RNA preprints: W14/2019

Circular RNA circGTIC1 drives gastric TIC self-renewal to initiate gastric tumorigenesis and metastasis. Liyan Wang, Bin Li, Xuhua Xiao, Xiaoyuan Yi, Feifei He

Risk variant in miR-544a binding site in CCDC170 is associated with osteoporosis. Xinhong Liu, Yang Wang, Qin Tan, Yunqi He, Xin Zhao

mRNA Degradation Rates Are Coupled to Metabolic Status in Mycobacteria. Diego A. Vargas-Blanco, Ying Zhou, Luis Gutierrez Zamalloa, Tim Antonelli, Scarlet S. Shell

FilTar: Using RNA-Seq data to improve microRNA target prediction accuracy in animals. Thomas Bradley, Simon Moxon

A heterochromatin-specific RNA export pathway facilitates piRNA production. Mostafa F. ElMaghraby, Peter Refsing Andersen, Florian Pühringer, Katharina Meixner, Thomas Lendl, Laszlo Tirian, Julius Brennecke

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

Molecular determinants of metazoan tricRNA biogenesis. Casey A. Schmidt, Joseph D. Giusto, Alicia Bao, Anita K. Hopper, A. Gregory Matera

RNA base pairing complexity in living cells visualized by correlated chemical probing. Anthony M. Mustoe, Nicole Lama, Patrick S. Irving, Samuel W. Olson, Kevin M. Weeks

dSreg: A bayesian model to integrate changes in splicing and RNA binding protein activity. Carlos Martí-Gómez, Enrique Lara-Pezzi, Fátima Sánchez-Cabo

MicroRNAs expressed from FSHR and aromatase genes target important ovarian functions. Ilmatar Rooda, Birgitta Kaselt, Andres Salumets, Agne Velthut-Meikas

Fast and unbiased purification of RNA-protein complexes after UV cross-linking. Erika C Urdaneta, Benedikt M Beckmann

Codon Bias Confers Stability to mRNAs via ILF2 in Humans. Fabian Hia, Sheng Fan Yang, Yuichi Shichino, Masanori Yoshinaga, Yasuhiro Murakawa, Alexis Vandenbon, Akira Fukao, Toshinobu Fujiwara, Markus Landthaler, Tohru Natsume, Shungo Adachi, Shintaro Iwasaki, Osamu Takeuchi

Quantitative Principles of cis-translational control by general mRNA sequence features in eukaryotes. Jingyi Jessica Li, Guo-Liang Chew, Mark D. Biggin

TDP-43 proteinopathy impairs neuronal mRNP granule mediated postsynaptic local translation and mRNA metabolism. Chia-En Wong, Kuen-Jer Tsai

The RNA binding protein DAZL functions as repressor and activator of maternal mRNA translation during oocyte maturation. Cai-Rong Yang, Gabriel Rajkovic, Enrico Maria Daldello, Xuan G. Luong, Jing Chen, Marco Conti

The rs6505162 C>A polymorphism in the miRNA-423 gene exhibits a protective element of coronary artery in a southern Chinese population with Kawasaki disease. Jiawen Li, Jinxin Wang, Xiaoping Su, Zhiyong Jiang, Xing Rong, Xueping Gu, Huixian Qiu, Lanlan Zeng, Hao Zheng, Xiaoqiong Gu, Maoping Chu

SSD1 suppresses phenotypes induced by the lack of Elongator-dependent tRNA modifications. Fu Xu, Anders Bystrom, Marcus Johansson

The piRNA Response to Retroviral Invasion of the Koala Genome. Tianxiong Yu, Birgit S. Koppetsch, Keith Chappell, Sara Pagliarani, Stephen Johnston, Zhiping Weng, William E. Theurkauf

Drosophila ribosomal protein S5b is essential for oogenesis and interacts with distinct RNAs. Jian Kong, Hong Han, Julie Bergalet, Louis Philip Benoit Bouvrette, Greco Hernández, Nam Sung Moon, Hojatollah Vali, Éric Lécuyer, Paul Lasko

