RNA preprints: W16/2018

An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys. Marilyn Parra, Ben W. Booth, Richard Weiszmann, Brian A. Yee, Gene W. Yeo, James B. Brown, Susan E. Celniker, John G. Conboy

Prader-Willi locus Snord116 RNA processing requires an active endogenous allele and neuron-specific splicing by Rbfox3/NeuN. Rochelle L Coulson, Weston T Powell, Dag H Yasui, Gayathri Dileep, James Resnick, Janine M LaSalle

Changes in neuronal immunofluorescence in the C- versus N-terminal domains of hnRNP H following D1 dopamine receptor activation. Qiu T Ruan, Neema Yazdani, Jacob A Beierle, Kathryn M Hixson, Kristen E Hokenson, Daniel J Apicco, Kimberly Luttik, Karen Zheng, Peter EA Ash, Karen Szumlinski, Shelley Russek, Benjamin Wolozin, Camron D Bryant

Impact of DNA sequencing and analysis methods on 16S rRNA gene bacterial community analysis in dairy products. Zhengyao Xue, Mary E Kable, Maria L Marco

Characterisation and functional predictions of canine long non-coding RNAs. Céline Le Béguec, Valentin Wucher, Laetitia Lagoutte, Edouard Cadieu, Nadine Botherel, Benoit Hédan, Clotilde De Brito, Anne-Sophie Guillory, Catherine André, Thomas Derrien, Christophe Hitte

In silico analysis of piRNAs in retina reveals potential targets in intracellular transport and retinal degeneration. Suganya Sivagurunathan, Nagesh Srikakulam, Jayamuruga Pandian Arunachalam, Gopal Pandi, Subbulakshmi Chidambaram

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

Widespread cis-regulation of RNA-editing in a large mammal. Thomas J Lopdell, Christine Couldrey, Kathryn Tiplady, Stephan R Davis, Russell G Snell, Bevin L Harris, Mathew D Littlejohn

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

Gene Set Enrichment Analysis (GSEA) of Upregulated Genes in Cocaine Addiction Reveals miRNAs as Potential Therapeutic Agents. Ishtiaque Ahammad, Sarbojoy Saha

Systematic evaluation of isoform function in literature reports of alternative splicing. Shamsuddin Bhuiyan, Sophia Ly, Minh Phan, Brandon Huntington, Ellie Hogan, Chao Chun Liu, James Liu, Paul Pavlidis

Direct inference of base-pairing probabilities with neural networks improves RNA secondary structure prediction with pseudoknots. Manato Akiyama, Yasubumi Sakakibara, Kengo Sato

Identification of a secretion-enhancing cis regulatory targeting element (SECReTE) involved in mRNA localization and protein synthesis. Osnat Cohen-Zontag, Lisha Qiu Jin Lim, Dvir Dahary, Tsviya Olender, Yitzhak Pilpel, Jeffrey Gerst

A cytoplasmic Argonaute protein promotes the inheritance of RNAi. Fei Xu, Xuezhu Feng, Xiangyang Chen, Chenchun Weng, Qi Yan, Ting Xu, Minjie Hong, Shouhong Guang

Six species of non-tuberculosis mycobacteria carry non-identical 16S rRNA gene copies. Keita Takeda, Kinuyo Chikamatsu, Yuriko Igarashi, Yuta Morishige, Yoshiro Murase, Akio Aono, Hiroyuki Yamada, Akiko Takaki, Satoshi Mitarai

Poly-Target Selection Identifies RNA Broad-Spectrum Inhibitors of HIV Reverse Transcriptases. Khalid K. Alam, Jonathan L. Chang, Margaret J. Lange, Phuong D.M. Nguyen, Andrew W. Sawyer, Donald H. Burke

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

A method for RNA structure prediction shows evidence for structure in lncRNAs. Riccardo Delli Ponti, Alexandros Armaos, Stefanie Marti, Gian Gaetano Tartaglia

 

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RNA preprints: W15/2018

Long non-coding RNAs in wild wheat progenitors. Alice Pieri, Mario Enrico Pè, Edoardo Bertolini

