RNA preprints: W47/2018

Remote control of alternative splicing in roots through TOR kinase. Ezequiel Petrillo, Stefan Riegler, Armin Fuchs, Lucas Servi, Micaela A. Godoy Herz, Maria Guillermina Kubaczka, Peter Venhuizen, Alois Schweighofer, Alberto R Kornblihtt, Craig Simpson, John W.S. Brown, Christian Meyer, Maria Kalyna, Andrea Barta

RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins. Jing Zhang, Jason Liu, Donghoon Lee, Jo-Jo Feng, Lucas Lochovsky, Shaoke Lou, Michael Rutenberg-Schoenberg, Mark Gerstein

Convolutional models of RNA energetics. Michelle J Wu

Pan-Cancer Repository of Validated Natural and Cryptic mRNA Splicing Mutations. Ben C. Shirley, Eliseos J. Mucaki, Peter K Rogan

Modulation of RNA-dependent interactions in stress granules prevents persistent TDP-43 accumulation in ALS/FTD. Mark Y. Fang, Sebastian Markmiller, William E. Dowdle, Anthony Q. Vu, Paul J. Bushway, Sheng Ding, Mark M. Mercola, Joseph W. Lewcock, Gene Yeo

Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs. Zhangming Yan, Norman Huang, Weixin Wu, Weizhogn Chen, Yiqun Jiang, Jingyao Chen, Xuerui Huang, Xingzhao Wen, Jie Xu, Qiushi Jin, Kang Zhang, Zhen Chen, Shu Chien, Sheng Zhong

Structural and biochemical studies define Nudt12 as a new class of RNA deNADding enzyme in mammalian cells. Ewa Grudzien-Nogalska, Yixuan Wu, Xinfu Jiao, Huijuan Cui, Ronald P. Hart, Liang Tong, Megerditch Kiledjian

The long noncoding RNA Hand2as orchestrates heart development through regulation of precise expression of HAND2. Xue Han, Jiejie Zhang, Yaxi Liu, Xiaoying Fan, Shanshan Ai, Yingjie Luo, Xin Li, Sai Luo, Hui Zheng, Yanzhu Yue, Zai Chang, Zhongzhou Yang, Fuchou Tang, Aibin He, Xiaohua Shen

Comprehensive analysis of miRNA and protein profiles within exosomes derived from canine lymphoid tumour cell lines. Hajime Asada, Hirotaka Tomiyasu, Takao Uchikai, Genki Ishihara, Yuko Goto-Koshino, Koichi Ohno, Hajime Tsujimoto

Beyond the seed: structural basis for supplementary mircoRNA targeting. Jessica Sheu-Gruttadauria, Yao Xiao, Luca F. R. Gebert, Ian J. MacRae

Cold Inducible RNA-binding protein (CIRBP) adjusts clock gene expression and REM sleep recovery after sleep deprivation. Marieke M.B. Hoekstra, Paul Franken, Yann Emmenegger

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

The key protein of endosomal mRNP transport Rrm4 binds translational landmark sites of cargo mRNAs. Lilli Olgeiser, Carl Haag, Susan Boerner, Jernej Ule, Anke Busch, Janine Koepke, Julian Konig, Michael Feldbrugge, Kathi Zarnack

Proteomic analysis of the Pseudomonas aeruginosa iron starvation response reveals PrrF sRNA-dependent regulation of amino acid metabolism, iron-sulfur cluster biogenesis, motility, and zinc homeostasis. Cassandra E. Nelson, Weiliang Huang, Luke K. Brewer, Angela T. Nguyen, Maureen A. Kane, Angela Wilks, Amanda G. Oglesby-Sherrouse

Landscape of RNA editing reveals new insights into the dynamic gene regulation of spermatogenesis based on integrated RNA-Seq. Xiaodan Wang, Zhenshuo Zhu, Xiaolong Wu, Hao Li, Tongtong Li, Qun Li, Peng Zhang, Leijie Li, Dongxue Che, Xia Xiao, Jinlian Hua, Mingzhi Liao

Functional dissection of the ARGONAUTE7 promoter. J Steen Hoyer, Jose L Pruneda-Paz, Ghislain Breton, Mariah A Hassert, Emily E Holcomb, Halley Fowler, Kaylyn M Bauer, Jacob Mreen, Steve A Kay, James C Carrington

Novel autoregulatory cases of alternative splicing coupled with nonsense-mediated mRNA decay. Dmitri Pervouchine, Iaroslav Popov, Andy Berry, Beatrice Borsari, Adam Frankish, Roderic Guig

Live-cell single RNA imaging reveals bursts of translational frameshifting. Kenneth R Lyon Jr., Luis U Aguilera, Tatsuya Morisaki, Brian Munsky, Timothy J Stasevich

The mechanism of Ccr4-Not recruitment to specific mRNAs involves sequence-selective tethering by RNA-binding proteins. Michael W. Webster, James A. W. Stowell, Lori A Passmore

