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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RNA preprints: week 39 edition

Discovery of global regulators of 3’ untranslated region processing in cancers with KAPAC. Andreas J Gruber, Ralf Schmidt, Souvik Ghosh, Georges Martin, Andreas R Gruber, Erik van Nimwegen, Mihaela Zavolan

Spatial RNA proximities reveal a bipartite nuclear transcriptome and territories of differential density and transcription elongation rates. Jorg Morf, Steven W. Wingett, Irene Farabella, Jonathan Cairns, Mayra Furlan-Magaril, Xin Liu, Frank F. Craig, Simon Andrews, Marc A. Marti-Renom, Peter Fraser

MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs. Saima Shahid, Gunjune Kim, Nathan R. Johnson, Eric Wafula, Feng Wang, Ceyda Coruh, Vivian Bernal-Galeano, Tamia Phifer, Claude W. dePamphilis, James H. Westwood, Michael Axtell

Genome-Wide Characterization Of Differential Transcript Usage In Arabidopsis thaliana. Dries Vaneechoutte, April Roberts Estrada, Ying-Chen Lin, Ann Loraine, Klaas Vandepoele

MicroRNA miR-128 represses LINE-1 (L1) retrotransposition by downregulating the nuclear import factor TNPO1. Adam Idica, Evgueni Sevrioukov, Dimitri Zisoulis, Matthias Hamdorf, Iben Daugaard, Pavan Kadandale, Irene Pedersen

Interferon-inducible miR-128 modulates HIV-1 replication by targeting TNPO3 mRNA. Irene Pedersen, Aurore Bochnakiem, Dimitri Zisoulis, Adam Idica, Anjie Zhen, Vineet KewalRamani, Iben Daugaard, Matthias Hamdorf, Scott Kitchen, KyeongEun Lee

A comprehensive characterization of cis-acting splicing-associated variants in human cancer. Yuichi Shiraishi, Keisuke Kataoka, Kenichi Chiba, Ai Okada, Yasunori Kogure, Hiroko Tanaka, Seishi Ogawa, Satoru Miyano

Proto-ribosome: a theoretical approach based on RNA relics. Jacques Demongeot

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RNA in preprints: Week 38 edition

Welcome to Week 38! Here is the work on RNA that came out as a preprint over the past week. Enjoy!

miRNAgFree: prediction and profiling of novel microRNAs without genome assembly. Ernesto L. Aparicio, Antonio Rueda, Bastian Fromm, Cristina Gómez-Martin, Ricardo Lebrón, Jose L Oliver, Juan A Marchal, Michail Kotsyfakis, Michael Hackenberg

HyperTRIBE: Upgrading TRIBE with enhanced editing. Weijin Xu, Reazur Rahman, Michael Rosbash

Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome. Cai Li, Boris Lenhard, Nicholas M. Luscombe

Promoter architecture determines co-translational regulation of mRNA. Maria Lorena Espinar Calvo, Miquel Angel Schikora Tamarit, Julia Domingo Espinos, Lucas B Carey

Interaction Between Host MicroRNAs and the Gut Microbiota in Colorectal Cancer. Ce Yuan, Michael Burns, Subbaya Subramanian, Ran Blekhman

Quantitating Translational Control: mRNA Abundance-Dependent and Independent Contributions and the mRNA Sequences That Specify Them. Jingyi Jessica Li, Guo-Liang Chew, Mark D. Biggin

Updating the 97% identity threshold for 16S‌ ribosomal RNA OTUs. Robert C Edgar

Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution. Sahin Naqvi, Daniel W Bellott, Kathy S Lin, David C Page

High-Throughput Identification of Genetic Variation Impact on pre-mRNA Splicing Efficiency. Scott I Adamson, Lijun Zhan, Brenton R Graveley

A Cdk9-PP1 kinase-phosphatase switch regulates the elongation-termination transition of RNA polymerase II. Pabitra K Parua, Gregory T Booth, Miriam Sansó, Bradley Benjamin, Jason C Tanny, John T Lis, Robert P Fisher

Cdk9 regulates a promoter-proximal checkpoint to modulate RNA Polymerase II elongation rate. Gregory T Booth, Pabitra K Parua, Miriam Sanso, Robert P Fisher, John T Lis

