RNA preprints: W4/2019

Extensive splicing across the Saccharomyces cerevisiae genome. Stephen Douglass, Calvin S Leung, Tracy L Johnson

Accurate detection of m6A RNA modifications in native RNA sequences. Huanle Liu, Oguzhan Begik, Morghan C Lucas, Christopher E Mason, Schraga Schwartz, John S Mattick, Martin A Smith, Eva Maria Novoa

Elucidating small RNA pathways in Arabidopsis thaliana egg cells. Stefanie Sprunck, Marc Urban, Nicholas Strieder, Maria Lindemeier, Andrea Bleckmann, Maurits Evers, Thomas Hackenberg, Christoph Moehle, Thomas Dresselhaus, Julia C. Engelmann

Whole Aegilops tauschii transcriptome investigation revealed nine novel miRNAs involved in stress response. Behnam Bakhshi, Ehsan Mohseni Fard

Broad antifungal resistance mediated by RNAi-dependent epimutation in the basal human fungal pathogen Mucor circinelloides. Zanetta Chang, R. Blake Billmyre, Soo Chan Lee, Joseph Heitman

Widespread selection for high and low secondary structure in coding sequences across all domains of life. Daniel Gebert, Julia Jehn, David Rosenkranz

The biofilm matrix scaffold of Pseudomonas species consists of non-canonically base paired extracellular DNA and RNA. Thomas W Seviour, Fernaldo Richtia Winnerdy, Wong Lan Li, Shi Xiangyan, Sudarsan Mugunthan, Gurjeet Singh Kohli, Heather M Shewan, Jason Stokes, Scott A Rice, Anh-Tuan Phan, Staffan Kjelleberg

Paternally-acting canonical RNA-directed DNA methylation pathway genes sensitize Arabidopsis endosperm to paternal dosage. Rajavasireddy P Satyaki, Mary Gehring

Splicing buffers suboptimal codon usage in human cells. Christine Mordstein, Rosina Savisaar, Robert S Young, Jeanne Bazile, Lana Talmane, Juliet Luft, Michael Liss, Martin S Taylor, Laurence D Hurst, Grzegorz Kudla

N6-methyladenosine dynamics during early vertebrate embryogenesis. Havard Aanes, Dominique Engelsen, Adeel Manaf, Endalkachew Ashenafi Alemu, Cathrine Broberg Vagbo, Leonardo Martin, Mads Lerdrup, Klaus Hansen, Sinnakaruppan Mathavan, Cecilia Winata, Robert B. Darnell, Peter Alestrom, Arne Klungland

Relevance of the iron-responsive element (IRE) pseudotriloop structure for IRP1/2 binding and validation of IRE-like structures using the yeast three-hybrid system. Shih-Cheng Chen, René C.L. Olsthoorn

Dynamic control of pathway expression with riboregulated switchable feedback promoters. Cameron J Glasscock, John T Lazar, Bradley W Biggs, Jack H Arnold, Min-Kyoung Kang, Danielle Tullman-Ercek, Keith E J Tyo, Julius B Lucks

Selective enrichment of A-to-I edited transcripts from cellular RNA using Endonuclease V. Steve D Knutson, Jennifer M Heemstra

Comparative identification of microRNAs in Apis cerana cerana workers’midguts responding to Nosema ceranae invasion. Rui Guo, Dafu Chen, Yu Du, Huazhi Chen, Haipeng Wang, Cuiling Xiong, Yanzhen Zheng, Chunsheng Hou, Qingyun Diao

Expression kinetics and innate immune response after electroporation and lipid nanoparticle mediated delivery of a self-amplifying mRNA in the skin of mice. Hanne Huysmans, Zifu Zhong, Joyca De Temmerman, Barbara L Mui, Ying K Tam, Sean Mc Cafferty, Arlieke Gitsels, Daisy Vanrompay, Niek Sanders

Comparative analysis of sfRNA in the genome of pre-epidemic and epidemic Zika viruses for host interacting proteins potentially related to the recent epidemic. Perumal Arumugam Desingu

RNA interactions with CTCF are essential for its proper function. Ricardo Saldana-Meyer, Javier Rodriguez-Hernaez, Mayilaadumveettil Nishana, Karina Jacome-Lopez, Elphege P. Nora, Benoit G. Bruneau, Mayra Furlan-Magaril, Jane Skok, Danny Reinberg

RadiationGeneSigDB: A database of oxic and hypoxic radiation response gene signatures and their utility in identification of hypoxia-regulated MicroRNA. Venkata Manem, Andrew Dhawan

miRNA activity contributes to accurate RNA splicing in C. elegans intestine and body muscle tissues. Kasuen Kotagama, Anna L Schorr, Hannah S Steber, Marco Mangone

