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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RNA preprints: W19/2018

A new full-length virus genome sequencing method reveals that antiviral RNAi changes geminivirus populations in field-grown cassava. Devang Mehta, Matthias Hirsch-Hoffmann, Mariam Were, Andrea Patrignani, Hassan Were, Wilhelm Gruissem, Hervé Vanderschuren

RsmV a small non-coding regulatory RNA in Pseudomonas aeruginosa that sequesters RsmA and RsmF from target mRNAs. Kayley H Janssen, Manisha Diaz, Cindy J Gode, Matthew C Wolfgang, Timothy L Yahr

Exponential fluorescent amplification of individual RNAs using clampFISH probes. Sara H Rouhanifard, Ian A Mellis, Margaret Dunagin, Sareh Bayatpour, Orsolya Symmons, Allison Cote, Arjun Raj

Decoupling the impact of microRNAs on translational repression versus RNA degradation in embryonic stem cells. Jacob Freimer, TJ Hu, Robert Blelloch

RNA polymerase II clustering through CTD phase separation. Marc Boehning, Claire Dugast-Darzacq, Marija Rankovic, Anders S Hansen, Tae-Kyung Yu, Herve Marie-Nelly, Goran Kokic, Gina M Dailey, Patrick Cramer, Xavier Darzacq, Markus Zweckstetter

CSB-dependent CDK9 degradation and RNA Polymerase II phosphorylation during Transcription Coupled Repair. Lise-Marie Donnio, Anna Lagarou, Gabrielle Sueur, Pierre-Olivier MARI, Giuseppina Giglia-Mari

MiRNA expression profiles of serum exosomes derived from individuals with latent and active tuberculosis. Lingna Lyu, Jinghui Wang, Hong-yan Jia, Liping Pan, Zi-hui Li, Feng-jiao Du, Bo-ping Du, Qi Sun, Zong-de Zhang

S phase R-loop formation is restricted by PrimPol-mediated repriming. Saša Šviković, Alastair Crisp, Sue Mei Tan-Wong, Thomas A. Guilliam, Aidan J. Doherty, Nick J Proudfoot, Guillaume Guilbaud, Julian E. Sale

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

Co-transcriptional loading of RNA export factors shapes the human transcriptome. Nicolas Viphakone, Ian M Sudbery, Catherine Heath, David Sims, Stuart A Wilson

The variations of human miRNAs and Ising like base pairing models. Jyoti Prasad Banerjee, Jayanta Kumar Das, Pabitra Pal Choudhury, Sayak Mukherjee, Sk. Sarif Hassan, Pallab Basu

MiR-29b-1-5p is altered in BRCA1 mutant tumours and is a biomarker in basal- like breast cancer. Michael Milevskiy, Gurveen Sandhu, Anna Wronski, Darren Korbie, Brooke Brewster, Annette Shewan, Stacey Edwards, Juliet French, Melissa Brown

Production of spliced long noncoding RNAs specifies regions with increased enhancer activity. Noa Gil, Igor Ulitsky

Pathogenic DDX3X mutations impair RNA metabolism and neurogenesis during fetal cortical development. Ashley L. Lennox, Ruiji Jiang, Lindsey Suit, Brieana Fregeau, Charles J. Sheehan, Kimberly A. Aldinger, Ching Moey, Iryna Lobach, Ghayda Mirzaa, Alexandra Afenjar, Dusica Babovic-Vuksanovic, Stéphane Bézieau, Patrick R. Blackburn, Jens Bunt, Lydie Burglen, Perrine Charles, Brian H.Y. Chung, Benjamin Cogné, Suzanne DeBrosse, Nataliya Di Donato, Laurence Faivre, Delphine Héron, A. Micheil Innes, Bertrand Isidor, Bethany L. Johnson-Kerner, Boris Keren, Amy Kimball, Eric W. Klee, Paul Kuentz, Sébastien Küry, Dominique Martin-Coignard, Cyril Mignot, Noriko Miyake, Caroline Nava, Mathilde Nizon, Diana Rodriguez, Lot Snijders Blok, Christel Thauvin, Julien Thevenon, Marie Vincent, Alban Ziegler, William Dobyns, Linda J. Richards, A. James Barkovich, Stephen N. Floor, Debra L. Silver, Elliott H. Sherr

