RNA preprints: W28/2018

Scoring of pathogenic non-coding variants in Mendelian diseases through supervised learning on ancient, recent and ongoing purifying selection signals in human. Barthelemy Caron, Yufei Luo, Antonio Rausell

Fast and interpretable alternative splicing and differential gene-level expression analysis using transcriptome segmentation with Yanagi. Mohamed K Gunady, Steve Mount, Hector Corrada Bravo

Single-cell isoform RNA sequencing (ScISOr-Seq) across thousands of cells reveals isoforms of cerebellar cell types. Ishaan Gupta, Paul G Collier, Bettina Haase, Ahmed Mahfouz, Anoushka Joglekar, Taylor Floyd, Frank Koopmans, Ben Barres, August B Smit, Steven Sloan, Wenjie Luo, Olivier Fedrigo, M Elizabeth Ross, Hagen U Tilgner

Molecular simulations of the monovalent-ion dependent Folding Thermodynamics of RNA. Dave Thirumalai, Natalia A Denesyuk

Long non-coding RNAs defining major subtypes of B cell precursor acute lymphoblastic leukemia. Alva Rani James, Michael P Schroeder, Martin Neumann, Lorenz Bastian, Cornelia Eckert, Nicola Gökbuget, Jutta Ortiz Tanchez, Cornelia Schlee, Konstandina Isaakidis, Stefan Schwartz, Thomas Burmeister, Arend von Stackelberg, Michael A Rieger, Stefanie Göllner, Martin Horstman, Martin Schrappe, Renate Kirschner-Schwabe, Monika Brüggemann, Carsten Müller-Tidow, Hubert Serve, Altuna Akalin, Claudia D. Baldus

Spatial organization of single mRNPs at different stages of the gene expression pathway. Srivathsan Adivarahan, Nathan Livingston, Beth Nicholson, Samir Rahman, Bin Wu, Olivia Rissland, Daniel Zenklusen

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, Brandon F Maziuk, Peter EA Ash, Karen Szumlinski, Shelley Russek, Benjamin Wolozin, Camron D Bryant

Selective axonal translation of prenylated Cdc42 mRNA isoform supports axon growth. Seung Joon Lee, Amar N Kar, Riki Kawaguchi, Priyanka Patel, Pabitra K Sahoo, Byron Aguilar, Kelsey D Lanz, Caylee McCain, Giovanni Coppola, Qun Lu, Jeffery L. Twiss

Silencing of ANKRD12 circRNA induces molecular and functional changes associated with invasive phenotypes. Thasni Karedath, Ikhlak Ahmed, Wafaa Al Ameri, Fatima Al-Dasim, Simeon S Andrews, Samson Samuel, Iman K Al Azwani, Yasmin Ali Mohamoud, Arash Rafii, Joel A Malek

MicroRNA miR-7 and miR-17-92 in POMC neurons are associated with sex-specific regulation of diet-induced obesity. Tao Sun, Yanxia Gao, Jiaheng Li, Zhen Zhang, Ruihan Zhang, Andrew Pollock

Reconstitution of mammalian Cleavage Factor II involved in 3′ processing of mRNA precursors. Peter Schaefer, Christian Tueting, Lars Schoenemann, Uwe Kuehn, Thomas Treiber, Nora Treiber, Christian Ihling, Anne Graber, Walter Keller, Gunter Meister, Andrea Sinz, Elmar Wahle

mRNP architecture in translating and stress conditions reveals an ordered pathway of mRNP compaction. Anthony Khong, Roy Parker

Structural differences between pri-miRNA paralogs promotes alternative Drosha cleavage and expands target repertoires. Xavier Bofill De Ros, Wojciech K Kasprzak, Yuba Bhandari, Lixin Fan, Quinn Cavanaugh, Minjie Jiang, Lisheng Dai, Acong Yang, Tie-Juan Shao, Bruce A Shapiro, Yun-Xing Wang, Shuo Gu

The expanded universe of prokaryotic Argonaute proteins. Sergei Ryazansky, Andrey Kulbachinskiy, Alexei Aravin

Processivity, velocity and universal characteristics of nucleic acid unwinding by helicases. Shaon Chakrabarti, Christopher Jarzynski, D. Thirumalai

Cicada endosymbionts have tRNAs that are correctly processed despite having genomes that do not encode all of the tRNA processing machinery. James T Van Leuven, Meng Mao, Gordon M Bennett, John McCutcheon

Alzheimer’s disease risk SNPs show no strong effect on miRNA expression in human lymphoblastoid cell lines. Inken Wohlers, Colin Schulz, Fabian Kilpert, Lars Bertram

Regulating prospero mRNA Stability Determines When Neural Stem Cells Stop Dividing. Lu Yang, Tamsin J. Samuels, Yoav Arava, Francesca Robertson, Aino I. Järvelin, Ching-Po Yang, Tzumin Lee, David Ish-Horowicz, Ilan Davis

The role of Aβ circRNA in Alzheimer′s disease: alternative mechanism of Aβ biogenesis from Aβ circRNA translation. Dingding Mo, Di Cui, Xinping Li

