RNA preprints: W41/2018

Population-scale study of eRNA transcription reveals bipartite functional enhancer architecture. Katla Kristjándsóttir, Yeonui Kwak, Nathaniel D Tippens, John T Lis, Hyun Min Kang, Hojoong Kwak

An In-Silico Mammalian Whole-Cell Model Reveals the Influence of Spatial Organization on RNA Splicing Efficiency. Zhaleh Ghaemi, Joseph Peterson, Martin Gruebele, Zaida Luthey-Schulten

The dynamic proteome of influenza A virus infection identifies M segment splicing as a host range determinant. Boris Bogdanow, Katrin Eichelbaum, Anne Sadewasser, Xi Wang, Immanuel Husic, Katharina Paki, Martha Hergeselle, Barbara Vetter, Jingyi Hou, Wei Chen, Lueder Wiebusch, Irmtraud M. Meyer, Thorsten Wolff, Matthias Selbach

A symmetric toggle switch explains the onset of random X inactivation in different mammals. Verena Mutzel, Ikuhiro Okamoto, Ilona Dunkel, Mitinori Saitou, Luca Giorgetti, Edith Heard, Edda G. Schulz

Modular modeling improves the predictions of genetic variant effects on splicing. Jun Cheng, Thi Yen Duong Nguyen, Kamil J Cygan, Muhammed Hasan Celik, William Fairbrother, Ziga Avsec, Julien Gagneur

Integrative analysis of Zika virus genome RNA structure reveals critical determinants of viral infectivity. Qiangfeng Cliff Zhang, Pan Li, Yifan Wei, Miao Mei, Lei Tang, Lei Sun, Wenze Huang, Jianyu Zhou, Chunlin Zou, Shaojun Zhang, Chengfeng Qin, Tao Jiang, Jianfeng Dai, Xu Tan

The microRNA, miR-18a, regulates NeuroD and photoreceptor differentiation in the retina of the zebrafish. Scott M Taylor, Emily Giuffre, Patience Moseley, Peter F Hitchcock

Bromodomain Protein, BRD4, Contributes to the Regulation of Alternative Splicing. Sheetal Uppal, Qingrong Chen, Daoud Meerzaman, Anne Gegonne, Dinah S Singer

Signal Transduction in Human Cell Lysate via Dynamic RNA Nanotechnology. Lisa M. Hochrein, Tianjia J. Ge, Maayan Schwarzkopf, Niles A. Pierce

The ghr-miR164 and GhNAC100 module participates in cotton plant defence against Verticillium dahlia. Jiahe Wu, Guang Hu, Yu Lei, Le Wang, Jianfen Liu, Ye Tang, Zhennan Zhang, Aiming Chen, Qingzhong Peng, Zuoren Yang

Drosophila Mutants that Are Motile but Respond Poorly to All Stimuli Tested: Mutants in RNA Splicing and RNA Helicase, Mutants in The Boss. Lar L. Vang, Julius Adler

Aminoacyl tRNA Synthetases as Malarial Drug Targets: A Comparative Bioinformatics Study. Dorothy Wavinya Nyamai, Ozlem Tastan Bishop

Specificity of RNA folding and its association with evolutionarily adaptive mRNA secondary structure. Gongwang Yu, Hanbing Zhu, Xiaoshu Chen, Jian-Rong Yang

jouvence, a new small nucleolar RNA required in the gut extends lifespan in Drosophila. Lucille Mellottee, Stephanie Soule, Abdelkrim Arab, Chongjian Chen, Jean-Rene Martin

Dynamic regulation of the Trypanosoma brucei transferrin receptor in response to iron starvation is mediated via the 3’UTR. Corinna Benz, Winston Lo, Nadin Fathallah, Ashley Connor-Guscott, Henry J Benns, Michael D. Urbaniak

A prognostic signature for lower-grade gliomas based on expression of long noncoding RNAs. Manjari Kiran, Ajay Chatrath, Xiwei Tang, Daniel Macrae Keenan, Anindya Dutta

Density dependent enhancement effect of Wolbachia and the host RNAi response to a densovirus in Aedes cells. Rhys Parry, Cameron Bishop, Lachlan De Hayr, Sassan Asgari

Development of a novel signature of long noncoding RNAs as a prognostic biomarker for esophageal cancer. Yan Miao, Jing Sui, Ying Zhang, Lihong Yin

DNA damage dependent hypomethylation regulates the pro-angiogenic LncRNA MEG9. Cristina Espinosa-Diez, RaeAnna Wilson, Rishima Mukherjee, Marlee Feltham, Clayton Hudson, Rebecca Ruhl, Sudarshan Anand