Neutrophil microvesicles drive atherosclerosis by delivering miR-155 to atheroprone endothelium. Ingrid Gomez, Ben Ward, Celine Souilhol, Chiara Recarti, Mark Ariaans, Jessica Johnston, Amanda Burnett, Marwa Mahmoud, Le Anh Luong, Laura West, Merete Long, Sion Parry, Rachel Woods, Carl Hulston, Birke Benedikter, Rohit Bazaz, Sheila Francis, Endre Kiss-Toth, Marc van Zandvoort, Andreas Schober, Paul Hellewell, Paul Evans, Victoria Ridger

Dlk1-Dio3 Locus-Derived LncRNAs Perpetuate Postmitotic Motor Neuron Cell Fate and Subtype Identity. Ya-Ping Yen, Wen-Fu Hsieh, Ya-Lin Lu, Ee Shan Liau, Ho-Chiang Hsu, Yen-Chung Chen, Ting-Chun Liu, Mien Chang, Joye Li, Shau-Ping Lin, Jui-Hung Hung, Jun-An Chen

DOT1L suppresses nuclear RNAi originating from enhancer elements in Caenorhabditis elegans. Ruben Esse, Ekaterina Gushchanskaia, Avery Lord, Alla Grishok

The interplay between small RNA pathways shapes chromatin landscape in C. elegans. Ekaterina Gushchanskaia, Ruben Esse, Qicheng Ma, Nelson Lau, Alla Grishok

RNA polymerase organizes into distinct spatial clusters independent of ribosomal RNA transcription in E. coli. Xiaoli Weng, Christopher Herrick Bohrer, Kelsey Bettridge, Arvin Cesar Lagda, Cedric Cagliero, Ding Jun Jin, Jie Xiao

Large-scale RNA editing profiling in different adult chicken tissues. Mohammad Reza Bakhtiarizadeh, Hamid Shafiei, Abdolreza Salehi

 

RNA preprints: W18/2018

Adaptive Partitioning of the tRNA Interaction Interface by Aminoacyl-tRNA-Synthetases. Andy Collins-Hed, David H Ardell

The suppressive cap-binding-complex factor 4EIP is required for normal differentiation. Christine Clayton, Monica Terrao, Kevin Kamanyi Marucha, Elisha Mugo, Dorothea Droll, Ihor Minia, Franziska Egler, Johanna Braun

Promoter activity buffering reduces the fitness cost of misregulation. Miquel Angel Schikora-Tamarit, Guillem Lopez-Grado i Salinas, Carolina Gonzalez Navasa, Irene Calderon, Xavi Marcos-Fa, Miquel Sas, Lucas Carey

Direct reprogramming of human epithelial cells into organoids by miR-106a-3p. Frederic Delom, Michel Puceat, Delphine Fessart

16S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses. Stephen Woloszynek, Zhengqiao Zhao, Jian Chen, Gail L. Rosen

A single N1-methyladenosine on the large ribosomal subunit rRNA impacts locally its structure and the translation of key metabolic enzymes. Sunny Sharma, Johannes David Hartmann, Peter Watzinger, Arvid Klepper, Christian Peifer, Peter Koetter, Denis LJ Lafontaine, Karl-Dieter Entian

Structural basis for the RNA-guided ribonuclease activity of CRISPR-Cas13d. Cheng Zhang, Silvana Konermann, Nicholas J Brideau, Peter Lotfy, Scott J Novick, Timothy Strutzenberg, Patrick R Griffin, Patrick D Hsu, Dmitry Lyumkis

Response to “No evidence of functional co-adaptation between clustered microRNAs”. Yirong Wang, Hong Zhang, Jian Lu

A Rev-CBP80-eIF4AI complex drives Gag synthesis from the HIV-1 unspliced mRNA. Daniela Toro-Ascuy, Bárbara Rojas-Araya, Francisco García-de-Gracia, Cecilia Rojas-Fuentes, Camila Pereira-Montecinos, Aracelly Gaete-Argel, Fernando Valiente-Echeverría, Théophile Ohlmann, Ricardo Soto-Rifo