The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A)-translation. Andrea Hildebrandt, Mirko Brüggemann, Susan Boerner, Cornelia Rücklé, Jan Bernhard Heidelberger, Annabelle Dold, Anke Busch, Heike Hänel, Andrea Voigt, Stefanie Ebersberger, Ingo Ebersberger, Jean-Yves Roignant, Kathi Zarnack, Julian König, Petra Beli

Tracing the evolution of the plastome and mitogenome in the Chloropicophyceae uncovered convergent tRNA gene losses and a variant plastid genetic code. Monique Turmel, Adriana Lopes dos Santos, Christian Otis, Roxanne Sergerie, Claude Lemieux

DPAC: a tool for Differential Poly(A) Site usage from poly(A) targeted RNAseq data. Andrew Laurence Routh

Targeted Cleavage and Polyadenylation of RNA by CRISPR-Cas13. Kelly M Anderson, Pornthida Poosala, Sean R Lindley, Douglas M Anderson

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RNA preprints: W3/2019

A single microRNA-Hox gene module controls complex movement in morphologically-distinct developmental forms of Drosophila. Raouf Issa, Joao Picao-Osorio, Nuno Rito, Maria Eugenia Chiappe, Claudio R. Alonso

3′UTR cleavage of transcripts localized in axons of sympathetic neurons. Catia Andreassi, Raphaelle Luisier, Hamish Crerar, Sasja Franke, Nicholas M. Luscombe, Giovanni Cuda, Marco Gaspari, Antonella Riccio

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

Mature sperm small RNA profile in the sparrow: implications for transgenerational effects of age on fitness. Wayo Matsushima, Kristiana Brink, Julia Schroeder, Eric Alexander Miska, Katharina Gapp

RNA Polymerase II is involved in 18S and 25S ribosomal RNA transcription, in Candida albicans. Jacob Fleischmann, Miguel Angel Rocha, Peter V Hauser

Targeting of RBM10 to S1-1 Nuclear Bodies: Targeting Sequences and its Biological Significance. Ling-Yu Wang, Sheng-Jun Xiao, Hiroyuki Kunimoto, Kazuaki Tokunaga, Hirotada Kojima, Masatsugu Kimura, Takahiro Yamamoto, Naoki Yamamoto, Zhao Hong, Koji Nishio, Hideo Yamane, Tokio Tani, Koichi Nakajima, Hiroyoshi Iguchi, Akira Inoue

Termination of non-coding transcription in yeast relies on both a CTD-interaction domain and a CTD-mimic in Sen1. Zhong Han, Olga Jasnovidova, Agnieszka Tudek, Karel Kubicek, Domenico Libri, Richard Stefl, Odil Porrua

Divergence of piRNA pathway proteins affects piRNA biogenesis but not TE transcript level. Luyang Wang, Daniel Barbash, Erin Kelleher

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

Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods. Carrie Wright, Anandita Rajpurohit, Emily E. Burke, Courtney Williams, Leonardo Collado-Torres, Martha Kimos, Nicholas J. Brandon, Alan J. Cross, Andrew E. Jaffe, Daniel R. Weinberger, Joo Heon Shin

Targeted Long-Read RNA Sequencing Demonstrates Transcriptional Diversity Driven by Splice-Site Variation in MYBPC3. Alexandra Dainis, Elizabeth Tseng, Tyson A Clark, Ting Hon, Matthew Wheeler, Euan Ashley

Early genome activation in Drosophila is extensive with an initial tendency for aborted transcripts and retained introns. Jamie C Kwasnieski, Terry L Orr-Weaver, David P Bartel

MicroRNA-222 regulates fluid shear stress-induced human nucleus pulposus cells degeneration through affecting c-Fos expression. Gaixiong Miao, Yicun Yao, Baoqing Ye, Libing Dai, Guowei Liang, Haixiong Miao , Yicun Yao , Baoqing Ye

Protein features for assembly of the RNA editing helicase 2 subcomplex (REH2C) in Trypanosome holo-editosomes. Vikas Kumar, Pawan K. Doharey, Shelly Gulati, Joshua Meehan, Mary Grace Martinez, Karissa Hughes, Blaine H.M. Mooers, Jorge Cruz-Reyes

Measuring amber initiator tRNA orthogonality in a genomically recoded organism. Russel M. Vincent, Bradley W. Wright, Paul R. Jaschke