Interplay Between Short-range Attraction and Long-range Repulsion Controls Reentrant Liquid Condensation of Ribonucleoprotein-RNA Complexes. Ibraheem Alshareedah, Taranpreet Kaur, Jason Ngo, Hannah Seppala, Liz-Audrey Djomnang Kounatse, Wei Wang, Mahdi Muhammad Moosa, Priya R Banerjee

Translation and Transforming Activity of a Circular RNA from Human Papillomavirus. Jiawei Zhao, Eunice E Lee, Jiwoong Kim, Bahir Chamseddin, Rong Yang, Yang Xie, Xiaowei Zhan, Richard Wang

3′-UTR shortening disrupts ceRNA crosstalk of housekeeping genes resulting in subtype-specific breast cancer development. Fan Zhenjiang, Soyeon Kim, Brenda Diergaarde, Hyun Jung Park

In silico analysis of coding SNPs and 3′-UTR associated miRNAs in DCAF17 gene that may affect the regulation and pathogenesis of Woodhouse-Sakati Syndrome. abdelrahman hamza abdelmoneim Sr., Asia M Elrashied, Alaa I Mohammed, Sara A Mirghani, Rania E Osman, Esraa O Gadim, Mohamed A Salih

Alternative Polyadenylation Modifies Target Sites of MicroRNAs with Clinical Potential for Breast Cancer Progression. Soyeon Kim, Yulong Bai, Brenda Diergaarde, George C. Tseng, Hyun Jung Park

BPPart and BPMax: RNA-RNA Interaction Partition Function and Structure Prediction for the Base Pair Counting Model. Ali Ebrahimpour-Boroojeny, Sanjay Rajopadhye, Hamidreza Chitsaz

 

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RNA preprints: W13/2019

Inhibition of arterivirus RNA synthesis by cyclophilin inhibitors is counteracted by mutations in replicase transmembrane subunits. Adriaan H. de Wilde, A. Linda Boomaars-van der Zanden, Anja W. M. de Jong, Montserrat Barcéna, Eric J. Snijder, Clara C. Posthuma

Codon Optimality Confers GC-Rich-Induced Stability to mRNAs in Humans. Fabian Hia, Sheng Fan Yang, Yuichi Shichino, Masanori Yoshinaga, Yasuhiro Murakawa, Alexis Vandenbon, Akira Fukao, Toshinobu Fujiwara, Markus Landthaler, Tohru Natsume, Shungo Adachi, Shintaro Iwasaki, Osamu Takeuchi

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, Yong-Hui Zheng, Xiaojun Wang

MuStARD: a Deep Learning method for intra- and inter- species scanning identification of small RNA molecules. Georgios K Georgakilas, Andrea Grioni, Konstantinos G Liakos, Eliska Malanikova, Fotis C Plessas, Panagiotis Alexiou

DDX3 depletion selectively represses translation of structured mRNAs. Lorenzo Calviello, Srivats Venkataramanan, Karol J. Rogowski, Emanuel Wyler, Malvika Tejura, Bao Thai, Jacek Krol, Witold Filipowicz, Markus Landthaler, Stephen N. Floor

Metabolic labeling of RNAs uncovers hidden features and dynamics of the Arabidopsis thaliana transcriptome. Emese Xochitl Szabo, Philipp Reichert, Marie-Kristin Lehniger, Marilena Ohmer, Marcella de Francisco Amorim, Udo Gowik, Christian Schmitz-Linneweber, Sascha Laubinger

Cross-talk between m6A and m1A regulators, YTHDF2 and ALKBH3 fine-tunes mRNA expression. Nga Lao, Niall Barron

An RNA guanine quadruplex regulated pathway to TRAIL-sensitization by DDX21. Ewan K.S. McRae, Steven J. Dupas, Evan P. Booy, Ramanaguru S. Piragasam, Richard P. Fahlman, Sean A. McKenna

Efficient and specific oligo-based depletion of rRNA. Amelie J. Kraus, Benedikt G. Brink, T. Nicolai Siegel

Xrn1 activity broadly represses RNA polymerase II occupancy at mammalian but not viral promoters during herpesvirus infection. Ella N Hartenian, Britt A Glaunsinger

The PIWI/piRNA response is relaxed in a rodent that lacks mobilizing transposable elements. Michael W. Vandewege, Roy N. Patt II, Dana K. Merriman, David A. Ray, Federico G. Hoffmann