Enhancing microRNA activity through increased endosomal release mediated by nigericin. Esteban A Orellana, Loganathan Rangasamy, Srinivasarao Tenneti, Ahmed M Abdelaal, Philip S. Low, Andrea L Kasinski

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

Model-based analysis of positive selection significantly expands the list of cancer driver genes, including RNA methyltransferases. Siming Zhao, Jun Liu, Pranav Nanga, Yuwen Liu, Ercument Cicek, Nicholas Knoblauch, Chuan He, Matthew Stephens, Xin He

miR-263b controls circadian rhythms and structural plasticity of small ventral lateral neurons by inhibition of Beadex. Xiaoge Nian, Wenfeng Chen, Weiwei Bai, Zhangwu Zhao, Yong Zhang

Posttranscriptional regulation of intestinal epithelial cell repair by RNA binding protein IMP1. Priya Chatterji, Kelly A Whelan, Sarah F Andres, Fernando Cid Samper, Lauren A Simon, Rei Mizuno, Emma T Lundsmith, David S.M Lee, Shun Liang, H.R. Sagara Wijeratne, Stefanie Marti, Lillian Chau, Patrick A Williams, Veronique Giroux, Benjamin J Wilkins, Gary D Wu, Premal Shah, Gian Gaetano Tartaglia, Kathryn E Hamilton


RNA preprints: W27/2018

Nearly all new protein-coding predictions in the CHESS database are not protein-coding. Irwin Jungreis, Michael L. Tress, Jonathan Mudge, Cristina Sisu, Toby Hunt, Rory Johnson, Barbara Uszczynska-Ratajczak, Julien Lagarde, James Wright, Paul Muir, Mark Gerstein, Roderic Guigo, Manolis Kellis, Adam Frankish, Paul Flicek, The GENCODE Consortium

Structural rearrangement of TFIIS- and TFIIF/TFIIE-like subunits in RNA polymerase I transcription complexes. Lucas Tafur, Yashar Sadian, Rene Wetzel, Felix Weis, Christoph W. Muller

RibonucleaseH1-targeted R-loops in surface antigen gene expression sites can direct trypanosome immune evasion. Emma Briggs, Kathryn Crouch, Leandro Lemgruber, Craig Lapsley, Richard McCulloch

Environmentally-induced epigenetic conversion of a piRNA cluster. Karine Casier, Valerie Delmarre, Nathalie Gueguen, Catherine Hermant, Elise Viode, Chantal Vaury, Stephane Ronsseray, Emilie Brasset, Laure Teysset, Antoine Boivin

microRNA-dependent regulation of biomechanical genes establishes tissue stiffness homeostasis. Albertomaria Moro, Tristan Driscoll, William Armero, Liana C. Boraas, Dionna Kasper, Nicolas Baeyens, Charlene Jouy, Venkatesh Mallikarjun, Joe Swift, Sang Joon Ahn, Donghoon Lee, Jing Zhang, Mengting Gu, Mark Gerstein, Martin Schwartz, Stefania Nicoli

The mirtron miR-1010 functions in concert with its host gene SKIP to maintain synaptic homeostasis. Christopher Amourda, Timothy E Saunders

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

Drosophila DNA/RNA methyltransferase contributes to robust host defense in ageing animals by regulating sphingolipid metabolism. Varada Abhyankar, Bhagyashree Kaduskar, Siddhesh Kamat, Deepti Deobagkar, Girish S Ratnaparkhi

Monochrome multiplex qPCR of 18S and 5.8S human rDNA. Chris B Ligerman, Richard M Cawthon

Role of Cnot6l in maternal mRNA turnover. Filip Horvat, Helena Fulka, Radek Jankele, Radek Malik, Jun Ma, Katerina Solcova, Radislav Sedlacek, Kristian Vlahovicek, Richard M Schultz, Petr Svoboda

Characterization of Telomeric Repeat-Containing RNA (TERRA) localization and protein interactions in Primordial Germ Cells of the mouse. Miguel Angel Brieno-Enriquez, Stefannie L. Moak, Anyul Abud-Flores, Paula Elaine Cohen

Genome-wide analysis of RNA sites consistently edited in human blood reveals interactions with mRNA processing genes and suggests correlations with biological and drug-related variables. Edoardo Giacopuzzi, Massimo Gennarelli, Chiara Sacco, Chiara Magri, Alessandro Barbon

Transposon silencing in the Drosophila female germline ensures genome stability in progeny embryos. Anne Ephrussi, Zeljko Durdevic, Ramesh S Pillai

Widespread separation of the polypyrimidine tract from 3′ AG by G tracts in association with alternative exons in metazoa and plants. Hai Nguyen, Jiuyong Xie

Altered hsrω lncRNA levels in activated Ras background further enhance Ras activity in Drosophila eye and induces more R7 photoreceptors. Mukulika Ray, Subhash C. Lakhotia

Rab1b and ARF5 are novel RNA-binding proteins involved in IRES-driven RNA localization. Javier Fernandez-Chamorro, Rosario Francisco-velilla, Jorge Ramajo, Encarna Martinez-Salas