RAI1 Regulates Activity-Dependent Nascent Transcription and Synaptic Scaling. Patricia M. Garay, Alex Chen, Takao Tsukahara, Rafi Kohen, J. Christian Althaus, Margarete A. Wallner, Roman J. Giger, Michael A. Sutton, Shigeki Iwase

AGO1 in association with NEAT1 lncRNA contributes to nuclear and 3D chromatin architecture in human cells. Muhammad Shuaib, Krishna Mohan Parsi, Hideya Kawaji, Manjula Thimma, Sabir Abdu Adroub, Alexandre Fort, Yanal Ghosheh, Tomohiro Yamazaki, Taro Mannen, Loqmane Seridi, Bodor Fallatah, Waad Albawardi, Timothy Ravasi, Piero Carninci, Tetsuro Hirose, Valerio Orlando

RNA preprints: W2/2019

Splicing inhibition enhances the antitumor immune response through increased tumor antigen presentation and altered MHC-I immunopeptidome. Alison Pierson, Romain Darrigrand, Marine Rouillon, Mathilde Boulpicante, Zafiarisoa Dolor Renko, Camille Garcia, Michael Ghosh, Marie-Charlotte Laiguillon, Camille Lobry, Mouad Alami, Sebastien Apcher

Inhibition of miR-22-3p reduces kidney disease associated with systemic lupus erythematosus. Danielle L Michell, Ashley Faust, Jared L Moore, Brenna D Appleton, Michelle Ormseth, Marisol Ramirez-Solano, Quanhu Sheng, Joseph F Solus, C. Michael Stein, Kasey C Vickers, Amy S Major

LncRNA Dnmt3aos regulates Dnmt3a expression leading to aberrant DNA methylation in macrophage polarization. Xueqin Li, Yingying Zhang, Mengying Zhang, Xiang Kong, Hui Yang, Min Zhong, Weiya Pei, Yang Xu, Xiaolong Zhu, Tianbing Chen, Jingjing Ye, Kun Lv

Hundreds of yeast mRNAs form a separately addressable, translation elongation-controlled regulon. Eleanna Kazana, Tobias von der Haar

Compartmentalized nonsense-mediated mRNA decay regulates synaptic plasticity and cognitive function via GluR1 signaling. Michael Notaras, Megan Allen, Francesco Longo, Nicole Volk, Miklos Toth, Noo Li Jeon, Eric Klann, Dilek Colak

Purification of Cross-linked RNA-Protein Complexes by Phenol-Toluol Extraction. Erika C Urdaneta, Carlos H Vieira-Vieira, Timon Hick, Hans-Herrmann Wessels, Davide Figini, Rebecca Moschall, Jan Medenbach, Uwe Ohler, Sander Granneman, Matthias Selbach, Benedikt M Beckmann

Tristetraprolin/ZFP36 regulates the turnover of autoimmune-associated HLA-DQ mRNAs. Laura Pisapia, Russell Hamilton, Federica FARINA, Vito D’Agostino, Pasquale Barba, Maria Strazzullo, Alessandro Provenzani, Carmela Gianfrani, Giovanna Del Pozzo

Interaction of modified oligonucleotides with nuclear proteins, formation of novel nuclear structures and sequence-independent effects on RNA processing. Loren L Flynn, Ruohan Li, May T Aung-Htut, Ianthe L Pitout, Jack A L Cooper, Alysia Hubbard, Lisa Griffiths, Charles Bond, Steve D Wilton, Archa H Fox, Sue Fletcher

RNA polymerase clamp movement aids dissociation from DNA but is not required for RNA release at intrinsic terminators. Michael J Bellecourt, Ananya Ray-Soni, Alex Harwig, Rachel Anne Mooney, Robert Landick

A novel rationale for targeting FXI: Insights from the hemostastic miRNA targetome for emerging anticoagulant strategies. Jamie Nourse, Sven Danckwardt

Polymerase recycling contributes to transcriptional noise. Massimo Cavallaro, Mark D. Walsh, Matt Jones, James Teahan, Simone Tiberi, Barbel Finkenstadt, Daniel Hebenstreit

MIR2052HG regulates ERα levels and aromatase inhibitor resistance through LMTK3 by recruiting EGR1. Junmei Cairns, James Ingle, Krishna Kalari, Lois E Shepherd, Michiaki Kubo, Matthew P Goetz, Richard M. Weinshilboum, Liewei Wang

Tau-mediated Disruption of the Spliceosome Triggers Cryptic RNA-splicing and Neurodegeneration in Alzheimer’s Disease. Yi-Chen Hsieh, Caiwei Guo, Hari K. Yalamanchili, Measho Abreha, Rami Al-Ouran, Yarong Li, Eric B. Dammer, James J. Lah, Allan I. Levey, David A. Bennett, Philip L. De Jager, Nicholas T. Seyfried, Zhandong Liu, Joshua M. Shulman