Time-resolved NMR monitoring of tRNA maturation. Pierre Barraud, Alexandre Gato, Matthias Heiss, Marjorie Catala, Stefanie Kellner, Carine Tisné

Splicing conservation signals in plant long non-coding RNAs. Jose Antonio Corona-Gomez, Irving Jair Garcia-Lopez, Peter F. Stadler, Selene L. Fernandez-Valverde

tailfindr: Alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing. Maximilian Krause, Adnan M. Niazi, Kornel Labun, Yamila N. Torres Cleuren, Florian S. Müller, Eivind Valen

The MITF-SOX10 regulated long non-coding RNA DIRC3 is a melanoma tumour suppressor. Elizabeth A Coe, Jennifer Y Tan, Michael Shapiro, Pakavarin Louphrasitthiphol, Andrew R Bassett, Ana C Marques, Colin R Goding, Keith W Vance

Synthetic 5’ UTRs can either up- or down-regulate expression upon RBP binding. Noa Katz, Roni Cohen, Oz Solomon, Beate Kaufmann, Orna Atar, Zohar Yakhini, Sarah Goldberg, Roee Amit

Efficiency of protein synthesis inhibition depends on tRNA and codon compositions. Sophia Rudorf

MiR-218: A Molecular Switch and Potential Biomarker of Susceptibility to Stress. Angelica Torres-Berrio, Dominique Nouel, Santiago Cuesta, Eric M. Parise, Jose Maria Restrepo-Lozano, Pier Larochelle, Eric J. Nestler, Cecilia Flores

Regulatory sites for known and novel splicing in human basal ganglia are enriched for disease-relevant information. Sebastian Guelfi, Karishma D’Sa, Juan Botía, Jana Vandrovcova, Regina H. Reynolds, David Zhang, Daniah Trabzuni, Leonoardo Collado-Torres, Andrew Thomason, Pedro Quijada Leyton, Sarah A. Gagliano, Mike A. Nalls, UK Brain Expression Consortium, Kerrin S. Small, Colin Smith, Adaikalavan Ramasamy, John Hardy, Michael E. Weale, Mina Ryten

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 G. Martinez, Karrisa Hughes, Blaine H.M. Mooers, Jorge Cruz-Reyes

The mRNA-bound proteome of Leishmania mexicana: novel genetic insight into an ancient parasite. Luis M. de Pablos, Tiago R. Ferreira, Adam A. Dowle, Sarah Forrester, Ewan Parry, Katherine Newling, Pegine B. Walrad

Extensive epitranscriptomic methylation of A and C residues on murine leukemia virus transcripts enhances viral gene expression. David G. Courtney, Andrea Chalem, Hal P. Bogerd, Brittany A. Law, Edward M. Kennedy, Christopher L. Holley, Bryan R. Cullen

MicroRNA levels in bone and blood change during bisphosphonate and teriparatide therapy in an animal model of postmenopausal osteoporosis. Roland Kocijan, Moritz Weigl, Susanna Skalicky, Elisabeth Geiger, James Ferguson, Gabriele Leinfellner, Patrick Heimel, Peter Pietschmann, Johannes Grillari, Heinz Redl, Matthias Hackl

Class I and II aminoacyl-tRNA synthetase tRNA groove discrimination created the first synthetase•tRNA cognate pairs and was therefore essential to the origin of genetic coding. Charles W. Carter Jr, Peter R. Wills

Pat1 activates late steps in mRNA decay by multiple mechanisms. Joseph H. Lobel, Ryan W Tibble, John D. Gross

Detection of Spacer Precursors Formed In Vivo During Primed CRISPR Adaptation. Anna A. Shiriaeva, Ekaterina Savitskaya, Kirill A. Datsenko, Irina O. Vvedenskaya, Iana Fedorova, Natalia Morozova, Anastasia Metlitskaya, Anton Sabantsev, Bryce E. Nickels, Konstantin Severinov, Ekaterina Semenova

RNase H1 and H2 are differentially regulated to eliminate RNA-DNA hybrids. Arianna Lockhart, Vanessa Borges Pires, Fabio Bento, Vanessa Kellner, Sarah Luke-Glaser, Brian Luke