The influenza A virus endoribonuclease PA-X usurps host mRNA processing machinery to limit host gene expression. Lea Gaucherand, Brittany K Porter, Summer K Schmaling, Christopher Harley Rycroft, Yuzo Kevorkian, Craig McCormick, Denys A Khaperskyy, Marta Gaglia

Metatranscriptome profiling of the dynamic transcription of mRNA and sRNA of a probiotic Lactobacillus strain in human gut. Qiuwen He, zhihong sun, Jianmin Qiao, Dong Chen, Jie Huang, Xiaotian Luo, Jia Ding, Jiachao Zhang, Qiangchuan Hou, Yi Zhang, Heping Zhang

DNA and RNA binding mediate the toxicity of arginine-rich peptides encoded by C9ORF72 GGGGCC repeats. Vanesa Lafarga, Oleksandra Sirozh, Irene Diaz-Lopez, Misaru Hisaoka, Eduardo Zarzuela, Jasminka Boskovic, Bogdan Jovanovic, Rafael Fernandez-Leiro, Javier Munoz, Georg Stoecklin, Ivan Ventoso, Oscar Fernandez-Capetillo

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RNA preprints: W40/2018

CRISPR Artificial Splicing Factors. Nathaniel Jillette, Albert W Cheng

PUMILIO hyperactivity drives premature aging of Norad-deficient mice. Florian Kopp, Mehmet Yalvac, Beibei Chen, He Zhang, Sungyul Lee, Frank Gillett, Mahmoud Elguindy, Sushama Sivakumar, Hongtao Yu, Yang Xie, Prashant Mishra, Zarife Sahenk, Joshua T Mendell

Mitochondrial RNA capping: highly efficient 5′-RNA capping with NAD+ and NADH by yeast and human mitochondrial RNA polymerase. Jeremy G. Bird, Urmimala Basu, David Kuster, Aparna Ramachandran, Ewa Grudzien-Nogalska, Megerditch Kiledjian, Dmitry Temiakov, Smita S. Patel, Richard H. Ebright, Bryce E. Nickels

Reversal of microRNA-blocked tumor suppressors by biphenyl- dicarboxylate impedes endotoxin-induced hepatic hyperplasia. Li-Li Tan, Dong-Mei Chen, Jian-Ping Song, Qin Xu, Chang-Qing Li, Qing-Ping Zeng

Viral RNA-dependent RNA polymerase inhibitor 7-deaza-2′-C-methyladenosine prevents death in a mouse model of West Nile virus infection. Ludek Eyer, Martina Fojtíková, Radim Nencka, Ivo Rudolf, Zdenek Hubálek, Daniel Ruzek

Epigenetic silencing of miRNA-338-5p and miRNA-421 drives SPINK1-positive prostate cancer. Vipul Bhatia, Anjali Yadav, Ritika Tiwari, Shivansh Nigam, Sakshi Goel, Shannon Carskadon, Nilesh Gupta, Apul Goel, Nallasivam Palanisamy, Bushra Ateeq

RNA polymerase I transcription fidelity, speed and processivity depend on the interplay of its lobe binding subunits. Herbert Tschochner, Philipp Emanuel Merkl, Michael Pilsl, Tobias Fremter, Gernot Längst, Philipp Milkereit, Joachim Griesenbeck

Pervasiveness of exoribonuclease-resistant RNAs in plant viruses suggests new roles for these conserved RNA structures. Anna-Lena Steckelberg, Quentin Vicens, Jeffrey Scott Kieft

RNA polymerases display collaborative and antagonistic group behaviors over long distances through DNA supercoiling. Sangjin Kim, Bruno Beltran, Irnov Irnov, Christine Jacobs-Wagner

A high-throughput screen identifies small molecule modulators of alternative splicing by targeting RNA G-quadruplexes. Jing Zhang, Samuel E. Harvey, Chonghui Cheng

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, Sakshi Tomar, David Jimenez-Morales, Mariah Dunlap, Julia A Kaye, Priya S Shah, Steve Finkbeiner, Nevan J Krogan, Melanie Ott

Dynamic G-quadruplexes on the surface of the human ribosome. Santi Mestre-Fos, Petar I. Penev, Suttipong Suttapitugsakul, Chieri Ito, Anton S. Petrov, Roger M. Wartell, Ronghu Wu, Loren Dean Williams

Defining the RNA Interactome by Total RNA-Associated Protein Purification. Vadim Shchepachev, Stefan Bresson, Christos Spanos, Elisabeth Petfalski, Lutz Fischer, Juri Rappsilber, David Tollervey

Insights into the structure-driven protein interactivity of RNA molecules. Natalia Sanchez de Groot, Alexandros Armaos, Ricardo Grana-Montes, Marion Alriquet, Giulia Calloni, Martin Vabulas, Gian Gaetano Tartagli