Identification and characterization of miRNA169 family members in banana (Musa acuminata L.) that respond to fusarium oxysporum f. sp. cubense infection in banana cultivars. Shun Song​​, Yi Xu​, Dongmei Huang, Muhammad Aleem Ashraf, Jingyang Li, Wei Hu, Zhiqiang Jin, Changying Zeng, Fenling Tang, Biyu Xu, Huicai Zeng, Yujia Li, Jianghui Xie

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RNA preprints: W46/2018

An integrative study on ribonucleoprotein condensates identifies scaffolding RNAs and reveals a new player in Fragile X-associated Tremor/Ataxia Syndrome. Fernando Cid-Samper, Iona Gelabert-Baldrich, Benjamin Lang, Nieves Lorenzo-Gotor, Riccardo Delli Ponti, Lies-Anne WFM Severijnen, Benedetta Bolognesi, Ellen Gelpi, Renate K. Hukema-Felten, Teresa Botta-Orfila, Gian Gaetano Tartaglia

Identifying the diagnostic value of microRNA-421 in gastric cancer patients: a meta-analysis. Yan Miao, Ying Zhang, Lina Wang, Lihong Yin

TriPepSVM – de novo prediction of RNA-binding proteins based on short amino acid motifs. Annkatrin Bressin, Roman Schulte-Sasse, Davide Figini, Erika C. Urdaneta, Benedikt M. Beckmann, Annalisa Marsico

Chromatin Compaction by Small RNAs and the Nuclear RNAi Machinery in C. elegans. Brandon D Fields, Scott Kennedy

Impact of a Patient-Derived Hepatitis C Viral RNA Genome with a Mutated MicroRNA Binding Site. Miguel Mata, Steven Neben, Karim Majzoub, Jan Carette, Peter Sarnow

The stem rust fungus Puccinia graminis f. sp. tritici induces waves of small RNAs with opposing profiles during wheat infection. Jana Sperschneider, Silke Jacques, Bo Xu, Narayana Upadhyaya, Rohit Mago, Karam Singh, Eric Stone, Ming-Bo Wang, Peter Dodds, Jennifer Taylor

Precursor miRNAs are trafficked along axons associated with vesicles and locally processed to regulate growth cone steering. Eloina Corradi, Antoneta Gavoci, Stephanie Strohbuecker, Michela Roccuzzo, Irene Dalla Costa, Archana Iyer, Simone Bridi, Gabriela Santoz Rodriguez, Cei Abreu-Goodger, Marie-Laure Baudet

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

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

Several phased siRNA annotation methods can frequently misidentify 24 nucleotide siRNA-dominated PHAS loci. Seth Polydore, Alice Lunardon, Michael J Axtell

Truncated, uncapped mRNA 5′ ends targeted by cytoplasmic recapping cluster at CAGE tags and some transcripts are alternatively spliced. Mikaela R Berger, Rolando Alvarado, Daniel L Kiss

Recruitment of human eIF4G1 or DAP5 to the 5′ untranslated regions of a subset of cellular mRNAs drives cap-independent translation. Solomon A Haizel, Usha Bhardwaj, Ruben L Gonzalez Jr., Somdeb Mitra, Dixie Gos

G-quadruplex formation on specific surface-exposed regions of the human ribosomal RNA. Santi Mestre-Fos, Petar I. Penev, Suttipong Suttapitugsakul, Chieri Ito, Anton S. Petrov, Roger M. Wartell, Ronghu Wu, Loren Dean Williams

Plant Extracellular Vesicles Contain Diverse Small RNA Species and Are Enriched in 10 to 17 Nucleotide “Tiny” RNAs. Patricia Baldrich, Brian D. Rutter, Hana Zandkarimi, Ram Podicheti, Blake Meyers, Roger Innes

RNA preprints: W45/2018

Slow transcriptional elongation causes embryonic lethality and perturbs kinetic coupling of long neural genes. Magdalena M Maslon, Ulrich Braunschweig, Stuart Aitken, Abigail R Mann, Fiona Kilanowski, Chris J Hunter, Benjamin J Blencowe, Alberto R Kornblihtt, Ian R Adams, Javier F. Caceres

The spermidine acetyltransferase SpeG regulates transcription of the small RNA RprA. Linda I. Hu, Ekaterina V. Filippova, Joseph Dang, Sergii Pshenychnyi, Jiapeng Ruan, Olga Kiryukhina, Wayne F. Anderson, Misty L. Kuhn, Alan Wolfe

Timing Polymerase Pausing with TV-PRO-seq. Jie Zhang, Massimo Cavallaro, Daniel Hebenstreit

Limited differential expression of miRNAs and other small RNAs in LPS-stimulated human monocytes. Daniel Lu, Tracy Yamawaki, Hong Zhou, Wen-Yu Chou, Mark Chhoa, Edwin Lamas, Sabine S Escobar, Heather A Arnett, Huanying Ge, Songli Wang, Chi-Ming Li

Statistical Mechanical Prediction of Ligand Perturbation to RNA Secondary Structure and Application to the SAM-I Riboswitch. Osama Alaidi, Fareed Aboul-ela