An essential RNA-binding lysine residue in the Nab3 RRM domain undergoes mono and trimethylation. Kwan Yin Lee, Anand Chopra, Kyle Biggar, Marc D. Meneghini

Co-occurrence of multiple CRISPRs and cas clusters suggests epistatic interactions. Aude Bernheim, David Bikard, Marie Touchon, Eduardo PC Rocha

Ultrasound- and microbubble-mediated targeted delivery of therapeutic microRNA-loaded nanocarriers to deep liver and kidney tissues in pigs. Tommaso Di Ianni, Rajendran J.C. Bose, Uday K. Sukumar, Sunitha Bachawal, Huaijun Wang, Arsenii Telichko, Carl D. Herickhoff, Elise Robinson, Sam Baker, José G. Vilches-Moure, Stephen A. Felt, Sanjiv S. Gambhir, Ramasamy Paulmurugan, Jeremy D. Dahl

TDP-43 proteinopathy impairs neuronal mRNP granule mediated postsynaptic local translation and mRNA metabolism. Chia-En Wong, Kuen-Jer Tsai

Axonal transport of an insulin-like peptide mRNA promotes stress recovery in C. elegans. Rashmi Chandra, Lisa Li, Zahabiya Husain, Shashwat Mishra, Joy Alcedo

Two molecules of Has1 RNA helicase function simultaneously in the biogenesis of small and large ribosomal subunits. Sivakumar Vadivel Gnanasundram, Isabelle C Kos-Braun, Martin Koš

Ribosome profiling at isoform level reveals an evolutionary conserved impact of differential splicing on the proteome. Marina Reixachs-Sole, Jorge Ruiz-Orera, M. Mar Alba, Eduardo Eyras

Inhibition of the Dead Box RNA Helicase 3 prevents HIV-1 Tat and cocaine-induced neurotoxicity by targeting microglia activation. Marina Aksenova, Justin Sybrandt, Biyun Cui, Vitali Sikirzhytski, Hao Ji, Diana Odhiambo, Matthew D Lucius, Jill R Turner, Eugenia Broude, Edsel Pena, Sofia Lizzaraga, Jun Zhu, Ilya Safro, Michael D Wyatt, Michael Shtutman

Strand displacement: a fundamental mechanism in RNA biology? Fan Hong, Petr Šulc

Evolving methods for rational de novo design of functional RNA molecules. Stefan Hammer, Christian Günzel, Mario Mörl, Sven Findeiß

RNA preprints: W12/2019

The lncRNA NEAT1_1 is dispensable for normal tissue homeostasis and cancer cell growth. Carmen Adriaens, Florian Rambow, Greet Bervoets, Toomas Silla, Mari Mito, Tomoki Chiba, Asahara Hiroshi, Tetsuro Hirose, Shinichi Nakagawa, Torben Heick Jensen, Jean-Christophe Marine

DNA methylation, microRNA expression profiles and their relationships with transcriptome in grass-fed and grain-fed Angus Cattle rumen tissue. Yaokun Li, José A. Carrillo, Yi Ding, Yanghua He, Chunping Zhao, Jianan Liu, Linsen Zan, Jiuzhou Song

Post-transcriptional mechanisms distinguish human and chimp forebrain progenitor cells. Daniela A Grassi, Per Ludvik Brattås, Jeovanis G Valdés, Melinda Rezeli, Marie E Jönsson, Sara Nolbrant, Malin Parmar, György Marko-Varga, Johan Jakobsson

ITGA2 is a target of miR-206 promoting cancer stemness and lung metastasis through enhanced ACLY and CCND1 expression in triple negative breast cancer. Valery Adorno-Cruz, Andrew D. Hoffmann, Xia Liu, Brian Wray, Ruth A. Keri, Huiping Liu

Functional RNA Structures in the 3’UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses. Roman Ochsenreiter, Ivo L. Hofacker, Michael T. Wolfinger

A type III CRISPR ancillary ribonuclease degrades its cyclic oligoadenylate activator. Januka S. Athukoralage, Shirley Graham, Sabine Grüschow, Christophe Rouillon, Malcolm F. White

