, Paul Phojanakong, Byron C. Hann, Angela N Brooks, Arun P. Wiita