RegTools: Integrated analysis of genomic and transcriptomic data for discovery of splicing variants in cancer. Yang-Yang Feng, Avinash Ramu, Kelsy C Cotto, Zachary L Skidmore, Jason Kunisaki, Donald F Conrad, Yiing Lin, William Chapman, Ravindra Uppaulri, Ramaswamy Govindan, Obi L Griffith, Malachi Griffith

A Large-Scale Binding and Functional Map of Human RNA Binding Proteins. Eric L Van Nostrand, Peter Freese, Gabriel A Pratt, Xiaofeng Wang, Xintao Wei, Steven M Blue, Daniel Dominguez, Neal A L Cody, Sara Olson, Balaji Sundararaman, Rui Xiao, Lijun Zhan, Cassandra Bazile, Louis Philip Benoit Bouvrette, Jiayu Chen, Michael O Duff, Keri Garcia, Chelsea Gelboin-Burkhart, Myles Hochman, Nicole J Lambert, Hairi Li, Thai B Nguyen, Tsultrim Palden, Ines Rabano, Shashank Sathe, Rebecca Stanton, Ashley L Louie, Stefan Aigner, Julie Bergalet, Bing Zhou, Amanda Su, Ruth Wang, Brian A Yee, Xiang-Dong Fu, Eric Lecuyer, Christopher B Burge, Brenton Graveley, Gene W Yeo

Evidence for an Integrated Gene Repression Mechanism based on mRNA Isoform Toggling in Human Cells. Ina Hollerer, Juliet C Barker, Victoria Jorgensen, Amy Tresenrider, Claire Dugast-Darzacq, Xavier Darzacq, Leon Y Chan, Robert Tjian, Elcin Unal, Gloria A Brar

Deciphering the rules of mRNA structure differentiation in vivo and in vitro with deep neural networks in Saccharomyces cerevisiae. Haopeng Yu, Wenjing Meng, Yuanhui Mao, Yi Zhang, Qing Sun, Shiheng Tao

Structure of transcribing RNA polymerase II-nucleosome complex. Lucas Farnung, Seychelle M. Vos, Patrick Cramer

Cold denaturation of RNA secondary structures with loop entropy and quenched disorder. Flavio Iannelli, Yevgeni Mamasakhlisov, Roland R. Netz

RNA polymerase interactions and elongation rate. V. Belitsky, G. M. Schütz

RNA preprints: W39/2018

Interaction paths promote spliceosome module integration and network-level robustness to cascading effects. Paulo R Guimaraes Jr., Mathias M Pires, Mauricio Cantor, Patricia P Coltri

Excised linear introns regulate growth in yeast. Jeffrey T Morgan, Gerald R Fink, David P Bartel

Evolutionary analysis of base-pairing interactions in DNA and RNA secondary structures. Michael Thomas Golden, Ben Murrell, Darren Martin, Jotun Hein

CLIP-Seq and massively parallel functional analysis of the CELF6 RNA binding protein reveals a role in destabilizing synaptic gene mRNAs through interaction with 3’UTR elements in vivo. Michael A Rieger, Dana M King, Barak A Cohen, Joseph D. Dougherty

Nuclear export of chimeric mRNAs depends on an lncRNA-triggered autoregulatory loop. Zhen-Hua Chen, Zhancheng Zen, Tian-Qi Chen, Cai Han, Yu-Meng Sun, Wei Huang, Lin-Yu Sun, Ke Fang, Xue-Qun Luo, Wen-Tao Wang, Michelle YQ Chen

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

Isolation of cancer stem cells by selection for miR-302 expressing cells. Karim Rahimi, Annette Christine Fuchtbauer, Fardin Fathi, Seyed Javad Mowla, Ernst-Martin Fuchtbauer

Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes. Boas Pucker, Samuel Fraser Brockington

Population-scale study of eRNA transcription reveals bipartite functional enhancer architecture. Katla Kristjándsóttir, Yeonui Kwak, Nathaniel D Tippens, John T Lis, Hyun Min Kang, Hojoong Kwak

Modeling RNA-binding protein specificity in vivo by precisely registering protein-RNA crosslink sites. Huijuan Feng, Suying Bao, Sebastien M Weyn-Vanhentenryck, Aziz Khan, Justin Wong, Ankeeta Shah, Elise D Flynn, Chaolin Zhang

MiR-146a-dependent regulation of CD24/AKT/β-catenin axis drives stem cell phenotype in oral cancer. Susanta Roychoudhury, Sangeeta Ghuwalewala, Dishari Ghatak, Sumit Das, Pijush Das, Ramesh Butti, Mahadeo Gorain, Gopal C Kundu

On the optimal design of metabolic RNA labeling experiments. Alexey Uvarovskii, Isabel Naarmann-de Vries, Christoph Dieterich