Assessing the role of long-noncoding RNA in nucleus accumbens in subjects with alcohol dependence. Gowon O. McMichael, John Drake, Eric Sean Vornholt, Kellen Cresswell, Vernell Williamson, Chris Chatzinakos, Mohammed Mamdani, Siddharth Hariharan, Kenneth S. Kendler, Michael F. Miles, Gursharan Kalsi, Brien P. Riley, Mikhail Dozmorov, Silviu-Alin Bacanu, Vladimir I. Vladimirov

Identification and classification of hubs in miRNA target gene networks in human neural stem/progenitor cells following Japanese encephalitis virus infection. Sriparna Mukherjee, Irshad Akbar, Reshma Bhagat, Bibhabasu Hazra, Arindam Bhattacharyya, Pankaj Seth, Dipanjan Roy, Anirban Basu

A regulatory RNA is associated to invasive meningococcal disease in Europe. Jens Karlsson, Hannes Eichner, Susanne Jacobsson, Edmund Loh

Tissue-specific MicroRNA Expression Alters Cancer Susceptibility Conferred by a TP53 Noncoding Variant. Qipan Deng, Hui Hu, Xinfang Yu, Shuanglin Liu, Lei Wang, Weiqun Chen, Chi Zhang, Zhaoyang Zeng, Ya Cao, Ling Li, Mingzhi Zhang, Steven Rosenfeld, Shideng Bao, Eric Hsi, Ken H Young, Zhongxin Lu, Yong Li

Phenotypical microRNA screen reveals a noncanonical role of CDK2 in regulating neutrophil migration. A.Y. Hsu, D. Wang, S. Liu, J. Lu, R. Syahirah, D.A. Bennin, A. Huttenlocher, D.M. Umulis, J. Wan, Q. Deng

Krüppel-like factor 2- induced microRNAs: implications for treatment of pulmonary hypertension. Hebah Sindi, Giusy Russomanno, Kyeong Beom Jo, Vahitha B. Abdul-Salam, Basma Qazi Chaudhry, Alexander J. Ainscough, Robert Szulcek, Harm Jan Bogaard, Claire C. Morgan, Soni Pullamsetti, Mai Alzaydi, Christopher J. Rhodes, Christina A. Eichstaedt, Ekkehard Grünig, Martin R. Wilkins, Beata Wojciak-Stothard

An Exon Skipping Screen Identifies Antitumor Drugs That Are Potent Modulators of Pre-mRNA Splicing, Suggesting New Therapeutic Applications. Yihui Shi, Walter Bray, Alexander J. Smith, Wei Zhou, Joy Calaoagan, Chandraiah Lagisetti, Lidia Sambucetti, Phillip Crews, R. Scott Lokey, Thomas R. Webb

miRspongeR: 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

Profiling Gene Specific Changes to RNA Editome in Preeclampsia. Saam Hasan, Shahriyar Mahdi Robbani, Tamanna Afroze, Gias U Ahsan, Muhammad Maqsud Hossain

microRNA mir-598-3p mediates susceptibility to stress-enhancement of remote fear memory. Meghan E Jones, Stephanie E. Sillivan, Sarah Jamieson, Gavin Rumbaugh, Courtney A. Miller

High-throughput RNA sequencing from paired lesional- and non-lesional skin reveals major alterations in the psoriasis circRNAome. Liviu-Ionut Moldovan, Thomas Birkballe Hansen, Morten Trillingsgaard Venø, Trine Line Hauge Okholm, Thomas Levin Andersen, Henrik Hager, Lars Iversen, Jørgen Kjems, Claus Johansen, Lasse Sommer Kristensen

Srrm234, but not canonical SR and hnRNP proteins drive inclusion of Dscam exon 9 variable exons. Pinar Ustaoglu, Irmgard U. Haussmann, Hongzhi Liao, Antonio Torres-Mendez, Roland Arnold, Manuel Irimia, Matthias Soller

Levels of sdRNAs in cytoplasm and their association with ribosomes are dependent upon stress conditions but independent from snoRNA expression. Anna M. Mleczko, Piotr Machtel, M. Walkowiak, A. Wasilewska, K. Bąkowska-Żywicka

3.1Å structure of yeast RNA polymerase II elongation complex stalled at a cyclobutane pyrimidine dimer lesion solved using streptavidin affinity grids. Indrajit Lahiri, Jun Xu, Bong Gyoon Han, Juntaek Oh, Dong Wang, Frank DiMaio, Andres E Leschziner