Misoprostol regulates Bnip3 repression and alternative splicing to control cellular calcium homeostasis during hypoxic stress. Jared T. Field, Matthew D. Martens, Wajihah Mughal, Yan Hai, Donald Chapman, Grant M. Hatch, Tammy L. Ivanco, William Diehl-Jones, Joseph W. Gordon

CRISPR-Cas blocks antibiotic resistance plasmid transfer between Enterococcus faecalis strains in the gastrointestinal tract. Valerie J Price, Sara W McBride, Breck Duerkop, Kelli L Palmer

DDX41 recognizes RNA/DNA retroviral reverse transcripts and is critical for in vivo control of MLV infection. Spyridon Stavrou, Alexya Aguilera, Kristin Blouch, Susan R Ross

Structural basis for transfer RNA mimicry by a bacterial Y RNA. Wei Wang, Xinguo Chen, Sandra L Wolin, Yong Xiong

The spatial and temporal dynamics of the nuclear RNAi-targeted RNA transcripts in Caenorhabditis elegans. Julie Zhouli Ni, Natallia Kalinava, Sofia Galindo Mendoza, Sam Guoping Gu

Negative Cooperativity between Gemin2 and RNA Determines RNA Selection and Release of the SMN Complex in snRNP Assembly. Hongfei Yi, Li Mu, Congcong Shen, Xi Kong, Yingzhi Wang, Yan Hou, Rundong Zhang

MECP2 duplication and mutations impair NSCs differentiation via miR-197 regulated ADAM10. Yumeng Wang, Yufang Zheng, Siyu Yang, Zhangmin Yang, Lin-na Zhang, Yan-qin He, Xiaohong Gong, Dong Liu, Richard H Finnell, Zilong Qiu, Yasong Du, Hongyan Wang

Enhancer control of miR-155 expression in Epstein-Barr virus infected B cells. C David Wood, Thomas Carvell, Andrea Gunnell, Opeoluwa O Ojeniyi, Cameron S Osborne, Michelle J West

M1A within cytoplasmic mRNAs at single nucleotide resolution: A reconciled transcriptome-wide map. Schraga Schwartz

A systematic survey of human tissue-specific gene expression and splicing reveals new opportunities for therapeutic target identification and evaluation. Robert Y Yang, Jie Quan, Reza Sodaie, Francois Aguet, Ayellet V Segre, John A Allen, Thomas A Lanz, Veronica Reinhart, Matthew Crawford, Samuel Hasson, GTEx Consortium, Kristin G Ardlie, Roderic Guigo, Hualin S Xi

Small RNAs gained during epididymal transit of sperm are essential for embryonic development in mice. Colin Conine, Fengyun Sun, Lina Song, Jaime Rivera-Perez, Oliver Rando

Efficient computation of co-transcriptional RNA-ligand interaction dynamics. Michael T Wolfinger, Christoph Flamm, Ivo L Hofacker

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

Identification of small regulatory RNAs involved in persister formation. Shanshan Zhang, Shuang Liu, Nan Wu, Wenhong Zhang, Ying Zhang

Biogenesis of a young, 22-nt microRNA in Phaseoleae species by precursor-programmed uridylation. Qili Fei, Yu Yu, Li Liu, Yu Zhang, Patricia Baldrich, Qing Dai, Xuemei Chen, Blake Meyers

RNA preprints: W17/2018

U1 snRNP regulates chromatin retention of noncoding RNAs. Yafei Yin, Jinlong Yuyang Lu, Xuechun Zhang, Wen Shao, Yanhui Xu, Pan Li, Yantao Hong, Qiangfeng Cliff Zhang, Xiaohua Shen

Human 5′ UTR design and variant effect prediction from a massively parallel translation assay. Paul J Sample, Ban Wang, David W Reid, Vladimir Presnyak, Iain McFadyen, David R Morris, Georg Seelig