Alternative splicing of bicistronic MOCS1 defines a novel mitochondrial protein maturation mechanism. Simon Julius Mayr, Juliane Roeper, Guenter Schwarz

Widespread gene duplication and adaptive evolution in the RNA interference pathways of the Drosophila obscura group. Danang Crysnanto, Darren Obbard

A mouse tissue atlas of small non-coding RNA. Alina Isakova, Stephen Quake

LTMG (Left truncated mixture Gaussian) based modeling of transcriptional regulatory heterogeneities in single cell RNA-seq data – a perspective from the kinetics of mRNA metabolism. Changlin Wan, Wennan Chang, Yu Zhang, Fenil Shah, Sha Cao, Xin Chen, Melissa Fishel, Qin Ma, Chi Zhang

Single-cell microRNA/mRNA co-sequencing reveals non-genetic heterogeneity and novel regulatory mechanisms. Nayi Wang, Ji Zheng, Zhuo Chen, Yang Liu, Burak Dura, Minsuk Kwak, Juliana Xavier-Ferrucio, Yi-Chien Lu, Miaomiao Zhang, Christine Roden, Jijun Cheng, Diane Krauss, Ye Ding, Rong Fan, Jun Lu

MicroRNA-223 protects neurons from degeneration in Experimental Autoimmune Encephalomyelitis. Barbara Morquette, Camille A. Juzwik, Sienna S. Drake, Marc Charabati, Julia Zhang, Marc-Andre Lecuyer, Dylan Galloway, Aline Dumas, Omar de Faria Junior, Mardja Bueno, Isabel Rambaldi, Craig Moore, Amit Bar-Or, Luc Vallieres, Alexander Prat, Alyson Fournier

Quantifying Local Randomness in Human DNA and RNA Sequences Using Erdos Motifs. Wentian Li, Dimitrios Thanos, Astero Provata

RNA preprints: W38/2018

Precursor microRNA Identification Using Deep Convolutional Neural Networks. Binh Thanh Do, Vladimir Golkov, Göktuğ Erce Gürel, Daniel Cremers

Pervasive selection against microRNA target sites in human populations. Andrea Hatlen, Antonio Marco

miRBaseConverter: An R/Bioconductor Package for Converting and Retrieving miRNA Name, Accession, Sequence and Family Information in Different Versions of miRbase. Taosheng Xu, Ning Su, Lin Liu, Junpeng Zhang, Hongqiang Wang, Weijia Zhang, Jie Gui, Kui Yu, Jiuyong Li, Thuc Duy Le

Improving The Performance Of The RNA Amber Force Field By Tuning The Hydrogen-Bonding Interactions. Petra Kuhrova, Vojtech Mlynsky, Marie Zgarbova, Miroslav Krepl, Giovanni Bussi, Robert B. Best, Michal Otyepka, Jiri Sponer, Pavel Banas

Over-expression of Hsp83 in grossly depleted hsrω lncRNA background causes synthetic lethality and l(2)gl phenocopy in Drosophila. Mukulika Ray, Sundaram Acharya, Sakshi Shambhavi, Subhash C Lakhotia

Olfaction regulates organismal proteostasis and longevity via microRNA-dependent signaling. Fabian Finger, Franziska Ottens, Alexander Springhorn, Tanja Drexel, Lucie Proksch, Sophia Metz, Luisa Cochella, Thorsten Hoppe

Identifying Changes in RNA Editome Unique to Major Depressive Disorder. Saam Hasan, Shahriyar Mahdi Robbani, Tamanna Afroze, Gias Uddin Ahsan, Muhammad Maqsud Hossain

lncDIFF: a novel distribution-free method for differential expression analysis of long non-coding RNA. Qian Li, Xiaoqing Yu, Ritu Chaudhary, Robbert JC Slebos, Christine H Chung, Xuefeng Wang

PolyA tracks and poly-lysine repeats are the Achilles heel of Plasmodium falciparum. Slavica Pavlovic Djuranovic, Jessey Erath, Ryan J Andrews, Peter O Bayguinov, Joyce J Chung, Douglas L Chalker, James AJ Fitzpatrick, Walter N Moss, Pawel Szczesny, Sergej Djuranovic

Transcriptome profiles and novel lncRNA identification of Aedes aegypti cells in response to dengue virus serotype 1. Azali Azlan, Sattam M. Obeidat, Muhammad Amir Yunus, Ghows Azzam

SplicedFamAlign: CDS-to-gene spliced alignment and identification of transcript orthology groups. Safa Jammali, Jean-David Aguilar, Esaie Kuitche, Aida Ouangraoua