MicroRNA-205 affects mouse granulosa cell apoptosis and estradiol synthesis by targeting CREB1. Zhang Pengju, Wang Jun, Lang Hongyan, Wang Weixia, Liu Xiaohui, Liu Haiyan, Tan Chengcheng, Li Xintao, Zhao Yumin, Wu Xinghong

Co-regulation of alternative splicing by hnRNPM and ESRP1 during EMT. Samuel Harvey, Yilin Xu, Xiaodan Lin, Xin D Gao, Yushan Qiu, Jaegyoon Ahn, Xinshu Xiao, Chonghui Cheng

Phase Separations Driven by RNA Scaffolds and Protein Sequestration in FXTAS. Teresa Botta-Orfila, Fernando Cid-Samper, Iona Gelabert-Baldrich, Benjamin Lang, Nieves Lorenzo-Gotor, Riccardo Delli Ponti, Lies-Anne WFM Severijnen, Benedetta Bolognesi, Ellen Gelpi, Renate K. Hukema-Felten, Gian Gaetano Tartaglia

Circular RNA expression in human hematopoietic cells is widespread and cell-type specific. Benoit P Nicolet, Sander Engels, Francesca Aglialoro, Emile van den Akker, Marieke M von Lindern, Monika C Wolkers

Translation elongation and mRNA stability are coupled through the ribosomal A-site. Gavin Hanson, Najwa Alhusaini, Nathan Morris, Thomas Sweet, Jeff Coller

RNAs as proximity labeling media for identifying nuclear speckle positions relative to the genome. Weizhong Chen, Zhangming Yan, Simin Li, Norman Huang, Xuerui Huang, Jin Zhang, Sheng Zhong

Predicting the Impact of cis-Regulatory Variation on Alternative Polyadenylation. Nicholas Bogard, Johannes Linder, Alexander B Rosenberg, Georg Seelig

A transmissible RNA pathway in honey bees. Eyal Maori, Yael Garbian, Vered Kunik, Rita Mozes-Koch, Osnat Malka, Haim Kalev, Niv Sabath, Ilan Sela, Sharoni Shafir

A planarian nidovirus expands the limits of RNA genome size. Amir Saberi, Anastasia A. Gulyaeva, John Brubacher, Phillip A. Newmark, Alexander Gorbalenya

ampvis2: an R package to analyse and visualise 16S rRNA amplicon data. Kasper S. Skytte Andersen, Rasmus H. Kirkegaard, Soeren M. Karst, Mads Albertsen

CUDA RNAfold. W B Langdon, Ronny Lorenz

Hippocampal knockdown of Piwil1 and Piwil2 enhances contextual fear memory in mice. Laura Jane Leighton, Wei Wei, Vikram S Ratnu, Xiang Li, Esmi L Zajaczkowski, Paola A Spadaro, Nitin Khandelwal, Arvind Kumar, Timothy W Bredy

MicroRNAs reinforce repression of PRC2 transcriptional targets independently and through a feed-forward regulatory network with PRC2. Haridha Shivram, Steven V Le, Vishwanath R Iyer

Identification of PTBP1 responsible for caspase dependent YRNA cleavage. Jun Ogata, Yuki Sugiura, Akinori Kanai, Masafumi Tanaka, Hirotaka Matsui, Masato Ohtsuka, Toshiya Inaba, Motoyuki Otsuka, Ai Kotani

The Translation Machinery Is Immune from miRNA Perturbations: A Cell-Based Probabilistic Approach. Shelly Mahlab-Aviv, Nathan Linial, Michal Linial

Heteromeric RNP assembly at LINEs controls lineage-specific RNA processing. Jan Attig, Federico Agostini, Clare Gooding, Aarti Singh, Anob M Chakrabarti, Nejc Haberman, Warren Emmett, Christopher WJ Smith, Nicholas M Luscombe, Jernej Ule

Key role of piRNAs in telomeric chromatin maintenance and telomere nuclear positioning in Drosophila germline. Elizaveta Radion, Valeriya Morgunova, Sergei Ryazansky, Natalia Akulenko, Sergey Lavrov, Yuri Abramov, Pavel Komarov, Sergey Glukhov, Ivan Olovnikov, Alla Kalmykova