Interactions between dosage compensation complex components Msl-1, Msl-2 and NURF component NURF301 with long non-coding RNA gene hsrω. Deo Prakash Chaturvedi

The mir-35 family links maternal germline sex to embryonic viability in C. elegans. Lars Kristian Benner, Katherine Perkins Prothro, Katherine McJunkin

RBM10 variants and RBM5 involve in alternative splicing of RBM10v1 pre-mRNA: RBM10v1 includes its own exon 4, but RBM10v2 and RBM5 skip it. Koji Nishio

Deep neural networks for interpreting RNA binding protein target preferences. Mahsa Ghanbari, Uwe Ohler

Guanine content of microRNAs is associated with their tumor suppressive and oncogenic roles in lung and breast cancers. Amit Cohen, Mario Alberto Burgos-Aceves, Yoav Smith

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

Modeling the dynamics of Let-7-coupled gene regulatory networks linking cell proliferation to malignant transformation. Claude Gerard, Frederic Lemaigre, Didier Gonze

RNA preprints: W1/2019

Dysregulation of splicing-related proteins in prostate cancer is controlled by FOXA1. John Gordon Foster, Rebecca Arkell, Marco Del Giudice, Chinedu Anene, Andrea Lauria, John Daniel Gerard Kelly, Nicholas Robert Lemoine, Salvatore Oliviero, Matteo Cereda, Prabhakar Rajan

PTBP1 mRNA isoforms and regulation of their translation. Luisa M Arake de Tacca, Mia C Pulos, Stephen N Floor, Jamie Cate

Detection of circulating extracellular mRNAs by modified small RNA-sequencing analysis. Kemal Marc Akat, Youngmin Anna Lee, Arlene Hurley, Pavel Morozov, Klaas E.A. Max, Miguel Brown, Kimberly Bogardus, Anuoluwapo Sopeyin, Kai Hildner, Thomas Diacovo, Markus F. Neurath, Martin Borggrefe, Thomas Tuschl

A widespread Xrn1-resistant RNA motif composed of two short hairpins. Ivar W Dilweg, Alexander P Gultyaev, Rene Olsthoorn

Secretion of an Argonaute protein by a parasitic nematode and the evolution of its siRNA guides. Franklin Wang-Ngai Chow, Georgios Koutsovoulos, Cesaré Ovando-Vázquez, Kyriaki Neophytou, Dominik R Laetsch, Jose R Bermúdez-Barrientos, Sujai Kumar, Elaine Robertson, Julie M Claycomb, Mark Blaxter, Cei Abreu-Goodger, Amy H Buck

Genetic interactions of histone acetyl-transferase enzymes encoding genes Gcn5 and Mof with hsrω lncRNA gene. Deo Prakash Chaturvedi

Disentangling sRNA-Seq data to study RNA communication between species. Jose Roberto Bermudez-Barrientos, Obed Ramirez-Sanchez, Franklin WN Chow, Amy H Buck, Cei Abreu-Goodger

Detecting Circular RNA from High-throughput Sequence Data with de Bruijn Graph. Xin Li, Yufeng Wu

SpliceV: Analysis and publication quality printing of linear and circular RNA splicing, expression and regulation. Nathan A Ungerleider, Erik K Flemington

Trapping a somatic endogenous retrovirus into a germline piRNA cluster immunizes the germline against further invasion. Celine Duc, Marianne Yoth, Nolwenn Mouniee, Silke Jensen, Chantal Vaury, Emilie Brasset

In vitro analysis of RNA polymerase II elongation complex dynamics. Yoo Jin Joo, Scott B. Ficarro, Yujin Chun, Jarrod A. Marto, Stephen Buratowski

Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features. Lisa Barros De Andrade e Sousa, Iris Jonkers, Laurene Syx, Julie Chaumell, Christel Picard, Benjamin Foret, Chong-Jian Chen, John T. Lis, Edith Heard, Edda G. Schulz, Annalisa Marsico

Overexpression of long noncoding RNA GAS5 suppresses tumorigenesis and development of gastric cancer by sponging miR-106a-5p through the Akt/mToR pathway. Shuaijun Dong, Xiefu Zhang, Dechun Liu

Systematic identification and characterization of Aedes aegypti long noncoding RNAs. Azali Azlan, Sattam M. Obeidat, Muhammad Amir Yunus, Ghows Azzam

