RNA preprints: Week 43 edition

Nuclear Abl Drives Extracellular-Vesicle Transfer of miR-34c to Induce Bystander Effects of Radiation. Shubhra Rastogi, Amini Hwang, Josolyn Chan, Jean YJ Wang

The DEAD box RNA helicase Ddx39a is essential for myocyte and lens development in zebrafish. Linlin Zhang, Beibei Li, Yuxi Yang, Ian C. Scott, Xin Lou

Assembly and translocation of a CRISPR-Cas primed acquisition complex. Maxwell W. Brown, Kaylee E. Dillard, Yibei Xiao, Adam E. Dolan, Erik T. Hernandez, Samuel Dahlhauser, Yoori Kim, Logan R. Myler, Eric Anslyn, Ailong Ke, Ilya Finkelstein

Terminal uridylyltransferases target RNA viruses as part of the innate immune system in animals. Jeremie Le Pen, Hongbing Jiang, Tomas Di Domenico, Emma Kneuss, Joanna Kosalka, Marcos Morgan, Christian Much, Konrad L. M. Rudolph, Anton J. Enright, Donal O’Carroll, David Wang, Eric A. Miska

Discovering Competing Endogenous RNA Interactions in Breast Cancer Molecular Subtypes. Gulden Olgun, Ozgur Sahin, Oznur Tastan

Data Science Issues in Understanding Protein-RNA Interactions. Anob M. Chakrabarti, Nejc Haberman, Arne Praznik, Nicholas M. Luscombe, Jernej Ule

Distribution of Purines and Pyrimidines over miRNAs of Human, Gorilla and Chimpanzee. Jayanta Kumar Das, Pabitra Pal Choudhury, Adwitiya Chaudhuri, Sk. Sarif Hassan, Pallab Basu

Genome-Wide Mining, Characterization and Development of miRNA-SSRs in Arabidopsis thaliana. Anuj Kumar, Aditi Chauhan, Sai Kumar Kompelli, Vijay Gahlaut, Johny Ijaq, Krishna Pal Singh, MNV Prasad Gajula, Prashanth Suravajhala, Amrendra Mishra, Harindra Singh Balyan, Pushpendra Kumar Gupta

Repetitive DNA reeling by the Cascade-Cas3 complex in nucleotide unwinding steps. Luuk Loeff, Stan J. J. Brouns, Chirlmin Joo

Csde1 cooperates with Strap to control translation of erythroid transcripts. Kat S. Moore, Nurcan Yagci, Floris van Alphen, Alexander B. Meijer, Peter A. C. ‘t Hoen, Marieke M. von Lindern

Ancient exapted transposable elements promote nuclear enrichment of long noncoding RNAs. Joana Carlevaro-Fita, Monalisa Das, Taisia Polidori, Carmen Navarro, Rory Johnson

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RNA preprints: Week 42 edition

Interleukins 4 and 13 Induce Exon Skipping of Mutant Dystrophin Pre-mRNA to Restore Dystrophin Production. SiewHui Low, Chen-Ming Fan

Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot. Jorjethe Roca, Naoto Hori, Yogambigai Velmurugu, Ranjani Narayanan, Prasanth Narayanan, Dave Thirumalai, Anjum Ansari

RNA velocity in single cells. Gioele La Manno, Ruslan Soldatov, Hannah Hochgerner, Amit Zeisel, Viktor Petukhov, Maria Kastriti, Peter Lonnerberg, Alessandro Furlan, Jean Fan, Zehua Liu, David van Bruggen, Jimin Guo, Erik Sundstrom, Goncalo Castelo-Branco, Igor Adameyko, Sten Linnarsson, Peter Kharchenko

Evidence of non-tandemly repeated rDNAs and their intragenomic heterogeneity in Rhizophagus irregularis. Taro Maeda, Yuuki Kobayashi, Hiromu Kameoka, Nao Okuma, Naoya Takeda, Katsushi Yamaguchi, Takahiro Bino, Shuji Shigenobu, Masayoshi Kawaguchi