RNA binding and HEPN nuclease activation are decoupled in CRISPR-Cas13a. Akshay Tambe, Alexandra East-Seletsky, Gavin J Knott, Jennifer A Doudna, Mitchell R O’Connell

The ERA-related GTPase AtERG2 associated with mitochondria 18S RNA is essential for early embryo development in Arabidopsis. Pengyu Cheng, Hongjuan Li, Linlin Yuan, Huiyong Li, Lele Xi, Junjie Zhang, Jin Liu, Yingdian Wang, Heping Zhao, Huixin Zhao, Shengcheng Han

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RNA in preprints: Week 37 edition

Ancient exapted transposable elements drive nuclear localisation of lncRNAs. Joana Carlevaro-Fita, Monalisa Das, Taisia Polidori, Carmen Navarro, Rory Johnson

Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells. Yoav Lubelsky, Igor Ulitsky

EIF4A3 associated splicing and nonsense mediated decay defined by a systems analysis with novel small molecule inhibitors. Alborz Mazloomian, Shinsuke Araki, Momoko Oohori, Damian Yap, Shoichi Nakao, Atsushi Nakanishi, Sohrab Shah, Samuel Aparicio.

High-throughput identification of RNA nuclear enrichment sequences. Chinmay J Shukla, Alexandra L McCorkindale, Chiara Gerhardinger, Keegan D Korthauer, Moran N Cabili, David M Shechner, Rafael A Irizarry, Philipp G Maass, John L Rinn

Biomarker evaluation of plasma microRNA-122, high-mobility group box-1 and keratin-18 in acute gallstone disease. Francesca Th’ng, Bastiaan Vliegenthart, Jonathan D Lea, Daniel J Antoine, James W Dear, Damian James Mole

Deep learning of the splicing (epi)genetic code reveals a novel candidate mechanism linking histone modifications to ESC fate decision. Yungang Xu, Yongcui Wang, Jiesi Luo, Weiling Zhao, Xiaobo Zhou

CRISPR-based Herd Immunity Limits Phage Epidemics in Bacterial Populations. Pavel Payne, Lukas Geyrhofer, Nicholas H. Barton, Jonathan P. Bollback

Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection. Ye Jimmie Chun, Jenny Chen, Alexandra-Chloe Villani, Meena Subramaniam, Rachel E Gate, Tushar Bhangale, Mark N Lee, Towfique Raj, Raktima Raychowdhury, Weibo Li, Noga Rogel, Selina H Imboywa, Portia I Chipendo, Cristin McCabe, Michelle H Lee, Irene Y Frohlich, Barbara E Stranger, Philip L De Jager, Aviv Regev, Tim Behrens, Nir Hacohen

Motif signatures of transcribed enhancers. Dimitrios Kleftogiannis, Haitham Ashoor, Nikolaos Zarokanellos, Vladimir B. Bajic

A potential link between tuberculosis and lung cancer through non-coding RNAs. Debmalya Barh, Sandeep Tiwari, Ranjith N. Kumavath, Vasco Azevedo

Mitochondrial Dual-coding Genes in Trypanosoma brucei. Laura E. Kirby, Donna Koslowsky

The U2AF homology motif kinase 1 (UHMK1) is upregulated upon hematopoietic cell differentiation. Isabella Barbutti, Joao Agostinho Machado-Neto, Vanessa Cristina Arfelli, Paula de Melo Campos, Fabiola Traina, Sara Teresinha Olalla Saad, Leticia Froehlich Archangelo

Paupar LncRNA Promotes KAP1 Dependent Chromatin Changes And Regulates Subventricular Zone Neurogenesis. Ioanna Pavlaki, Farah Alammari, Bin Sun, Neil Clark, Tamara Sirey, Sheena Lee, Dan J. Woodcock, Chris P. Ponting, Francis G. Szele, Keith W. Vance

Antisense transcription-dependent chromatin signature modulates sense transcription and transcript dynamics. Thomas Brown, Francoise S. Howe, Struan C. Murray, Emily Seward, Scott Rata, Andrew Angel, Jane Mellor

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