RNA preprints: W8/2019

Precise removal of Calm1 long 3′ UTR isoform by CRISPR-Cas9 genome editing impairs dorsal root ganglion development in mice. Hannah N Gruner, Bongmin Bae, Maebh Lynch, Daniel Oliver, Kevin So, Grant S Mastick, Wei Yan, Pedro Miura

Phospho-sRNA-seq reveals extracellular mRNA/lncRNA fragments as potential biomarkers in human plasma. Maria D. Giraldez, Ryan M. Spengler, Alton Etheridge, Annika Jane Goicochea, Missy Tuck, Sung Won Choi, David J. Galas, Muneesh Tewari

Local-to-global signal transduction at the core of the Mn2+ sensing riboswitch. Krishna C Suddala, Ian R Price, Michal Janeček, Petra Kührová, Shiba Dandpat, Jiří Šponer, Pavel Banáš, Ailong Ke, Nils G Walter

Comprehensive Assessment of Sequence and Expression of Circular-RNAs in Progenitor Cell Types of the Developing Mammalian Cortex. Martina Dori, Leila Haj Abdullah Alieh, Daniel Cavalli, Simone Massalini, Mathias Lesche, Andreas Dahl, Federico Calegari

Neutrophil-extracellular trap-associated RNA (naRNA) and LL37 enable self-amplifying inflammation in psoriasis. 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

Conditional Prediction of RNA Secondary Structure Using NMR Chemical Shifts. Kexin Zhang, Aaron Terrence Frank

dbMTS: a comprehensive database of putative human microRNA target site SNVs and their functional predictions. Chang Li, Michael D. Swartz, Bing Yu, Xiaoming Liu

Single molecule real time (SMRT) full length RNA-sequencing reveals novel and distinct mRNA isoforms in human bone marrow cell subpopulations. Anne Deslattes Mays, Marcel O Schmidt, Garrett Graham, Elizabeth Tseng, Primo Baybayan, Robert Sebra, Sanda Miloslav, Jean-Baptiste Mazarati, Anna T Riegel, Anton Wellstein

Transcriptome stability profiling identifies novel and functional MIRNA targets in melanoma cells. Piyush Joshi, Tatsuya Seki, Shinobu Kitamura, Andrea Bergano, Bongyong Lee, Ranjan J Perera

MicroRNA-mediated control of developmental lymphangiogenesis. Hyun Min Jung, Ciara Hu, Alexandra M Fister, Andrew E Davis, Daniel Castranova, Van N Pham, Lisa M Price, Brant M Weinstein

Automated analysis of small RNA datasets with RAPID. Sivarajan Karunanithi, Martin Simon, Marcel H Schulz

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

ACValidator: a novel assembly-based approach for in silico validation of circular RNAs. Shobana Sekar, Philipp Geiger, Jonathan Adkins, Geidy Serrano, Thomas Beach, Winnie S Liang

mRNA adenosine methylase (MTA) deposits m6A on pri-miRNAs to modulate miRNA biogenesis in Arabidopsis thaliana. Susheel Sagar Bhat, Dawid Bielewicz, Natalia Grzelak, Tomasz Gulanicz, Zsuzsanna Bodi, Lukasz Szewc, Matuesz Bajczyk, Jakub Dolata, Dariusz J. Smolinski, Rupert G. Fray, Artur Jarmolowski, Zofia Szweykowska-Kulinska

Dengue and Zika virus 5’-UTRs harbor IRES functions. Yutong Song, JoAnn Mugavero, Charles B Stauft, Eckard Wimmer

Single mRNP analysis by super-resolution microscopy and fluorescence correlation spectroscopy reveals that small mRNP granules represent mRNA singletons. Angels Mateu-Regue, Jan Christiansen, Frederik Otzen Bagger, Christian Hellriegel, Finn Cilius Nielsen

Systematic identification of circular RNAs and corresponding regulatory networks unveil their potential roles in the midgut of Apis cerana cerana workers. Dafu Chen, Huazhi Chen, Yu Du, Sihai Geng, Cuiling Xiong, Yanzhen Zheng, Chunsheng Hou, Qingyun Diao, Rui Guo

Identifying A- and P-site locations on ribosome-protected mRNA fragments using Integer Programming. Nabeel Ahmed, Pietro Sormanni, Prajwal Ciryam, Michele Vendruscolo, Christopher M Dobson, Edward P O’Brien

Programmable DNA cleavage by Ago nucleases from mesophilic bacteria Clostridium butyricum and Limnothrix rosea. Anton Kuzmenko, Denis Yudin, Sergei Ryazansky, Andrey Kulbachinskiy, Alexei Aravin