HuD is a neural enhancer of global translation acting on mTORC1-responsive genes and sponged by the Y3 small non-coding RNA. Paola Zuccotti, Toma Tebaldi, Daniele Peroni, Marcel Köhn, Lisa Gasperini, Valentina Potrich, Tatiana Dudnakova, Guido Sanguinetti, Luciano Conti, Paolo Macchi, David Tollervey, Stefan Hüttelmaier, Alessandro Quattrone

A max-margin training of RNA secondary structure prediction integrated with the thermodynamic model. Manato Akiyama, Kengo Sato, Yasubumi Sakakibara

ciRS-7 exonic sequence is embedded in a long non-coding RNA locus. Steven Barrett, Kevin R. Parker, Caroline Horn, Miguel Mata, Julia Salzman

Genome-Wide Mining, Characterization and Development of miRNA-SSRs in Arabidopsis thaliana. Anuj Kumar, Aditi Aditi Chauhan, Sai Kumar Kompelli, Vijay Gahlaut, Johny Ijaq, Krishna Pal Singh, MNV Prasad Gajula, Prashanth Suravajhala, Amrendra Mishra, Harindra Singh Balyan, Pushpendra Kumar Gupta

Multi-step regulation of transcription kinetics explains the non-linear relation between RNA polymerase II density and mRNA expression in Dosage Compensation. Pouria Dasmeh

Csde1 cooperates with Strap to control translation of erythroid transcripts. Kat S. Moore, Nurcan Yagci, Floris van Alphen, Alexander B. Meijer, Peter A. C. ‘t Hoen, Marieke M. von Lindern

Feature versus Raw Sequence: Deep Learning Comparative Study on Predicting Pre-miRNA. Jaya Thomas, Sonia Thomas, Lee Sael

Automatic simulation of RNA editing in plants for the identification of novel putative Open Reading Frames. Fabio Fassetti, Claudia Giallombardo, Ofelia Leone, Luigi Palopoli, Simona E Rombo, Pierluigi Ruffolo, Adolfo Saiardi

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RNA preprints: Week 41 edition

Paternal easiRNAs regulate parental genome dosage in Arabidopsis. German Martinez, Philip Wolff, Zhenxing Wang, Jordi Moreno-Romero, Juan Santos-Gonzalez, Lei Liu Conze, Christopher DeFraia, Keith Slotkin, Claudia Kohler

microRNA-triggered transposon small RNAs mediate genome dosage response. Filipe Borges, Jean-Sebastien Parent, Frederic van Ex, Philip Wolff, German Martinez, Claudia Kohler, Robert A Martienssen

Csde1 binds transcripts involved in protein homeostasis and controls their expression in erythropoiesis. Kat S. Moore, Nurcan Yagci, Floris van Alphen, Nahuel A. Paolini, Rastislav horos, Ntsiki M. Held, Riekelt H. Houtkooper, Emile van den Akker, Alexander B. Meijer, Peter A. C. ‘t Hoen, Marieke von Lindern

N6-methyladenosine modification and the YTHDF2 reader protein play cell type specific roles in lytic viral gene expression during Kaposi’s sarcoma-associated herpesvirus infection. Charles Hesser, John Karijolich, Dan Dominissini, Chuan He, Britt A. Glaunsinger

The kinetics of pre-mRNA splicing in the Drosophila genome: influence of gene architecture. Athma A Pai, Telmo Henriques, Kayla McCue, Adam Burkholder, Karen Adelman, Christopher B Burge

The Antiviral and Cancer Genomic DNA Deaminase APOBEC3H Is Regulated by a RNA-Mediated Dimerization Mechanism. Reuben Harris, Nadine Shaban, Ke Shi, Kate Lauer, Michael Carpenter, Christopher Richards, Michael Lopresti, Daniel Salamango, Jiayi Wang, Surajit Banerjee, William Brown, Hideki Aihara