The RNA-Binding Protein DND1 Acts Sequentially as a Negative Regulator of Pluripotency and a Positive Regulator of Epigenetic Modifiers Required for Germ Cell Reprogramming. Victor A Ruthig, Matthew B Friedersdorf, Jason A Garness, Steve C Munger, Corey Bunce, Jack D Keene, Blanche Capel

Short exon prediction based on multiscale products of a genomic-inspired multiscale bilateral filtering. Xiaolei Zhang, Weijun Pan

Unbiased screen of RNA tailing enzymes at single-nucleotide resolution reveals a poly(UG) polymerase required for genome integrity and RNA silencing. Melanie A. Preston, Douglas F. Porter, Fan Chen, Natascha Buter, Christopher P. Lapointe, Sunduz Keles, Judith Kimble, Marvin Wickens

Extrinsic Noise Suppression in Micro RNA Mediated Incoherent Feedforward Loops. Alberto Carignano, Sumit Mukherjee, Abhyudai Singh, Georg Seelig

miRNA analysis with Prost! reveals evolutionary conservation of organ-enriched expression and post-transcriptional modifications in three-spined stickleback and zebrafish. Thomas Desvignes, Peter Batzel, Jason Sydes, B. Frank Eames, John H. Postlethwait

Narrow equilibrium window for complex coacervation of tau and RNA under cellular conditions. Yanxian Lin, James McCarty, Jennifer N. Rauch, Kris T. Delaney, Kenneth S. Kosik, Glenn H. Fredrickson, Joan-Emma Shea, Songi Han

A Novel Method for the Capture-based Purification of Whole Viral Native RNA Genomes. Cedric C.S. Tan, Sebastian Maurer-Stroh, Yue Wan, October M. Sessions, Paola Florez de Sessions

SilentMutations (SIM): a tool for analyzing long-range RNA-RNA interactions in viral genomes and structural RNAs. Daniel Desiro, Martin Hoelzer, Bashar Ibrahim, Manja Marz

RNA preprints: W37/2018

The biochemical basis of microRNA targeting efficacy. Sean E McGeary, Kathy S Lin, Charlie Y Shi, Namita Bisaria, David P Bartel

AptCompare: optimized de novo motif discovery of RNA aptamers via HTS-SELEX. Kevin R Shieh, Christina Kratschmer, Keith E Maier, John M Greally, Matthew Levy, Aaron Golden

Intensive and Specific Feedback Self-control of the Argonauts and MicroRNA Targeting Activity. Degeng Wang, Audrey Gill, Fangyuan Zhang

A novel interaction between Gβγ and RNA polymerase II regulates cardiac fibrosis. Shahriar M Khan, Ryan D Martin, Celia Bouazza, Jace Jones-Tabah, Andy Zhang, Sarah MacKinnon, Phan Trieu, Sarah Gora, Paul BS Clarke, Jason C Tanny, Terence E Hebert

An adaptive stress-induced tRNA depletion response mediates codon-based gene repression and growth suppression. Doowon Huh, Maria C Passarelli, Lisa Fish, Henrik Molina, Elizabeth A McMillan, Hani Goodarzi, Sohail F Tavazoie

CD95/Fas ligand mRNA is toxic to cells. William Putzbach, Ashley Haluck-Kangas, Quan Q Gao, Aishe A Sarshad, Elizabeth T Bartom, Austin M. Stults, Abdul S Qadir, Markus Hafner, Marcus E Peter

Transite: A computational motif-based analysis platform that identifies RNA-binding proteins modulating changes in gene expression. Konstantin Krismer, Shohreh Varmeh, Molly A. Bird, Anna Gattinger, Yi Wen Kong, Thomas Bernwinkler, Daniel A. Anderson, Andreas Heinzel, Brian A. Joughin, Ian G. Cannell, Michael B. Yaffe

Quantitative proteomics reveals key roles for post-transcriptional gene regulation in the molecular pathology of FSHD. Sujatha Jagannathan, Yuko Ogata, Philip Gafken, Stephen J Tapscott, Robert K Bradley

Identification of potential microRNAs associated with Herpesvirus family based on bioinformatic analysis. Kevin Lamkiewicz, Emanuel Barth, Manja Marz, Bashar Ibrahim

The key protein of endosomal mRNP transport binds translational landmark sites of cargo mRNAs.Lilli Olgeiser, Carl Haag, Susan Boerner, Jernej Ule, Anke Busch, Julian Konig, Michael Feldbrugge, KathiZarnack

Inferring Sequence-Structure Preferences of RNA-Binding Proteins with Convolutional Residual Networks. Peter K Koo, Praveen Anand, Steffan B. Paul, Sean R. Eddy