Circular RNA profiling in the oocyte and cumulus cells reveals that circARMC4 is essential for porcine oocyte maturation. Zubing Cao, Di Gao, Tengteng Xu, Ling Zhang, Xu Tong, Dandan Zhang, Yiqing Wang, Wei Ning, Xin Qi, Yangyang Ma, Kaiyuan Ji, Tong Yu, Yunsheng Li, Yunhai Zhang

Structure-guided enhancement of selectivity of chemical probe inhibitors targeting bacterial seryl-tRNA synthetase. Ricky Cain, Ramya Salimraj, Avinash S. Punekar, Dom Bellini, Colin W. G. Fishwick, Lloyd Czaplewski, David J. Scott, Gemma Harris, Christopher G. Dowson, Adrian J. Lloyd, David I. Roper

Musashi binding elements in Zika and related Flavivirus 3’UTRs: A comparative study in silico. Adriano de Bernardi Schneider, Michael T. Wolfinger

Quantitation of cis-translational control by general mRNA sequence features in five eukaryotes. Jingyi Jessica Li, Guo-Liang Chew, Mark D Biggin

RNA preprints: W11/2019

Comprehensive Classification of the RNaseH-like domain-containing Proteins in Plants. Shuai Li, Kunpeng Liu, Qianwen Sun

Sen1 is required for RNA Polymerase III transcription termination in an R-loop independent manner. Julieta Rivosecchi, Marc Larochelle, Camille Teste, Frédéric Grenier, Amélie Malapert, Emiliano P. Ricci, Pascal Bernard, François Bachand, Vincent Vanoosthuyse

MicroRNA Overexpression screen reveals a noncanonical role of CDK2 in regulating neutrophil migration. Alan Y. Hsu, Decheng Wang, Sheng Liu, Justice Lu, Ramizah Syahirah, David A. Bennin, Anna Huttenlocher, Jun Wan, Qing Deng

Genome-wide profiling of microRNAs and prediction of mRNA targets in 17 bovine tissues. Min Wang, Amanda J Chamberlain, Claire P Prowse-Wilkins, Christy J Vander Jagt, Timothy P Hancock, Jennie E Pryce, Benjamin G Cocks, Mike E Goddard, Benjamin J Hayes

Single-base mapping of m6A by an antibody-independent method. Zhang Zhang, Li-Qian Chen, Yu-Li Zhao, Cai-Guang Yang, Ian A Roundtree, Zijie Zhang, Jian Ren, Wei Xie, Chuan He, Guan-Zheng Luo

MicroRNA-transcriptome networks in whole blood and monocytes of women undergoing preterm labor. Alison G. Paquette, Oksana Shynlova, Xiaogang Wu, Mark Kibschull, Kai Wang, Nathan D. Price, Stephen J Lye

Plasma Circular RNA Panel to Diagnose Hepatitis B Virus-Related Hepatocellular Carcinoma. Jian Yu, Meng-chao Wang, Wen-bing Ding, Xing-gang Guo, Jian Xu, Qing-guo Xu, Yuan Yang, Shu-han Sun, Jing-feng Liu, Lun-xiu Qin, Hui Liu, Fu Yang, Wei-ping Zhou

Germ Granules Functions are Memorized by Transgenerationally Inherited Small RNAs. Itamar Lev, Itai Antoine Toker, Yael Mor, Anat Nitzan, Guy Weintraub, Ornit Bhonkar, Itay Ben Shushan, Uri Seroussi, Julie M. Claycomb, Hila Gingold, Ronen Zaidel-Bar, Oded Rechavi

NET-prism enables RNA polymerase-dedicated transcriptional interrogation at nucleotide resolution. Constantine Mylonas, Peter Tessarz

Non-coding AUG circRNAs constitute an abundant and conserved subclass of circles. Lotte VW Stagsted, Katrine M Nielsen, Iben Daugaard, Thomas B Hansen

Inducible overexpression of zebrafish microRNA-722 suppresses chemotaxis of human neutrophil like cells. Alan Y. Hsu, Sheng Liu, Kent A. Brasseale, Ramizah Syahirah, Jun Wan, Qing Deng