Tissue-specific mouse mRNA isoform networks. Gaurav Kandoi, Julie Dickerson

ANP32A and ANP32B are key factors in the Rev dependent CRM1 pathway for nuclear export of HIV-1 unspliced mRNA. Yujie Wang, Haili Zhang, Lei Na, Cheng Du, Zhenyu Zhang, Yonghui Zheng, Xiaojun Wang

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RNA preprints: W7/2019

An alternatively spliced zebrafish jnk1a transcript has an essential and non-redundant role in development of the first heart field derived proximal ventricular chamber. Adrian Santos-Ledo, Sam J Washer, Tamilvendhan Dhanaseelan, Paul Chrystal, Tania Papoutsi, Deborah Henderson, Bill Chaudhry

How the initiating ribosome copes with (p)ppGpp to translate mRNAs. Daria S Vinogradova, Pavel Kasatsky, Elena Maksimova, Victor Zegarra, Alena Paleskava, Andrey L Konevega, Pohl Milon

Comprehensive circular RNA expression profiles in intermuscular fat from lean and obese pigs. Zhiguo Miao, Jinzhou Zhang, Shan Wang, Panpeng Wei

Oligoribonuclease functions as a diribonucleotidase to bypass a key bottleneck in RNA degradation. Soo-Kyoung Kim, Justin D Lormand, Cordelia A Weiss, Karin A Eger, Husan Turdiev, Asan Turdiev, Wade C Winkler, Holger Sondermann, Vincent T Lee

Full-length mRNA sequencing reveals principles of poly(A) tail length control. Ivano Legnini, Jonathan Alles, Nikos Karaiskos, Salah Ayoub, Nikolaus Rajewsky

Alanine tRNAs translate environment into behavior in Caenorhabditis elegans. Diana Andrea Fernandes De Abreu, Thalia Salinas-Giege, Laurence Marechal-Drouard, Jean-Jacques Remy

lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation. Kaveh Daneshvar, M. Behfar Ardehali, Isaac A Klein, Arcadia J Kratkiewicz, Chan Zhou, Amin Mahpour, Brett M Cook, Wenyang Li, Joshua V Pondick, Sean P Moran, Richard A Young, Robert E Kingston, Alan C Mullen

Glia-derived exosomal miR-274 targets Sprouty in trachea and synaptic boutons to modulate growth and responses to hypoxia. Yi-Wei Tsai, Hsin-Ho Sung, Jian-Chiuan Li, Chun-Yen Yeh, Pei-Yi Chen, Ying-Ju Cheng, Chun-Hong Chen, Yu-Chen Tsai, Cheng-Ting Chien

Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR. Gemma Danks, Heloisa Galbiati, Martina Raasholm, Yamila N Torres Cleuren, Eivind Valen, Pavla Navratilova, Eric M Thompson

A mechanism for ligand gated strand displacement in ZTP riboswitch transcription regulation. Eric J Strobel, Luyi Cheng, Katherine E Berman, Paul D Carlson, Julius B Lucks

Structure of the Ebola virus nucleoprotein – RNA complex. Robert N Kirchdoerfer, Erica Ollmann Saphire, Andrew B Ward

Control of Shoot Meristem Size by an Aminoacyl tRNA Synthetase, OKI1, in Arabidopsis. Munenori Kitagawa, Rachappa S Balkunde, Huyen Thanh Bui, David S Jackson

MicroRNA-143 plays a protective role in ischemia-induced retinal neovascularization. Jiang-Hui Wang, Jinying Chen, Damien Ling, Leilei Tu, Vikrant Singh, Moeen Riaz, Fan Li, Selwyn M Prea, Zheng He, Bang V Bui, Alex W Hewitt, Peter van Wijngaarden, Gregory J Dusting, Guei-Sheung Liu

Decoding and recoding phase behavior of TDP43 reveals that phase separation is not required for splicing function. Hermann Broder Schmidt, Ariana Barreau, Rajat Rohatgi

MiR-590-5p sensitises pancreatic ductal adenocarcinoma cells by blocking autophagy via targeting ATG3. Leping Yang, Fazhao Li, Jun He, Susun Liu, Yawei Zhang

The Telomerase Reverse Transcriptase (TERT) and p53 Regulate Mammalian PNS and CNS Axon Regeneration downstream of c-Myc. JIn-Jin Ma, Ren-Jie Xu, Xin Ju, Wei-Hua Wang, Zong-Ping Luo, Chang-Mei Liu, Lei Yang, Bin Li, Jian-Quan Chen, Bin Meng, Hui-Lin Yang, Feng-Quan Zhou, Saijilafu