A post-transcriptional program of chemoresistance by AU-rich elements/TTP in cancer quiescence. Sooncheol Lee, Douglas Micalizzi, Samuel S Truesdell, Syed IA Bukhari, Myriam Boukhali, Jennifer Lombardi-Story, Yasutaka Kato, Ipsita Dey-Guha, Benjamin T Nicholson, Min-Kyung Choo, David T Myers, Dongjun Lee, Maria A Mazzola, Radhika Raheja, Adam Langenbucher, Nicholas J Haradhvala, Michael Lawrence, Roopali Gandhi, David A Sweetser, David Sykes, Wilhelm Haas, Daniel A Haber, Shyamala Maheswaran, Shobha Vasudevan

Evolutionary analysis of base-pairing interactions in DNA and RNA secondary structures. Michael Thomas Golden, Ben Murrell, Darren Martin, Jotun Hein

Precursor microRNA Identification Using Deep Convolutional Neural Networks. Binh Thanh Do, Vladimir Golkov, Göktuğ Erce Gürel, Daniel Cremers

Functional lability of RNA-dependent RNA polymerases in animals. Natalia Pinzón, Stéphanie Bertrand, Lucie Subirana, Isabelle Busseau, Hector Escrivá, Hervé Seitz

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

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

RNA preprints: W36/2018

Transcripts from multicopy gene families localizing to mouse Y long arm encode piRNAs and proteins. Rachel A Jesudasan, Kankadeb Mishra, Pranatharthi Annapurna, Anurag Chaturvedi, Nissankararao M Praveena, Jomini L Alex, Sivarajan Karunanidhi, Hemakumar M Reddy

Intensive and Specific Feedback Self-control of MicroRNA Targeting Activity. Degeng Wang, Audrey Gill, Fangyuan Zhang

Musashi binding elements in Zika and related Flavivirus 3’UTRs: A comparative study in silico. Adriano de Bernardi Schneider, Michael T Wolfinger

USP21 and OTUD3 Antagonize Regulatory Ribosomal Ubiquitylation and Ribosome-Associated Quality Control. Danielle M Garshott, Elayanambi Sundaramoorthy, Marilyn Leonard, Eric J Bennett

Modeling slow-processing of toxin messenger RNAs in type-I Toxin-Antitoxin systems: post-segregational killing and noise filtering. Yusuke Himeoka, Namiko Mitarai

Deep sequencing of circulating exosomal microRNA allows non-invasive glioblastoma diagnosis. Saeideh Ebrahimkhani, Fatemeh Vafaee, Susannah Hallal, Heng Wei, Maggie Lee, Paul Young, Laveniya Satgunaseelan, Brindha Shivalingam, Catherine Suter, Michael Buckland, Kimberley Kaufman

Secondary structure of pre-mRNA introns for genes of 15q11-12 locus. Mapping of functionally significant motives of RNA binding proteins and f nucleosome positioning signals. Viya Borisovna Fedoseyeva, Irina Alexandrovna Zharinova, Alexander Anatolyevich Alexandrov

RNA-antimicrobial peptide complexes activate a self-sustaining TLR- and NETosis-mediated cycle of neutrophil activation. Franziska Herster, Zsofia Bittner, Sabine Dickhoefer, David Eisel, Tatjana Eigenbrod, Thomas Knorpp, Nicole Schneiderhan-Marra, Markus W Loeffler, Dominik Hartl, Lukas Freund, Knut Schaekel, Martin Heiser, Kamran Ghoreschi, Alexander N. R. Weber

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

FUS controls the processing of snoRNAs into smaller RNA fragments that can regulate gene expression. Patrycja Plewka, Michal Szczesniak, Agata Stepien, Marek Zywicki, Andrzej Pacak, Martino Colombo, Izabela Makalowska, Marc-David Ruepp, Katarzyna Dorota Raczynska

Maternal Circulating MicroRNAs Control the Placental Response to Alcohol. Alexander M Tseng, Amanda H Mahnke, Alan B Wells, Nihal A Salem, Andrea M Allan, Victoria H.J. Roberts, Natali Newman, Nicole A.R. Walter, Christopher D Kroenke, Kathleen A Grant, Lisa K Akison, Karen M Moritz, Christina D Chambers, Rajesh C Miranda

Extracting information from RNA SHAPE data: Kalman filtering approach. Sana Vaziri, Patrice Koehl, Sharon Aviran

Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns. Alison D Tang, Cameron M Soulette, Marijke J van Baren, Kevyn Hart, Eva Hrabeta-Robinson, Catherine J Wu, Angela N Brooks

miRBaseConverter: An R/Bioconductor Package for Converting and Retrieving miRNA Name, Accession, Sequence and Family Information in Different Versions of miRbase. Taosheng Xu, Ning Su, Lin Liu, Junpeng Zhang, Hongqiang Wang, Jie Gui, Kui Yu, Jiuyong Li, Thuc Duy Le