Riboglow: a multicolor riboswitch-based platform for live cell imaging of mRNA and small non-coding RNA in mammalian cells. Esther Braselmann, Aleksandra J Wierzba, Jacob T Polaski, Mikolaj Chrominski, Zachariah Holmes, Sheng-Ting Hung, Dilara Batan, Joshua Wheeler, Roy Parker, Ralph Jimenez, Dorota Gryko, Robert T. T Batey, Amy E Palmer

Taxonomy annotation and guide tree errors in 16S rRNA databases. Robert C Edgar

Specific miRNA-GPCR networks regulate Sox9a/Sox9b activities to promote gonadal renewal in zebrafish. Jizhou Yan, Xinlu Du, Huiping Guo, Ying Zhang, Jiacheng Wu, Mingyou Li, Xianxin Hua

Polypyrimidine Tract Binding Protein blocks microRNA-124 biogenesis to enforce its neuronal specific expression. Kyu-Hyeon Yeom, Simon Mitchell, Anthony J Linares, Sika Zheng, Chia-Ho Lin, Xiao-Jun Wang, Alexander Hoffmann, Douglas L Black

Uncoupling DNA- and RNA-directed DNA methylation at Rasgrf1. Erin T. Chu, David H. Taylor, Margaret Hofstedt, Paul D. Soloway

RNA preprints: W14/2018

Detecting Differential Variable microRNAs via Model-Based Clustering. Xuan Li, Yuejiao Fu, Xiaogang Wang, Dawn L DeMeo, Kelan Tantisira, Scott T. Weiss, Weiliang Qiu

SPORTS1.0: a tool for annotating and profiling non-coding RNAs optimized for rRNA- and tRNA- derived small RNAs. Junchao Shi, Euna Ko, Kenton M Sanders, Qi Chen, Tong Zhou

Muscleblind regulates Drosophila Dscam2 cell-type-specific alternative splicing. Joshua Shing Shun Li, Kevin Nzumbi Mutemi, S Sean Millard

The Evolution of Small-RNA-Mediated Silencing of an Invading Transposable Element. Erin S. Kelleher, Ricardo B. R. Azevedo, Yichen Zheng

Isolation and sequencing of AGO-bound RNAs reveals characteristics of mammalian stem-loop processing in vivo. Ian M Silverman, Sager J Gosai, Nicholas Vrettos, Shawn W Foley, Nathan D Berkowitz, Zissimos Mourelatos, Brian D Gregory

The trypanocidal benzoxaborole AN7973 inhibits trypanosome mRNA processing. Daniela Begolo, Isabel M Vincent, Federica Giordani, Michael J Witty, Timothy G Rowan, Zakaria Bengaly, Kirsten Gillingwater, Yvonne Freund, Michael P Barrett, Christine E Clayton

Small RNA-mediated genomic silencing promotes telomere stability in the absence of telomerase. Charles Longtine, Stephen Frenk, Shawn Ahmed

Global changes in mRNA abundance drive differential shuttling of RNA binding proteins, linking cytoplasmic RNA degradation to transcription. Sarah Gilbertson, Joel D Federspiel, Ella Hartenian, Ileana M Cristea, Britt Glaunsinger

Intron-containing RNA from the HIV-1 provirus activates type I interferon and inflammatory cytokines. Sean Matthew McCauley, Kyusik Kim, Anetta Nowosielska, Ann Dauphin, William Edward Diehl, Jeremy Luban

Genome variants associated with RNA splicing variation in bovine are extensively shared between tissues. Ruidong Xiang, Ben J. Hayes, Christy J. Vander Jagt, Iona M. MacLeod, Majid Khansefid, Phil J. Bowman, Zehu Yuan, Claire P. Prowse-Wilkins, Coralie M. Reich, Brett A. Mason, Josie B. Garner, Leah C. Marett, Yizhou Chen, Sunduimijid Bolormaa, Hans D. Daetwyler, Amanda J. Chamberlain, Michael E. Goddard

Robustness of bristle number to temperature and genetic background varies with bristle type and is regulated by miR-9a. Alexis Matamoro-Vidal, Thomas Tully, Virginie Courtier-Orgogozo