Covariation analysis with improved parameters reveals conservation in lncRNA structures. Rafael C A Tavares, Anna M Pyle, Srinivas Somarowthu

Microrna-184 And Its Lncrna Sponge Uca1 Are Induced In Wounded Keratinocytes In A Store-Operated Calcium Entry-Dependent Manner. Adam Richardson, Daniel J Owens, Kehinde Ross

RNA preprints: W26/2018

RBM-5 modulates U2AF large subunit-dependent alternative splicing in C. elegans. Chuanman Zhou, Xiaoyang Gao, Surong Hu, Wenjing Gan, Jing Xu, Yongchao C. Ma, Long MA

IFN-γ induces epithelial-to-mesenchymal transition of cancer cells via an unique microRNA processing. Jer-Tsong Hsieh, U-Ging Lo, Rey-Chen Pong, Diane Yang, Leah Gandee, Elizabeth Hernandez, Andrew Dang, Chun-Jung Lin, John Santoyo, Shi-Hong Ma Ma, Rajni Sonavane, Jun Huang, Shu-Fen Tseng, Loredana Moro, Arnaldo Augusto Arbini, Payal Kapur, Ganesh V Raj, Dalin He, Chih-Ho Lai, Ho Lin

Mediator is essential for small nuclear and nucleolar RNA transcription in yeast. Jason P Tourigny, Moustafa M Saleh, Gabriel E Zentner

The exon junction complex undergoes a compositional switch that alters mRNP structure and nonsense-mediated mRNA decay activity. Justin W Mabin, Lauren A Woodward, Robert Patton, Zhongxia Yi, Mengxuan Jia, Vicki Wysocki, Ralf Bundschuh, Guramrit Singh

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

Barnaba: Software for Analysis of Nucleic Acids Structures and Trajectories. Sandro Bottaro, Giovanni Bussi, Giovanni Pinamonti, Sabine Reisser, Wouter Boomsma, Kresten Lindorff-Larsen

Dynamic m6A methylation facilitates mRNA triaging to stress granules. Maximilian Anders, Irina Chelysheva, Ingrid Goebel, Timo Trenkner, Jun Zhou, Yuanhui Mao, Silvia Verzini, Shu-Bing Qian, Zoya Ignatova

Genome-wide mapping reveals conserved and diverged R-loop activities in the unusual genetic landscape of the African trypanosome genome. Emma Briggs, Graham Hamilton, Kathryn Crouch, Craig Lapsley, Richard McCulloch

The pyriproxyfen metabolite 4’OH- pyriproxyfen disrupts thyroid hormone signaling and enhances Musashi-1 levels in neuroprogenitors. Petra Spirhanzlova, Sebastien Le Mevel, Karn Wejaphikul, Bilal Mughal, Jean-David Gothie, Anthony Sebillot, Lucille Butruille, Michelle Leemans, Theo Visser, Sylvie Remaud, Jean-Baptiste Fini, Barbara Demeneix

IRES-mediated ribosome repositioning directs translation of a +1 overlapping ORF that enhances viral infection. Craig H Kerr, Qing S Wang, Kyung-Mee Moon, Kathleen Keatings, Douglas W Allan, Leonard J Foster, Eric Jan

3′ Branch Ligation: A Novel Method to Ligate Non-Complementary DNA to Recessed or Internal 3′ OH Ends in DNA or RNA. Lin Wang, Yang Xi, Wenwei Zhang, Weimao Wang, Hanjie Shen, Xiaojue Wang, Xia Zhao, Andrei Alexeev, Brock Peters, Alayna Albert, Xu Xu, Han Ren, Ou Wang, Killeen Kirkconnell, Helena Perazich, Sonya Clark, Evan Hurowitz, Ao Chen, Xun Xu, Radoje Drmanac, Yuan Jiang

Proteogenomics of adenosine-to-inosine RNA editing in the fruit fly. Ksenia G Kuznetsova, Anna A Kliuchnikova, Irina Y Ilina, Alexey L Chernobrovkin, Svetlana E Novikova, Tatyana E Farafonova, Dmitry S Karpov, Mark V Ivanov, Anton O Goncharov, Olga E Voronko, Shamsudin S Nasaev, Ekaterina V Ilgisonis, Victor G Zgoda, Roman A Zubarev, Mikhail V Gorshkov, Sergei A Moshkovskii

TEsmall identifies small RNAs associated with targeted inhibitor resistance in melanoma. Kathryn O’Neill, Wen-Wei Liao, Ami Patel, Molly Gale Hammell

Structure probing data enhances RNA-RNA interaction prediction. Milad Miladi, Soheila Montaseri, Rolf Backofen, Martin Raden

Antisense lncRNA transcription drives stochastic Protocadherin α promoter choice. Daniele Canzio, Chiamaka Nwakeze, Adan Horta, Sandy Rajkumar, Eliot Coffey, Erin Duffy, Rachel Duffié, Matt Simon, Stavros Lomvardas, Tom Maniatis