RNA preprints: W20/2018

Site specific target binding controls RNA cleavage efficiency by the Kaposi’s sarcoma-associated herpesvirus endonuclease SOX. Aaron Stephen Mendez, Carolin Vogt, Jens Bohne, Britt A Glaunsinger

Extracellular HBV RNAs are heterogeneous in length and circulate as virions and capsid-antibody-complexes in chronic hepatitis B patients. Lu Bai, Xiaonan Zhang, Weixia Li, Min Wu, Jiangxia Liu, Maya Kozlowski, Liang Chen, Jiming Zhang, Yuxian Huang, Zhenghong Yuan

Multifunctional RNA-binding proteins mediate ecdysone-dependent germline stem cell self-renewal in Drosophila. Danielle S Finger, Vivian V Holt, Elizabeth T Ables

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

Evidence of an Unusual Poly(A) RNA Signature Detected by High-throughput Chemical Mapping. Roger Wellington-Oguri, Eli Fisker, Michelle Wiley, Mat Zada, Eterna Players

Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia. Gerard Minuesa, Steven K Albanese, Arthur Chow, Alexandra Schurer, Sun-Mi Park, Christina Z. Rotsides, James Taggart, Andrea Rizzi, Levi N. Naden, Timothy Chou, Saroj Gourkanti, Daniel Cappel, Maria C Passarelli, Lauren Fairchild, Carolina Adura, Fraser J Glickman, Jessica Schulman, Christopher Famulare, Minal Patel, Joseph K Eibl, Gregory M Ross, Derek S Tan, Christina S Leslie, Thijs Beuming, Yehuda Goldgur, John D Chodera, Michael G Kharas

A discriminator code–based DTD surveillance ensures faithful glycine delivery for protein biosynthesis in bacteria. Rajan Sankaranarayanan, Santosh Kumar Kuncha, Katta Suma, Komal Ishwar Pawar, Jotin Gogoi, Satya Brata Routh, Sambhavi Pottabathini, Shobha P Kruparani

Ularcirc: Visualisation and enhanced analysis of circular RNAs via back and canonical forward splicing. David T. Humphreys, Nicolas Fossat, Patrick P.L. Tam, Joshua W. K. Ho

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

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

Cerox1 and microRNA-488-3p noncoding RNAs jointly regulate mitochondrial complex I catalytic activity. Tamara M Sirey, Kenny Roberts, Wilfried Haerty, Oscar Bedoya-Reina, Sebastian Rogatti-Granados, Jennifer Tan, Nick Li, Lisa Heather, Sarah Cooper, Ana Marques, Chris Ponting

TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes. Maria Waldl, Bernhard C. Thiel, Roman Ochsenreiter, Alexander Holzenleiter, João Victor de Araujo Oliveira, Maria Emília M. T. Walter, Michael T. Wolfinger, Peter F. Stadler

Construction and analysis of mRNA, miRNA, lncRNA, and TF regulatory networks reveal the key genes in prostate cancer. Su-Liang Li, Yun Ye, Sheng-Yu Wang

Engineered Genetic Redundancy Relaxes Selective Constraints upon Endogenous Genes in Viral RNA Genomes. Silvia Ambros, Francisca De la Iglesia, Sttefany M. Rosario, Anamarija Butkovic, Santiago F. Elena

Molecular analysis of long non-coding RNA GAS5 and microRNA-34a expression signature in common solid tumors: A pilot study. Eman A Toraih, Saleh Ali Alghamdi, Aya El-Wazir, Marwa H Hosny, Mohammad H Hussein, Motaz S Khashana, Manal S Fawzy

Discovery of microRNA-like RNAs during early fruiting body development in the model mushroom Coprinopsis cinerea. Amy Yuet-Ting Lau, Xuanjin Cheng, Chi Keung Cheng, Wenyan Nong, Man Kit Cheung, Raymond Hon-Fu Chan, Jerome Ho Lam Hui, Hoi Shan Kwan

S-MiRAGE: A quantitative, secreted RNA-based reporter of gene expression and cell persistence. Kinshuk Mitra, William N Feist, Simone Alfossi, Enrique Fuentes-Mattei, Maria Ines Almeida, Jean J Kim, George A Calin, Aryeh Warmflash

Splicing and epigenetic factors jointly regulate epidermal differentiation. Sabine E.J. Tanis, Pascal W.T. Jansen, Huiqing Zhou, Michiel Vermeulen, Klaas W. Mulder

Cohesin interacts with a panoply of splicing factors required for cell cycle progression and genomic organization. Jung-Sik Kim, Xiaoyuan He, Jie Liu, Zhijun Duan, Taeyeon Kim, Julia Gerard, Brian Kim, William S. Lane, William S. Noble, Bogdan Budnik, Todd Waldman

Messenger RNAs transcribed from yeast linear cytoplasmic plasmids possess unconventional 5′ and 3′ UTRs and suggest a novel mechanism of translation. Vaclav Vopalensky, Michal Sykora, Tomas Masek, Martin Pospisek

RBPMetaDB: A comprehensive annotation of mouse RNA-Seq datasets with perturbations of RNA-binding proteins. Jin Li, Su-Ping Deng, Jacob Vieira, James Thomas, Valerio Costa, Ching-San Tseng, Franjo Ivankovic, Alfredo Ciccodicola, Peng Yu

Deficiency for Piwi results in transmission of a heritable stress that promotes longevity via DAF-16/Foxo. Bree Heestand, Matt Simon, Stephen Frenk, Shawn Ahmed

DAF-16/Foxo suppresses the transgenerational sterility of prg-1 piRNA mutants via a systemic small RNA pathway. Matt Simon, Maya Spichal, Bree Heestand, Stephen Frenk, Ashley Hedges, Malik Godwin, Alicia Wellman, Aisa Sakaguchi, Shawn Ahmed

EternaBrain: Automated RNA design through move sets from an Internet-scale RNA videogame. Rohan Koodli, Benjamin Keep, Katherine R Coppess, Fernando Portela, Eterna Players, Rhiju Das

RNA components of the spliceosome regulate tissue- and cancer-specific alternative splicing. Heidi Dvinge, Jamie Guenthoer, Peggy L Porter, Robert K Bradley

N4-acetylcytidine and 5-formylcytidine are present in Saccharomyces cerevisiae mRNAs. Mehmet Tardu, Qishan Lin, Kristin Koutmou

 

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