Metabolic balancing by miR-276 shapes the mosquito reproductive cycle and Plasmodium falciparum development. Lena Lampe, Marius Jentzsch, Elena A Levashina

Exosome-mediated MIR211 modulates tumor microenvironment via the DUSP6-ERK5 axis and contributes to BRAFV600E inhibitor resistance in melanoma. Bongyong Lee, Anupama Sahoo, John Marchica, Junko Sawada, Sanjay Sahoo, Fabiana I. A. L. Layng, Darren Finlay, Joseph Mazar, Piyush Joshi, Masanobu Komatsu, Kristiina Vuori, Garth Powis, Petrus R. de Jong, Animesh Ray, Ranajan J. Perera

mRNA structure regulates protein expression through changes in functional half-life. David M. Mauger, B. Joseph Cabral, Vladimir Presnyak, Stephen V. Su, David W. Reid, Brooke Goodman, Kristian Link, Nikhil Khatwani, John Reynders, Melissa J. Moore, Iain J. McFadyen

Comprehensive network analysis reveals alternative splicing-related lncRNAs in hepatocellular carcinoma. Junqing Wang, Yixin Chen, Keli Xu, Yin-yuan Mo, Yunyun Zhou

Expression changes confirm predicted single nucleotide variants affecting mRNA splicing. Eliseos J Mucaki, Peter K Rogan

Changes in Ovary Transcriptome and Alternative Splicing at Estrus from Xiang Pigs with Large and Small Litter Size. Fu P Zhang, Xue Q Ran

The length of the expressed 3′ UTR is an intermediate molecular phenotype linking genetic variants to complex diseases. Elisa Mariella, Federico Marotta, Elena Grassi, Stefano Gilotto, Paolo Provero

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

Analysis of genetically driven alternative splicing identifies FBXO38 as a novel COPD susceptibility gene. Aabida Saferali, Jeong H Yun, Margaret M Parker, Phuwanat Sakornsakolpat, Robert P Chase, Andrew Lamb, Brian D Hobbs, Marike H Boezen, Xiangpeng Dai, Kim de Jong, Terri H Beaty, Wenyi Wei, Xiaobo Zhou, Edwin K Silverman, Michael H Cho, Peter J Castaldi, Craig P Hersh, COPDGene Investigators, and the International COPD Genetics Consortium Investigators

SCANVIS: a tool for SCoring, ANnotating and VISualing splice junctions. Phaedra Agius, Heather Geiger, Nicolas Robine

Egalitarian binding partners, Dynein Light Chain and Bicaudal-D, act sequentially to link mRNA to the Dynein motor. Chandler H. Goldman, Rajalakshmi Veeranan-Karmegam, Hannah Neiswender, Graydon B. Gonsalvez

A universal fluorescence-based toolkit for real-time quantification of DNA and RNA nuclease activity. Emily C Sheppard, Sally Rogers, Nicholas J Harmer, Richard Chahwan

Genome-wide identification and analysis of A-to-I RNA editing events in the malignantly transformed cell lines from BEP2D induced by α-particles radiation. Qiaowei Liu, Hao Li, Lukuan You, Tao Li, Lingling Li, Pingkun Zhou, Xiaochen Bo, Hebing Chen, Xiaohua Chen, Yi Hu

Evaluations of short telomere risk-associated single nucleotide polymorphisms in telomerase reverse transcriptase gene on telomere length maintenance. Jialin Xu, Matthew A Trudeau, Andrew J Sandford, Judy MY Wong

Identification of lncRNAs associated with early stage breast cancer and their prognostic implications. Deva Magendhra Rao Arunagiri Kuha, Krishna Patel, Sunitha Korivi Jyothi, Meenakumari Balaiah, Shirley Sundersingh, Sridevi Velusami, Rajkumar Thangarajan, Akhilesh Pandey, Aditi Chatterjee, Harsha Gowda, Samson Mani

Environmental pheromone and endocrine signals correct heterochronic developmental phenotypes caused by insufficient expression of let-7 family microRNAs in C. elegans. Orkan Ilbay, Victor Ambros

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

A novel retroviral vector system to analyze expression from mRNA with retained introns using fluorescent proteins and flow cytometry. Patrick E.H. Jackson, Jing Huang, Monika Sharma, Sara K. Rasmussen, Marie-Louise Hammarskjold, David Rekosh

Modeling ribosome dwell times and relationships with tRNA loading and codon usage in mammals. Cedric Gobet, Benjamin Weger, Julien Marquis, Eva Martin, Frederic Gachon, Felix Naef

PLIT: An alignment-free computational tool for identification of long non-coding RNAs in plant transcriptomic datasets. S. Deshpande, J. Shuttleworth, J. Yang, S. Taramonli, M. England

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

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