Role of MPK4 in pathogen-associated molecular pattern-triggered alternative splicing in Arabidopsis. Bazin Jeremie, Kiruthiga Gayathri Mariappan, Thomas Blein, Ronny Volz, Martin Crespi, Heribert Hirt

Tombusvirus p19 captures RNase III-cleaved double-stranded RNAs formed by overlapping sense and antisense transcripts in E. coli. Linfeng Huang, Padraig Deighan, Jingmin Jin, Yingxue Li, Elaine Lee, Shirley S. Mo, Heather Hoover, Sahar Abubucker, Nancy Finkel, Larry McReynolds, Ann Hochschild, Judy Lieberman

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

Evolutionary implications of the microRNA- and piRNA complement of Lepidodermella squamata (Gastrotricha). Bastian Fromm, Juan Pablo Tosar, Felipe Aguilera, Marc Riemer Friedlander, Lutz Bachmann, Andreas Hejnol

RNA preprints: W52/2018

A systems view of spliceosomal assembly and branchpoints with iCLIP. Michael Briese, Nejc Haberman, Christopher Sibley, Anob Chakrabarti, Zhen Wang, Julian Konig, David Perera, Vihandha Wickramasinghe, Ashok Venkitaraman, Nicholas Luscombe, Christopher Smith, Tomaz Curk, Jernej Ule

RNA Polymerase II Independent Recruitment of SPT6 at Transcription Start Sites in Arabidopsis. Chen Chen, Jie Shu, Chenlong Li, Raj K. Thapa, Vi Nguyen, Kangfu Yu, Zechun Yuan, Susanne E. Kohalmi, Jun Liu, Frederic Marsolais, Shangzhi Huang, Yuhai Cui

Structures of the Human Spliceosomes Before and After Release of the Ligated Exon. Xiaofeng Zhang, Xiechao Zhan, Chuangye Yan, Wenyu Zhang, Dongliang Liu, Jianlin Lei, Yigong Shi

Multiplexed detection of RNA using MERFISH and branched DNA amplification. Chenglong Xia, Hazen P Babcock, Jeffrey R Moffitt, Xiaowei Zhuang

RNA sequencing identifies dysregulated circular RNAs in early-stage breast cancer. Vittal Rangan Arvinden, Deva Magendhra Rao Arinagiri Kuha, Meenakumari Balaiah, Priya Ramanathan, Shirley Sundersingh, Sridevi Velusami, Rajkumar Thangarajan, Zdenko Herceg, Samson Mani

A Regulatory Loop between the Retinoid-Related Orphan Nuclear Receptor NHR-23 and let-7 family microRNAs Modulates the C. elegans Molting Cycle. Ruhi Patel, Alison R Frand

Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API. Thomas Desvignes, Phillipe Loher, Karen Eilbeck, Jeffery Ma, Gianvito Urgese, Bastian Fromm, Jason Sydes, Ernesto Aparicio-Puerta, Victor Barrera, Roderic Espin, Eric Londin, Aristeidis G Telonis, Elisa Ficarra, Marc R Friedlander, John H Postlethwait, Isidore Rigoutsos, Michael Hackenberg, Ioannis S Vlachos, Marc K. Halushka, Lorena Pantano

Transgenic Mice and Pluripotent Stem Cells Express EGFP under the Control of miR-302 Promoter. Karim Rahimi, Sara Parsa, Mehrnoush Nikzaban, Seyed Javad Mowla, Fardin Fathi

The miR-338-3p involve in response to acute radiation syndrome by targeting DYRK2 in Tibet minipig. Wang Yujue, Yue Min, Guo Kai, Wu Shaojie, Tian Yuguang

miRNAs, target genes expression and morphological analysis on the heart in gestational protein-restricted offspring. José A.R. Gontijo, Heloisa Balan Assalin, Patrícia Aline Boer

A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs. Alexandra L McCorkindale, Philipp Wahle, Sascha Werner, Irwin Jungreis, Peter Menzel, Chinmay J Shukla, Ruben Lopes Pereira Abreu, Rafael Irizarry, Irmtraud Meyer, Manolis Kellis, Robert P Zinzen

Differential expression of microRNAs in Alzheimer’s disease brain, blood and cerebrospinal fluid: a systematic review and meta-analysis. Petros Takousis, Angélique Sadlon, Jessica Schulz, Inken Wohlers, Valerija Dobricic, Lefkos Middleton, Christina M. Lill, Robert Perneczky, Lars Bertram

A machine-learning classifier trained with microRNA ratios to distinguish melanomas from nevi. Rodrigo Torres, Ursula E Lang, Miroslav Hejna, Samuel J Shelton, Nancy M Joseph, Alan Hunter Shain, Iwei Yeh, Maria L Wei, Michael C. Oldham, Boris C Bastian, Robert L Judson-Torres