A non-Dicer RNase III and four other novel factors required for RNAi-mediated transposon suppression in the human pathogenic yeast C. neoformans. Jordan E. Burke, Adam D. Longhurst, Prashanthi Natarajan, Beiduo Rao, S. John Liu, Jade Sales-Lee, Yasaman Mortensen, James J. Moresco, Jolene K. Diedrich, John R. Yates III, Hiten D. Madhani

RBPSponge: genome-wide identification of lncRNAs that sponge RBPs. Saber HafezQorani, Aissa Houdjedj, Mehmet Arici, Abdesselam Said, Hilal Kazan

Direct proteolytic control of an extracytoplasmic function RNA polymerase sigma factor. Bohdan Bilyk, Sora Kim, Tania A Baker, Ryan F Seipke

Somatic mutations in miRNA genes in lung cancer – potential functional consequences of non-coding sequence variants. Paulina Galka-Marciniak, Martyna Olga Urbanek-Trzeciak, Paulina Maria Nawrocka, Agata Dutkiewicz, Maciej Giefing, Marzena Anna Lewandowska, Piotr Kozlowski

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

Hearing impairment due to Mir183/96/182 mutations suggests both loss and gain of function effects. Morag A Lewis, Francesca Di Domenico, Neil J Ingham, Haydn M Prosser, Karen P Steel

Direct interaction of PIWI and DEPS-1 is essential for piRNA function and condensate ultrastructure in Caenorhabditis elegans. Kin Man Suen, Fabian Braukmann, Richard Butler, Dalila Bensaddek, Alper Akay, Chi-Chuan Lin, Neel Doshi, Alexandra Sapetschnig, Angus I Lamond, John E Ladbury, Eric Alexander Miska

A Musashi-Related Protein Is Essential For Gametogenesis In Arabidopsis. Laura A Moody, Ester Rabbinowitsch, Hugh G Dickinson, Roxaana Clayton, David M Emms, Jane Langdale

Two ecotype-related long non-coding RNAs in the environmental control of root growth. Thomas Blein, Coline Balzergue, Thomas Roulé, Marc Gabriel, Laetitia Scalisi, Céline Sorin, Aurélie Christ, Etienne Delannoy, Marie-Laure Martin-Magniette, Laurent Nussaume, Caroline Hartmann, Daniel Gautheret, Thierry Desnos, Martin Crespi

The RNA encoding the microtubule-associated protein tau has extensive structure that affects its biology. Jonathan L Chen, Walter N Moss, Adam Spencer, Peiyuan Zhang, Jessica L Childs-Disney, Matthew D Disney

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

AptaBlocks Online – A web-based toolkit for the in-silico assembly of RNA complexes. Jan Hoinka, Yijie Wang, Teresa M. Przytycka

HIV-1 virus cycle replication: a review of RNA polymerase II transcription, alternative splicing and protein synthesis. Miguel Ramos Pascual

RNA preprints: W10/2019

Small RNA expression pattern in multiply inbred lines and their hybrids of maize embryo. Yong-Xin Liu

Nanopore sequencing of full-length circRNAs in human and mouse brains reveals circRNA-specific exon usage and intron retention. Karim Rahimi, Morten T. Venø, Daniel M. Dupont, Jørgen Kjems

Functional RNA Structures in the 3’UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses. Roman Ochsenreiter, Ivo L. Hofacker, Michael T. Wolfinger

FUS ALS-causative mutations impact FUS autoregulation and the processing of RNA-binding proteins through intron retention. Jack Humphrey, Nicol Birsa, Carmelo Milioto, David Robaldo, Matthew Bentham, Seth Jarvis, Cristian Bodo, Maria Giovanna Garone, Anny Devoy, Alessandro Rosa, Irene Bozzoni, Elizabeth Fisher, Marc-David Ruepp, Giampietro Schiavo, Adrian Isaacs, Vincent Plagnol, Pietro Fratta

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, Charlie Bond, Steve D Wilton, Archa H Fox, Sue Fletcher

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 Griselda Jacob, Frederick Richards, Adrian Buckroyd, Sanjay Sinha, Christopher W.J. Smith

Base pairing interactions between substrate RNA and H/ACA guide RNA modulate the kinetics of pseudouridylation, but not the affinity of substrate binding by H/ACA small nucleolar Ribonucleoproteins. Erin Katelyn Kelly, Ute Kothe