Deciphering human ribonucleoprotein regulatory networks. Neelanjan Mukherjee, Hans-Hermann Wessels, Svetlana Lebedeva, Marcin Sajek, Thalia Farazi, Mahsa Ghanbari, Aitor Garzia, Alina Munteanu, Aleksandra Mihailovic, Jessica Spitzer, Kemal Akat, Thomas Tuschl, Uwe Ohler

Evidence for a potential role of miR-1908-5p and miR-3614-5p in autoimmune disease risk using genome-wide analyses. Inken Wohlers, Lars Bertram, Christina Lill

Mettl14 is required for mouse post-implantation development by facilitating epiblast maturation. Qing-Yuan Sun, Tie Gang Meng, Xukun Lu, Lei Guo, Guan Mei Hou, Qian Nan Li, Xue Shan Ma, Lin Huang, Li Hua Fan, Zheng Hui Zhao, Xiang Hong Ou, Ying Chun Ouyang, Heide Schatten, Lei Li, Zhen Bo Wang

PinMol: Python application for designing molecular beacons for live cell imaging of endogenous mRNAs. Livia V. Bayer, Omar S. Omar, Diana P. Bratu, Irina E. Catrina

Stability of local secondary structure determines selectivity of viral RNA chaperones. Jack P.K. Bravo, Alexander Borodavka, Anders Barth, Antonio N Calabrese, Peter Mojzes, Joseph J.B. Cockburn, Don C Lamb, Roman Tuma

A Nested 2-Level Cross-validation Ensemble Learning Pipeline Suggests a Negative Pressure Against Crosstalk snoRNA-mRNA Interactions in Saccharomyces cerevisae. Antoine Soule, Jean-Marc Steyaert, Jerome Waldispuhl

Sequential regulation of maternal mRNAs through a conserved cis-acting element in their 3’ UTRs. Pooja Flora, Siu Wah Wong-Deyrup, Elliot Martin, Ryan Palumbo, Mohamad Nasrallah, Andrew Oligney, Patrick Blatt, Dhruv Patel, Gabriele Fuchs, Prashanth Rangan

Knockdown of GAS5 restores ox-LDL-induced impaired autophagy flux via upregulating miR-26a in human endothelial cells. Weijie Liang, Taibing Fan, Lin Liu, Lianzhong Zhang

The cellular NMD pathway restricts Zika virus infection and is targeted by the viral capsid protein. Krystal A Fontaine, Kristoffer E Leon, Mir Mubashir Khalid, David Jimenez-Morales, Mariah Dunlap, Julia A Kaye, Priya S Shah, Steven Finkbeiner, Nevan J Krogan, Melanie Ott

Identification of microRNA clusters cooperatively acting on Epithelial to Mesenchymal Transition in Triple Negative Breast Cancer. Laura Cantini, Gloria Bertoli, Claudia Cava, Thierry Dubois, Andrei Zinovyev, Michele Caselle, Isabella Castiglioni, Emmanuel Barillot, Loredana Martignetti

RNA preprints: W13/2018

Protein structure and function analyses to understand the implication of mutually exclusive splicing. Su Datt Lam, Christine Orengo, Jonathan Lees

Small RNA-mediated genomic silencing promotes telomere stability in the absence of telomerase. Charlie Longtine, Stephen Frenk, shawn ahmed

Endogenous miRNA sponges mediate the generation of oscillatory dynamics for a non-coding RNA network. Andrew Dhawan, Adrian L. Harris, Francesca M Buffa, Jacob G Scott

Estimating RNA structure chemical probing reactivities from reverse transcriptase stops and mutations. Angela M Yu, Molly E. Evans, Julius B. Lucks

In vitro assembly of an early spliceosome defining both splice sites. Kaushik Saha, Mike Minh Fernandez, Tapan Biswas, Charles Leonard Lumba, Gourisankar Ghosh

A post-transcriptional regulatory code for mRNA stability during the zebrafish maternal-to-zygotic transition. Charles E Vejnar, Mario Abdel Messih, Carter M Takacs, Valeria Yartseva, Panos Oikonomou, Romain Christiano, Marlon Stoeckius, Stephanie Lau, Miler T Lee, Jean-Denis Beaudoin, Hiba Darwich-Codore, Tobias C Walther, Saeed Tavazoie, Daniel Cifuentes, Antonio J Giraldez