A Novel Method for the Capture-based Purification of Whole Viral Native RNA Genomes. Cedric C.S. Tan, Sebastian Maurer-Stroh, Yue Wan, October M. Sessions, Paola Florez de Sessions

Several phased siRNA annotation methods can produce frequent false-positives for 24 nucleotide RNA-dominated loci in plants. Seth Polydore, Alice Lunardon, Michael J Axtell

A SKI subcomplex specifically required for the degradation of ribosome-free RNA regions. Elodie Zhang, Varun Khanna, Abdelkader Namane, Antonia Doyen, Estelle Dacheux, Bernard Turcotte, Alain Jacquier, Micheline Fromont-Racine

Dimerisation of APOBEC1 is dispensable for its RNA editing activity. Martina Chieca, Marco D Montini, Francesco Severi, Riccardo Pecori, Silvestro G Conticello

Identification of miRNAs and associated pathways regulated by Leukemia Inhibitory Factor in trophoblastic cell lines. Diana M. Morales-Prieto, Emanuel Barth, Ruby N. Gutièrrez-Samudio, Wittaya Chaiwangyen, Stephanie Ospina-Prieto, Bernd Gruhn, Ekkehard Schleußner, Manja Marz, Udo R. Markert

Active site closure stabilizes the backtracked state of RNA polymerase. Matti Turtola, Janne Makinen, Georgiy A Belogurov

Comparative analysis of miR-155 tissue expression profiles of different breeds of chicken. Chaolai Man, Sifan Xu, Yang Chang, Guanxian Wu, Wangting Zhang

The functional circular RNA, ciRS-7 (CDR1as), is biosynthesized using back-splicing promoted by inverted mammalian-wide MIRs but not primate-specific Alus. Rei Yoshimoto, Karim Rahimi, Karoline K Ebbesen, Thomas Hansen, Jorgen Kjems, Akila Mayeda

Dazl regulates germ cell survival through a network of polyA proximal mRNA interactions. Leah L Zagore, Thomas J Sweet, Molly M Hannigan, Sebastien M Weyn-Vanhentenryck, Raul Jobava, Maria Hatzoglou, Chaolin Zhang, Donny D Licatalosi

Transcriptomic analyses reveal groups of co-expressed, syntenic lncRNAs in four species of the genus Caenorhabditis. Cinta Pegueroles, Susana Iraola-Guzman, Uciel P Chorostecki, Ewa Ksiezopolska, Ester Saus, Toni Gabaldon

The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders. Cheen Euong Ang, Qing Ma, Orly Wapinski, ShengHua Fan, Ryan A Flynn, Bradley Coe, Masahiro Onoguchi, Victor H Olmos, Brian T Do, Lynn Dukes-Rimsky, Jin Xu, Qian Yi Lee, Koji Tanabe, LiangJiang Wang, Ulrich Elling, Josef Penninger, Kun Qu, Evan E Eichler, Anand Srivastava, Marius Wernig, Howard Chang

MiR-16-1* and miR-16-2* possess strong tumor suppressive and anti-metastatic properties in osteosarcoma. Vadim V. Maximov, Saleh Khawaled, Zaidoun Salah, Lina Jaber, Nataly Bengaiev, Ahlam Barhoum, Marco Galasso, Eylon Yavin, Rami I. Aqeilan

Regulation of Cell-Type-Specific Transcriptomes by miRNA Networks During Human Brain Development. Tomasz J Nowakowski, Neha Rani, Mahdi Golkaram, Hongjun R Zhou, Beatriz Alvarado, Kylie Huch, Jay West, Anne Leyrat, Alex A Pollen, Arnold R Kriegstein, Linda R Petzold, Kenneth S Kosik

RNA preprints: W35/2018

The RNA helicase UPF1 associates with mRNAs co-transcriptionally and is required for the release of mRNAs from transcription sites. Anand Kumar Singh, Subhendu Roy Choudhury, Sandip De, Jie Zhang, Stephen Kissane, Vibha Dwivedi, Preethi Ramanathan, Luisa Orsini, Daniel Hebenstreit, Saverio Brogna

PARylation regulates stress granule dynamics, phase separation, and neurotoxicity of disease-related RNA-binding proteins. Yongjia Duan, Aiying Du, Jinge Gu, Gang Duan, Chen Wang, Zhiwei Ma, Le Sun, Beituo Qian, Xue Deng, Kai Zhang, Kuili Tian, Yaoyang Zhang, Hong Jiang, Cong Liu, Yanshan Fang

DSCAM-AS1 promotes tumor growth of breast cancer by reducing miR-204-5p and upregulating RRM2. Wen-Hui Liang, Na Li, Zhi-Qing Yuan, Xin-Lai Qian, Zhi-Hui Wang