A tRNA modification balances carbon and nitrogen metabolism by regulating phosphate homeostasis, to couple metabolism to cell cycle progression. Ritu Gupta, Adhish Walvekar, Shun Liang, Zeenat Rashida, Premal Shah, Sunil Laxman

Detection of a novel mutation G511T in the 530 loop in 16S rRNA in multi drugs resistant Mycobacterium tuberculosis isolated from Sudanese patients. Yousif Mohammed Alfatih, Abeer Babiker Idris, Hadeel Gassim Hassan, Eman O M Nour, Nihad M A Elhaj, Salah-Eldin El-Zaki, Muataz M Eldirdery, Rahma H Ali, Nuha Y Ibrahim, Asrar M Elegail, Mohamed Ahmed Salih

miRsponge: an R/Bioconductor package for the identification and analysis of miRNA sponge interaction networks and modules. Junpeng Zhang, Lin Liu, Taosheng Xu, Yong Xie, Chunwen Zhao, Jiuyong Li, Thuc Duy Le

Biophysical characterizations of the recognition of the AAUAAA polyadenylation signal. Keith Hamilton, Yadong Sun, Liang Tong

Proteasome inhibitor-induced modulation reveals the spliceosome as a specific therapeutic vulnerability in multiple myeloma. Hector Han-Li Huang, Ian D. Ferguson, Alexis M. Thornton, Christine Y. T. Lam, Yu-Hsiu Tony Lin, Prabhakar Bastola, Margarette C. Mariano, Makeba D. Marcoulis, Julia Malato, Paul Phojanakong, Byron C. Hann, Angela N Brooks, Arun P. Wiita

RNA preprints: W51/2018

Dicer-like 5 deficiency confers temperature-sensitive male sterility in maize. Chong Teng, Han Zhang, Reza Hammond, Kun Huang, Blake Meyers, Virginia Walbot

Expression of the miR-302/367 microRNA cluster is regulated by a conserved long non-coding host gene. Karim Rahimi, Annette Christine Fuchtbauer, Fardin Fathi, Seyed Javad Mowla, Ernst-Martin Fuchtbauer

Molecular determinants of metazoan tricRNA biogenesis. Casey A. Schmidt, Joseph D. Giusto, A. Gregory Matera

Control of noncoding RNA production and histone levels by a 5′ tRNA fragment. Ana Boskovic, Xin Yang Bing, Ebru Kaymak, Oliver J Rando

Bayesian inference and comparison of stochastic transcription elongation models. Jordan Douglas, Richard Kingston, Alexei Drummond

Decoding the Epitranscriptional Landscape from Native RNA Sequences. Thidathip Wongsurawat, Piroon Jenjaroenpun, Trudy M Wassenaar, Taylor D Wadley, Visanu Wanchai, Nisreen N Akel, Aime T Franco, Michael L Jennings, David W Ussery, Intawat Nookaew

Computational Discovery of Evolutionary Conserved Enterovirus 71 RNA Secondary Structures. Nathan Fridlyand, Alexander N Lukashev, Andrey Chursov, Franco M Venanzi, Jonathan W Yewdell, Albert A Sufianov, Alexander Shneider

Deconvoluting Stress-Responsive Proteostasis Signaling Pathways for Pharmacologic Activation using Targeted RNA-sequencing. Julia M.D. Grandjean, Lars Plate, Richard I. Morimoto, Michael J. Bollong, Evan T. Powers, R Luke Wiseman

Identifying A- and P-site locations on ribosome-protected mRNA fragments using Integer Programming. Nabeel Ahmed, Pietro Sormanni, Prajwal Ciryam, Michele Vendruscolo, Christopher M Dobson, Edward P O’Brien

In vivo measurements reveal a single 5′ intron is sufficient to increase protein expression level in C. elegans. Matthew M Crane, Bryan Sands, Christian J Battaglia, Brock J Johnson, Soo Yun, Matt Kaeberlein, Roger Brent, Alexander Mendenhall

Dynamic ensemble of HIV-1 RRE stem IIB reveals non-native conformations that disrupt the Rev binding site. Chia-Chieh Chu, Raphael Plangger, Christoph Kreutz, Hashim M. Al-Hashimi

Predicting circRNA-RBP interaction sites using a codon-based encoding and hybrid deep neural networks. Kaiming Zhang, Xiaoyong Pan, Yang Yang, Hong-Bin Shen

Functional characterization of Arabidopsis ARGONAUTE 3 in reproductive tissue. Pauline E Jullien, Stefan Grob, Antonin Marchais, Nathan Pumplin, Clement Chevalier, Caroline Otto, Gregory Schott, Olivier Voinnet