Base-resolution mapping reveals distinct m1A methylome in nuclear- and mitochondrial-encoded transcripts. Xiaoyu Li, Xushen Xiong, Meiling Zhang, Kun Wang, Ying Chen, Jun Zhou, Yuanhui Mao, Jia Lv, Danyang Yi, Xiao-Wei Chen, Chu Wang, Shu-Bing Qian, Chengqi Yi

Sequence, Structure and Context Preferences of Human RNA Binding Proteins. Daniel Dominguez, Peter Freese, Maria S. Alexis, Amanda Su, Myles Hochman, Tsultrim Palden, Cassandra Bazile, Nicole J. Lambert, Eric L. Van Nostrand, Gabriel A. Pratt, Gene W. Yeo, Brenton Graveley, Christopher B. Burge

The optimization of mRNA expression level by its intrinsic properties — insights from codon usage pattern and structural stability of mRNA. Manish Prakash Victor, Debarun Acharya, Tina Begum, Tapash Chandra Ghosh

LIN28 selectively modulates a subclass of let-7 microRNAs. Dmytro Ustianenko, Hua-Sheng Chiu, Sebastien M. Weyn-Vanhentenryck, Pavel Sumazin, Chaolin Zhang

Salicylic acid perturbs sRNA-gibberellin regulatory network in immune response of potato to Potato virus Y infection. Maja Kriznik, Marko Petek, David Dobnik, Ziva Ramsak, Spela Baebler, Stephan Pollmann, Jan Kreuze, Jana Zel, Kristina Gruden

Transcriptomic Dynamics of a non-coding trinucleotide repeat expansion disorder SCA12 in iPSC derived neuronal cells: signatures of interferon induced response. Deepak Kumar, Parashar Dhapola, Ashaq Hussain, Rintu Kutum, Achal Kumar Srivastava, Mitali Mukerji, Odity Mukherjee, Mohammed Faruq

A unique, spliced varicella-zoster virus latency transcript represses expression of the viral transactivator gene 61. Daniel P. Depledge, Werner J. D. Ouwendijk, Tomohiko Sadaoka, Shirley E. Braspenning, Yasuko Mori, Randall Cohrs, Georges Verjans, Judith Breuer

Development of a riboswitch-based platform for live cell imaging of RNAs in mammalian cells. Esther Braselmann, Aleksandra J Wierzba, Jacob T Polaski, Mikołaj Chromiński, Dilara Batan, Dorota Gryko, Robert T Batey, Amy E Palmer

A mechanism for prime-realignment during influenza A virus replication. Judith Oymans, Aartjan te Velthuis

High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing. Julien Lagarde, Barbara Uszczynska-Ratajczak, Silvia Carbonell, Silvia Perez-Lluch, Amaya Abad, Carrie Davis, Thomas R. Gingeras, Adam Frankish, Jennifer Harrow, Roderic Guigo, Rory Johnson

Combined analysis of genome sequencing and RNA-motifs reveals novel damaging non-coding mutations in human tumors. Babita Singh, Juan Luis L Trincado Alonso, PJ Tatlow, Stephen R Piccolo, Eduardo Eyras

Backbone brackets and arginine tweezers delineate class I and class II aminoacyl tRNA synthetases. Florian Kaiser, Sebastian Bittrich, Sebastian Salentin, Christoph Leberecht, V. Joachim Haupt, Sarah Krautwurst, Michael Schroeder, Dirk Labudde

RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination. Nila Roy Choudhury, Gregory Heikel, Maryia Trubitsyna, Peter Kubik, Jakub Stanislaw Nowak, Shaun Webb, Sander Granneman, Christos Spanos, Juri Rappsilber, Alfredo Castello Palomares, Gracjan Michlewski

Initiation, elongation and realignment during influenza virus mRNA synthesis. Aartjan te Velthuis, Judith Oymans