Mechanistic characterization of RASGRP1 variants identifies an hnRNP K-regulated transcriptional enhancer contributing to SLE susceptibility. Julio E Molineros, Bhupinder Singh, Chikashi Terao, Yukinori Okada, Jakub Kaplan, Barbara McDaniel, Shuji Akizuki, Celi Sun, Carol Webb, Loren L Looger, Swapan K Nath

Unearthing Regulatory Axes of Breast Cancer circRNAs Networks to Find Novel Targets and Fathom Pivotal Mechanisms. Farzaneh Afzali, Mahdieh Salimi

Extracellular vesicle-mediated RNA release in Histoplasma capsulatum. Lysangela R Alves, Roberta Peres da Silva, David A Sanchez, Daniel Zamith-Miranda, Marcio L Rodrigues, Samuel Goldenberg, Rosana Puccia, Joshua D Nosanchuk

Sterol-O acyltransferase 1 is inhibited by gga-miR-181a-5p and gga-miR-429-3p through the TGFβ pathway in endodermal epithelial cells of Japanese quail. Han-Jen Lin, Chiao-Wei Lin, Harry J Mersmann, Shih-Torng Ding

HRPK-1, a conserved KH-domain protein, modulates microRNA activity during Caenorhabditis elegans development. Anna Zinovyeva, Li Li, Isana Veksler-Lublinsky

Widespread gene duplication and adaptive evolution in the RNA interference pathways of the Drosophila obscura group. Danang Crysnanto, Darren Obbard

The Gag Protein PEG10 Binds to RNA and Regulates Trophoblast Stem Cell Lineage Specification. Mona Abed, Erik Verschueren, Hanna Budayeva, Peter Liu, Donald Kirkpatrick, Rohit Reja, Sarah Kummerfeld, Joshua Webster, Sarah Gierke, Mike Reichelt, Keith Anderson, Robert Newman, Merone Roose-Girma, Zora Modrusan, Hazal Pektas, Emin Maltepe, Kim Newton, Vishva Dixit

Quantitative high-throughput tests of ubiquitous RNA secondary structure prediction algorithms via RNA/protein binding. Winston R Becker, Inga Jarmoskaite, Kalli Kappel, Pavanapuresan P Vaidyanathan, Sarah K Denny, Rhiju Das, William J Greenleaf, Daniel Herschlag

Deciphering the ‘m6A code’ via quantitative profiling of m6A at single-nucleotide resolution. Miguel Angel Garcia-Campos, Sarit Edelheit, Ursula Toth, Ran Shachar, Ronit Nir, Lior Lasman, Alexander Brandis, Jacob H. Hanna, Walter Rossmanith, Schraga Schwartz

The solution structure of Dead End bound to AU-rich RNA reveals an unprecedented mode of tandem RRM-RNA recognition required for mRNA repression. Malgorzata M Duszczyk, Harry Wischnewski, Tamara Kazeeva, Fionna E Loughlin, Christine von Schroetter, Ugo Pradère, Jonathan Hall, Constance Ciaudo, Frédéric H.-T. Allain

Bid as a novel interacting partner of IRE1 differentially regulating its RNAse activity. Samirul Bashir, Khalid Majid Fazili

The evolution of the 9aaTAD domain in Sp2 proteins: inactivation with valines and intron reservoirs. Martin Piskacek, Marek Havelka, Kristina Jendruchova, Andrea Knight, Liam Peter Keegan

Transcriptome-wide dynamics of extensive m6A mRNA methylation during Plasmodium falciparum blood-stage development. Sebastian Baumgarten, Jessica M. Bryant, Ameya Sinha, Thibaud Reyser, Peter R. Preiser, Peter C. Dedon, Artur Scherf

SF3B1ness score: screening SF3B1 mutation status from over 60,000 transcriptomes based on a machine learning approach. Yuichi Shiraishi, Kenichi Chiba, Ai Okada

The mechanism of RNA base fraying: molecular dynamics simulations analyzed with core-set Markov state models. Giovanni Pinamonti, Fabian Paul, Frank Noé, Alex Rodriguez, Giovanni Bussi

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

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

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