Transcription factor TAp73 and microRNA-449 complement each other to support multiciliogenesis. Merit Wildung, Tilman Uli Esser, Katie Baker Grausam, Cornelia Wiedwald, Larisa Volceanov-Hahn, Dietmar Riedel, Sabine Beuermann, Li Li, Jessica Lynn Simcox Zylla, Ann-Kathrin Guenther, Magdalena Wienken, Evrim Ercetin, Zhiyuan Han, Felix Bremmer, Orr Shomroni, Stefan Andreas, Haotian Zhao, Muriel Lizé

The Landscape Of Circular RNA Expression In The Human Brain. Akira Gokoolparsadh, Firoz Anwar, Irina Voineagu

Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching. Ruixue Wan, Rui Bai, Chuangye Yan, Jianlin Lei, Yigong Shi

miR-216b-5p is Down-Regulated in Human Breast Cancer and Inhibits Proliferation and Progression by Targeting HDAC8 Oncogene. Mohammad-Nazir Menbari, Karim Rahimi, Abbas Ahmadi, Samira Mohammadi-Yeganeh, Anvar Elyasi, Nikoo Darvishi, Vahedeh Hosseini, Mohammad Abdi

De novo Design of Translational RNA Repressors. Paul D Carlson, Cameron J Glasscock, Julius B Lucks

MicroRNA-deficient embryonic stem cells acquire a functional Interferon response. Jeroen Witteveldt, Lisanne Iris Knol, Sara Macias

Analysis of small RNA silencing in Zymoseptoria tritici – wheat interactions. Graeme J. Kettles, Bernhard J. Hofinger, Pingsha Hu, Carlos Bayon, Jason J. Rudd, Dirk Balmer, Mikael Courbot, Kim E. Hammond-Kosack, Gabriel Scalliet, Kostya Kanyuka

Spliceosomal Prp8 intein at the crossroads of protein and RNA splicing. Cathleen M. Green, Zhong Li, Olga Novikova, Valjean R. Bacot-Davis, Fenghan Gao, Nilesh K. Banavali, Hongmin Li, Marlene Belfort

mTORC1 Restricts Hepatitis C Virus Replication Through ULK1-mediated Suppression of miR-122 and Facilitates Post-replication Events. Manish Kumar Johri, Hiren Vasantrai Lashkari, Dhiviya Vedagiri, Divya Gupta, Krishnan Harshan

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

Small RNA bidirectional crosstalk during the interaction between wheat and Zymoseptoria tritici. Xin Ma, Nicolas Bologna, Javier Palma-Guerrero

ASCOT identifies key regulators of neuronal subtype-specific splicing. Jonathan P. Ling, Christopher Wilks, Rone Charles, Devlina Ghosh, Lizhi Jiang, Clayton P. Santiago, Bo Pang, Anand Venkataraman, Brian S. Clark, Abhinav Nellore, Ben Langmead, Seth Blackshaw

Design of a Synthetic sRNA-based Feedback Filter Module. Nicolas Delalez, Aivar Sootla, George H. Wadhams, Antonis Papachristodoulou

A role for gut microbiota in m6A epitranscriptomic mRNA modifications in different host tissues. Sabrina Jabs, Christophe Becavin, Marie-Anne Nahori, Vincent Guerinau, David Touboul, Amine Ghozlane, Marie-Agnes Dillies, Pascale Cossart

Thermosensitive alternative splicing senses and mediates temperature adaptation in Drosophila. Naveh Evantal, Ane Martin Anduaga, Osnat Bartok, Ines Lucia Patop, Ron Weiss, Sebastian Kadener

The whole genome sequence and mRNA transcriptome of the tropical cyclopoid copepod Apocyclops royi. Tue Sparholt Jørgensen, Bolette Lykke Holm Nielsen, Bent Petersen, Patrick Denis Browne, Benni Winding Hansen, Lars Hestbjerg Hansen

RNA preprints: W50/2018

GeTallele: a mathematical model and a toolbox for integrative analysis and visualization of DNA and RNA allele frequencies. Piotr M Słowiński, Muzi Li, Paula Restrepo, Nawaf Alomran, Liam Spurr, Christian Miller, Krasimira Tsaneva-Atanasova, Anelia Horvath

Basal Role for Nrf2-transgne on transcriptional (mRNA/miRNA) regulation in the mouse myocardium. Arun Jyothidasan, Gobinath Shanmugam, John Zhang, Brain Dally, David Crossman, Rajasekaran Namakkal Soorappan