Helicase Promotes Replication Re-initiation from an RNA Transcript. Bo Sun, Anupam Singh, Shemaila Sultana, James Inman, Smita Patel, Michelle Wang

The conservation landscape of the human ribosomal RNA gene repeats. Saumya Agrawal, Austen R.D. Ganley

Buffering gene expression noise by microRNA based feedforward regulation. Pavol Bokes, Michal Hojcka, Abhyudai Singh

Circulating microRNA biomarkers for metastatic disease in neuroblastoma patients. Fjoralba Zeka, Alan Van Goethem, Katrien Vanderheyden, Fleur Demuynck, Tim Lammens, Anneleen Decock, Hetty H Helsmoortel, Joelle Vermeulen, Rosa Noguera, Ana P Berbegall, Valerie Combaret, Gudrun Schleiermacher, Genevieve Laureys, Alexander Schramm, Johannes H Schulte, Sven Rahmann, Julie Bienertova Vasku, Pavel Mazanek, Marta Jeison, Shifra Ash, Michael D Hogarty, Mirthala Moreno-Smith, Eveline Barbieri, Jason Shohet, Frank Berthold, Frank Speleman, Matthias Fischer, Katleen De Preter, Pieter Mestdagh, Jo Vandesompele

A speed-fidelity trade-off determines the mutation rate and virulence of an RNA virus. William Fitzsimmons, Robert J. Woods, John T. McCrone, Andrew Woodman, Jamie J. Arnold, Madhumita Yennawar, Richard Evans, Craig E. Cameron, Adam S. Lauring

Intron retention as a novel source of cancer neoantigens. Alicia C Smart, Claire A Margolis, Harold Pimentel, Meng Xiao He, Diana Miao, Dennis Adeegbe, Tim Fugmann, Kwok Kin Wong, Eliezer M Van Allen

The miR-96 and RAR&gamma signaling axis governs androgen signaling and prostate cancer 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

TP53 Intron Derived Concentrations Implicate p53. Kevin G Bermeister, Jonathan Dyne, Xinghao Yu

ADAR2 mediated Q/R editing of GluK2 regulates homeostatic plasticity of kainate receptors. Sonam Gurung, Ashley J Evans, Kevin A Wilkinson, Jeremy Henley

Association Between Colonic Level of microRNA 31 and Subtypes of Adult and Pediatric Crohn’s Disease. Benjamin P Keith, Jasmine B Barrow, Nevzat Kazgan, Neil D Shah, Greg R Gipson, Wendy A Pitman, Shruti J Saxena, Elisabeth A Wolber, Matthew S Schaner, Michelle Hoffner O’Connor, Omar K Tradd, Matthew Kanke, Takahiko Toyonaga, Nicole Chaumont, Timothy S Sadiq, Mark J Koruda, Paul A Cotney, Nancy Allbritton, Dimitri G Trembath, Francisco Sylvester, Terrence S Furey, Praveen Sethupathy, Shehzad Z Sheikh

Transgenerational sterility of Piwi pathway mutants in response to germ granule dysfunction. Katherine Kretovich Billmyre, Bree Heestand, Maya Spichal, Stephen Frenk, Shawn Ahmed

Expanding the size limit of RNA viruses: Evidence of a novel divergent nidovirus in California sea hare, with a ~35.9 kb virus genome. Humberto J Debat

Genetic analysis of RNA polymerase I unveils new role of the Rpa12 subunit during transcription. Tommy Darrière, Michael Pilsl, Adrien Chauvier, Titouan Genty, Sylvain Audibert, Christophe Dez, Isabelle Leger-Silvestre, Christophe Normand, Olga Calvo, Carlos Fernández-Tornero, Herbert Tschochner, Olivier Gadal

Transcription Factor Regulation of RNA polymerase’s Torsional Capacity. Jie Ma, Chuang Tan, Xiang Gao, Robert Fulbright, Jeffery Roberts, Michelle D. Wang

A Single Mechanism of Biogenesis, Initiated and Directed by PIWI Proteins, Explains piRNA Production in Most Animals. Phillip Zamore, Ildar Gainetdinov, Cansu Colpan, Katharine Cecchini

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