The role of m6A-RNA methylation in stress response regulation. Mareen Engel, Simone Roeh, Carola Eggert, Paul M. Kaplick, Lisa Tietze, Janine Arloth, Peter Weber, Monika Rex-Haffner, Mira Jakovcevski, Manfred Uhr, Matthias Eder, Carsten T. Wotjak, Mathias V. Schmidt, Jan M. Deussing, Elisabeth B. Binder, Alon Chen

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RNA preprints: Week 40 edition

Large-scale screening of rare genetic variants in humans reveals frequent splicing disruptions. Rocky Cheung, Kimberly D. Insigne, David Yao, Christina P. Burghard, Eric M. Jones, Daniel B. Goodman, Sriram Kosuri

Transgenerational dynamics of rDNA copy number in Drosophila male germline stem cells. Kevin L. Lu, Jonathan O. Nelson, Natalie Warsinger-Pepe, Yukiko M. Yamashita

Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs in Drosophila melanogaster. Michael P. Meers, Karen Adelman, Robert J. Duronio, Brian D. Strahl, Daniel J. McKay, A. Gregory Matera

Pausing controls branching between productive and non-productive pathways during initial transcription. David Dulin, David L. V. Bauer, Anssi M. Malinen, Jacob J. W. Bakermans, Martin Kaller, Zakia Morichaud, Ivan Petushkov, Martin Depken, Konstantin Brodolin, Andrey Kulbachinskiy, Achillefs N. Kapanidis

miR-128 inhibits telomerase activity by targeting TERT mRNA. Herlinda Guzman, Katie Sanders, Adam Idica, Aurore Bochnakian, Douglas Jury, Iben Daugaard, Dimitri G. Zisoulis, Irene Pedersen

Gestational low-protein intake enhances the whole kidney miR-192 and miR-200 family expression and epithelial-to-mesenchymal transition in adult male offspring. Leticia B. Sene, Vitor Hugo G. Rizzi, Jose A. R. Gontijo, Patricia A. Boer

Cell Cycle Control by Nuclear Sequestration of CDC20 and CDH1 mRNA in Plant Stem Cells. Weibing Yang, Raymond Wightman, Elliot M. Meyerowitz

Predicting microRNA targeting efficacy in Drosophila. Vikram Agarwal, Alexander O. Subtelny, Prathapan Thiru, Igor Ulitsky, David P. Bartel

The miR-96/RARγ signaling axis governs androgen signaling and PCa progression. Mark D. Long, Prashant K. Singh, James R. Russell, Gerard Llimos, Spencer Rosario, Abbas Rizvi, Henry Withers, Patrick R. van den Berg, Jason Kirk, Lara E. Sucheston-Campbell, Dominic J. Smiraglia, Moray J. Campbell

The Elastic Network Contact Model applied to RNA: enhanced accuracy for conformational space prediction. Olivier Mailhot, Vincent Frappier, Francois Major, Rafael Najmanovich

Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements. Samuel H. Lewis, Kaycee A. Quarles, Yujing Yang, Melanie Tanguy, Lise Frezal, Stephen A. Smith, Prashant P. Sharma, Richard Cordaux, Clement Gilbert, Isabelle Giraud, David H. Collins, Phillip D. Zamore, Eric A. Miska, Peter Sarkies, Francis M. Jiggins

Initiation, elongation and realignment during influenza virus mRNA synthesis. Aartjan te Velthuis, Judith Oymans

The plastid-nucleus located DNA/RNA binding protein WHIRLY1 regulates microRNA-levels during stress. Aleksandra Swida-Barteczka, Anja Krieger-Liszkay, Wolfgang Bilger, Ulrike Voigt, Goetz Hensel, Zofia Szweykowska-Kulinska, Karin Krupinska

miR-128-induced LINE-1 restriction is dependent on down-regulation of hnRNPA1. Irene Pedersen, Lianna Fung, Herlinda Guzman, Evgueni Sevrioukov, Adam Idica, Eddie Park, Aurore Bochnakien, Iben Daugaard, Douglas Jury, Ali Mortazavi, Dimitri Zisoulis

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