Exonic unpaired elements modulate pre-mRNA structure for splice site recognition. Kaushik Saha, Tapan Biswas, Mike Minh Fernandez, Whitney England, Robert Spitale, Gourisankar Ghosh

Coding and non-coding RNA dysregulation in bipolar disorder. Jurjen Luykx, Fabrizio Giuliani, Giuliano Giuliani, Jan Veldink

A fungal ribonuclease-like effector protein inhibits plant host ribosomal RNA degradation. Pietro D Spanu, Helen G Pennington, Rhian Jones, Seomun Kwon, Giulia Bonciani, Hannah Thieron, Thomas Chandler, Peggy Luong, Sian Morgan, Michal Przydacz, Tolga O. Bozkurt, Sarah Bowden, Melanie Craze, Emma Wallington, James Garnett, Mark Kwaitaal, Ralph Panstruga, Ernesto Cota

Germline silencing of UASt depends on the piRNA pathway. Yi-Chun Huang, Henry Moreno, Sarayu Row, Dongyu Jia, Wu-Min Deng

The cellular NMD pathway restricts Zika virus infection and is targeted by the viral capsid protein. Krystal A Fontaine, Kristoffer E Leon, Mir Mubashir Khalid, David Jimenez-Morales, Julia Kaye, Priya Shah, Steven Finkbeiner, Nevan Krogan, Melanie Ott

Quantitative characterization of translational riboregulators using an in vitro transcription-translation system. Anis Senoussi, Jonathan Lee Tin Wah, Yoshihiro Shimizu, Jerome Robert, Alfonso Jaramillo, Sven Findeiss, Ilka M Axmann, Andre Estevez-Torres

Complete guide RNA design for CRISPR-mediated regulation of human long noncoding RNA transcription. Amir Saberi, Renjun Zhu, Chulan Kwon

Identification of microRNA clusters cooperatively acting on Epithelial to Mesenchymal Transition in Triple Negative Breast Cancer. Laura Cantini, Gloria Bertoli, Claudia Cava, Thierry Dubois, Andrei Zinovyev, Michele Caselle, Isabella Castiglioni, Emmanuel Barillot, Loredana Martignetti

Numerous recursive sites contribute to accuracy of splicing of long introns in flies. Athma A Pai, Joseph Paggi, Karen Adelman, Christopher B Burge

Intronic non-coding RNAs within ribosomal protein coding genes can regulate biogenesis of yeast ribosome. Akshara Pande, Rani Sharma, Bharat Ravi Iyengar, Vinod Scaria, Beena Pillai, Samir K Brahmachari

Onset of differentiation is posttranscriptionally controlled in adult neural stem cells. Avni Baser, Yonglong Dang, Maxim Skabkin, Guelce Guelcueler Balta, Georgios Kalamakis, Susanne Kleber, Manuel Goepferich, Roman Schefzik, Alejandro Santos Lopez, Enric Llorens Bobadilla, Carsten Schultz, Bernd Fischer, Ana Martin-Villalba

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

The formation of intramolecular secondary structure brings mRNA ends in close proximity. Wan-Jung C Lai, Mohammad Kayedkhordeh, Erica V Cornell, Elie Farah, Stanislav Bellaousov, Robert Rietmeijer, David H Mathews, Dmitri N Ermolenko

Small non-coding RNA expression in developing mouse nephron progenitor cells. Yu Leng Phua, Andrew Clugston, Kevin Hong Chen, Dennis Kostka, Jacqueline Ho

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

Competing endogenous RNA network: Potential entrants to gene editing in Hepatocellular Carcinoma. Ayman Shafei, Marwa Matboli, Mahmoud Ali, Ziad Nagy, Maged Reda, Mohamed Salah, Ahmed Hamdy, Mahmoud Abdelgawad, Ahmed Ashry, Mohammad Tarek, Osama Saber, Ahmed Azazy, Badr Mohamed, Mohamed Hassan, Nashwa El-Khazragy, Sherif El-Khamisy