Engineered transfer RNAs for suppression of premature termination codons. John D Lueck, Jae Seok Yoon, Alfredo Perales-Puchalt, Adam L Mackey, Daniel T Infield, Mark A Behlke, Marshall R Pope, David B Weiner, William R Skach, Paul B McCray, Christopher A Ahern

Differential amplicons for the evaluation of RNA integrity extracted from complex environmental samples. Fabien Cholet, Umer Zeeshan Ijaz, Cindy Jane Smith

CLIP-Seq and massively parallel functional analysis of the CELF6 RNA binding protein reveals a role in destabilizing synaptic gene mRNAs through interaction with 3’UTR elements in vivo. Michael A Rieger, Dana M King, Barak A Cohen, Joseph D. Dougherty

UNCROSS2: identification of cross-talk in 16S rRNA OTU tables. Robert Edgar

The RNA-Binding Protein DND1 Acts Sequentially as a Negative Regulator of Pluripotency and a Positive Regulator of Epigenetic Modifiers Required for Germ Cell Reprogramming. Victor A Ruthig, Matthew B Friedersdorf, Jason A Garness, Steve C Munger, Corey Bunce, Jack D Keene, Blanche Capel

IsoformSwitchAnalyzeR: Analysis of changes in genome-wide patterns of alternative splicing and its functional consequences. Kristoffer Vitting-Seerup, Albin Sandelin

MiR-505-3p is a Repressor of the Puberty Onset in Female Mice. Yuxun Zhou, li tong, maochun wang, xueying chang, sijia wang, kai li, Junhua Xiao

A quantitative and predictive model for RNA binding by human Pumilio proteins. Inga Jarmoskaite, Sarah K. Denny, Pavanapuresan P. Vaidyanathan, Winston R. Becker, Johan O.L. Andreasson, Curtis J. Layton, Kalli Kappel, Varun Shivashankar, Raashi Sreenivasan, Rhiju Das, William J. Greenleaf, Daniel Herschlag

CTP synthase regulation by miR-975 controls cell proliferation and differentiation in Drosophila melanogaster. Wai-Kan Woo, Najat Dzaki, Ghows Azzam

Staufen2 mediated RNA recognition and localization requires combinatorial action of multiple domains. Simone Heber, Imre Gaspar, Jan-Niklas Tants, Johannes Günther, Sandra M Fernández Moya, Robert Janowski, Anne Ephrussi, Michael Sattler, Dierk Niessing

An homeotic post-transcriptional network controlled by the RNA-binding protein RBMX. Paola Zuccotti, Daniele Peroni, Valentina Potrich, Alessandro Quattrone, Erik Dassi

Pat1 promotes processing body assembly by enhancing the phase separation of the DEAD-box ATPase Dhh1 and RNA. Ruchika Sachdev, Maria Hondele, Miriam Linsenmeier, Pascal Vallotton, Christopher F Mugler, Paolo Arosio, Karsten Weis

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

Pathogenicity and selective constraint on variation near splice sites. Jenny Lord, Giuseppe Gallone, Patrick J. Short, Jeremy F. McRae, Holly Ironfield, Elizabeth H. Wynn, Sebastian S. Gerety, Liu He, Bronwyn Kerr, Diana S. Johnson, Emma McCann, Esther Kinning, Frances Flinter, I. Karen Temple, Jill Clayton-Smith, Meriel McEntagart, Sally Ann Lynch, Shelagh Joss, Sofia Douzgou, Tabib Dabir, Virginia Clowes, Vivienne P. M. McConnell, Wayne Lam, Caroline F. Wright, David R. FitzPatrick, Helen V. Firth, Jeffrey C. Barrett, Matthew E. Hurles, on behalf of the Deciphering Developmental Disorders study

β-actin mRNA interactome mapping by proximity biotinylation. Joyita Mukherjee, Orit Hermesh, Nicolas Nalpas, Mirita Franz-Wachtel, Boris Macek, Ralf-Peter Jansen

miPIE: NGS-based Prediction of miRNA Using Integrated Evidence. Robert J Peace, Mohsen Sheikh Hassani, James R Green

Anti-microRNA screen uncovers miR-17 family within miR-17~92 cluster as the primary driver of kidney cyst growth. Matanel Yheskel, Ronak Lakhia, Andrea Flaten, Vishal Patel

Identification of microRNA-27a as a key regulator of cholesterol homeostasis. Abrar Ali Khan, Vinayak Gupta, Ananthamohan Kalyani, Vikas Arige, Santosh Reddy, Manoj Kumar Barthwal, Madhu Dikshit, Bhanuprakash Reddy, Nitish Ranjan Mahapatra