MicroRNA-27a mitigates hyperlipidemia and atherosclerosis by modulating cholesterol homeostasis. Abrar Ali Khan, Heena Agarwal, S Santosh Reddy, Vikas Arige, Vinayak Gupta, Ananthamohan Kalyani, G Bhanuprakash Reddy, Madhu Dikshit, Manoj K Barthwal, Nitish Ranjan Mahapatra

Integrated analysis of sex-biased mRNA and miRNA expression profiles in the gonad of the discus fish (Symphysodon aequifasciatus). yuanshuai Fu, Zhe Xu, Zaizhong Chen, Bin Wen, Jianzhong Gao

The impact of sex on alternative splicing. Guy Karlebach, Diogo F.T. Veiga, Anne Deslattes Mays, Anil K Kesarwani, Daniel Danis, Georgios Kararigas, Xingmin Aaron Zhang, Joshy George, Guru Ananda, Robin Steinhaus, Peter Hansen, Dominik Seelow, Chris Bizon, Rebecca Boyles, Chris Ball, Julie A McMurry, Melissa A Haendel, Jeremy Yang, Tudor Oprea, Mitali Mukerji, Olga Anczukow, Jacques Banchereau, Peter N Robinson

Dynamics of microRNA expression during mouse prenatal development. Rabi Murad, Sorena Rahmanian, Alessandra Breschi, Weihua Zeng, Brian A Williams, Mark Mackiewicz, Brian Roberts, Sarah Meadows, Dianne Moore, Carrie Davis, Diane Trout, Chris Zaleski, Alexander Dobin, Lei-Hoon Sei, Jorg Drenkow, Alex Scavelli, Thomas R Gingeras, Barbara Wold, Richard M. Myers, Roderic Guigo, Ali Mortazavi

Spontaneous driving forces give rise to protein-RNA condensates with coexisting phases and complex material properties. Steven Boeynaems, Alex S Holehouse, Venera Weinhardt, Denes Kovacs, Joris Van Lindt, Carolyn Larabell, Ludo Van Den Bosch, Rhiju Das, Peter Tompa, Rohit V Pappu, Aaron Gitler

The telomeric Cdc13-Stn1-Ten1 complex regulates RNA polymerase II transcription. Olga Calvo, Nathalie Grandin, Antonio Jordan-Pla, Esperanza Minambres, Noelia Gonzalez-Polo, Jose E Perez-Ortin, Michel Charbonneau

Short hairpin RNAs artifactually impair cell growth and suppress clustered microRNA expression. John Powers, Edroaldo Lummertz da Rocha, Daniel Pearson, Pavlos Missios, Tarja Yvanka de Soysa, Jessica Barragan, Patrick Cahan, George Daley

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

An RNA-binding region regulates CTCF clustering and chromatin looping. Anders S Hansen, Tsung-Han S Hsieh, Claudia Cattoglio, Iryna Pustova, Xavier Darzacq, Robert Tjian

Exploring the role of Polycomb recruitment in Xist-mediated silencing of the X chromosome in ES cells. Aurelie Bousard, Ana Claudia Raposo, Jan Jakub Zylicz, Christel Picard, Vanessa Borges Pires, Yanyan Qi, Laurene Syx, Howard Y. Chang, Edith Heard, Simao Teixeira da Rocha

Guided nuclear exploration increases CTCF target search efficiency. Anders S Hansen, Assaf Amitai, Claudia Cattoglio, Robert Tjian, Xavier Darzacq

One-dimensional sliding assists σ70-dependent promoter binding by Escherichia coli RNA polymerase. Iddo Heller, Margherita Marchetti, Abhishek Mazumder, Anirban Chakraborty, Agata M. Malinowska, Wouter H. Roos, Richard H. Ebright, Erwin J.G. Peterman, Gijs J.L. Wuite

Novel Computational Method to Define RNA PSRs Explains Influenza A Virus Nucleotide Conservation. Andrey Chursov, Nathan Fridlyand, Albert A Sufianov, Oleg I Kiselev, Irina Baranovskaya, Andrey Vasin, Jonathan W Yewdell, Alexander Shneider

mtDNA eQTLs and the m1A 16S rRNA modification explain mtDNA tissue-specific gene expression pattern in humans. Tal Cohen, Chen Mordechai, Alal Eran, Dan Mishmar

Synonymous SNPs of viral genes facilitate virus to escape host antiviral RNAi immunity. Xiaobo Zhang, Yuechao Sun, Yu Zhang

Revisiting the window of opportunity for co-transcriptional splicing efficiency and fidelity. Vahid Aslanzadeh, Jean Beggs