Nonsynonymous A-to-I RNA editing contributes to burden of deleterious missense variants in healthy individuals. Te-Lun Mai, Trees-Juen Chuang

FMRP association with and regulation of Fragile X granules exhibit circuit-dependent requirements for the KH2 RNA binding domain. Ellen C Gingrich, Katherine A Shepard, Molly E Mitchell, Kirsty Sawicka, Jennifer C Darnell, Michael R Akins

Pan-cancer analysis on microRNA-mediated gene activation. Hua Tan, Shan Huang, Zhigang Zhang, Xiaohua Qian, Peiqing Sun, Xiaobo Zhou

Differential phase partition of a PICS complex is required for piRNA processing and chromosome segregation in C. elegans. Chenming Zeng, Chenchun Weng, Xiaoyang Wang, Yong-Hong Yan, Wen-Jun Li, Demin Xu, Minjie Hong, Shanhui Liao, Xuezhu Feng, Meng-Qiu Dong, Chao Xu, Shouhong Guang

Photoperiod-dependent expression of MicroRNA in Drosophila. Mirko Pegoraro, Eran Tauber

ARF5/MONOPTEROS directly regulates miR390 expression in the Arabidopsis thaliana primary root meristem. Mouli Ghosh Dastidar, Andrea Scarpa, Ira Maegele, Paola Ruiz Duarte, Patrick von Born, Lotte Bald, Virginie Jouannet, Alexis Maizel

Axonal localization of the Fragile X family of RNA binding proteins is conserved across mammals. Katherine A Shepard, Lulu I T. Korsak, Michael Akins

PETISCO is a novel protein complex required for 21U RNA biogenesis and embryonic viability. Ricardo J Cordeiro Rodrigues, Antonio Miguel de Jesus Domingues, Svenja Hellmann, Sabrina Dietz, Bruno de Albuquerque, Christian Renz, Helle D. Ulrich, Falk Butter, Rene Kettin

Evidence of a noncoding transcript of the RIPK2 gene overexpressed in head and neck tumor. Eloiza Helena Tajara, Ulises MM Villagra, Bianca R da Cunha, Giovana M Polachini, Tiago Henrique, Carlos H. T. P. da Silva, Olavo A Feitosa, Erica E. Erica E. Fukuyama, Rossana V.M. López, Emmanuel Dias-Neto, Fabio D. Nunes, Patricia Severino

Single cell transcriptomes reveal characteristics of miRNA in gene expression noise reduction. Tao Hu, Lei Wei, Shuailin Li, Tianrun Cheng, Xuegong Zhang, Xiaowo Wang

TriPepSVM – de novo prediction of RNA-binding proteins based on short amino acid motifs. Annkatrin Bressin, Roman Schulte-Sasse, Davide Figini, Erika C. Urdaneta, Benedikt M. Beckmann, Annalisa Marsico

A unique No-Go Decay cleavage in mRNA exit-tunnel of ribosome produces 5′-OH ends phosphorylated by Rlg1. Albertas Navickas, Sebastien Chamois, Renette Saint-Fort, Julien Henri, Claire Torchet, Lionel Benard

RNA is a critical element for the sizing and the composition of phase-separated RNA-protein condensates. Marina Garcia-Jove Navarro, Shunnichi Kashida, Racha Chouaib, Sylvie Souquere, Gerard Pierron, Dominique Weil, Zoher Gueroui

PRMT1-mediated methylation of the Large Drosha Complex regulates microRNA biogenesis. Tiziana Bonaldi, Valeria Spadotto, Roberto Giambruno, Enrico Massignani, Marija Mihailovich, Francesca Patuzzo, Francesco Ghini, Francesco Nicassio

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

Nanopore native RNA sequencing of a human poly(A) transcriptome. Rachael E Workman, Alison Tang, Paul S. Tang, Miten Jain, John R Tyson, Philip C Zuzarte, Timothy Gilpatrick, Roham Razaghi, Joshua Quick, Norah Sadowski, Nadine Holmes, Jaqueline Goes de Jesus, Karen Jones, Terrance P Snutch, Nicholas James Loman, Benedict Paten, Matthew W Loose, Jared T Simpson, Hugh E. Olsen, Angela N Brooks, Mark Akeson, Winston Timp

Novel autoregulatory cases of alternative splicing coupled with nonsense-mediated mRNA decay. Dmitri Pervouchine, Iaroslav Popov, Andy Berry, Beatrice Borsari, Adam Frankish, Roderic Guigo

Structure, dynamics and roX2-lncRNA binding of tandem double-stranded RNA binding domains dsRBD1,2 of Drosophila helicase Maleless. Pravin Kumar Ankush Jagtap, Marisa Mueller, Pawel Masiewicz, Soeren von Buelow, Nele Merret Hollmann, Bernd Simon, Andreas W Thomae, Peter B Becker, Janosch Hennig

Core components of endosomal mRNA transport are evolutionarily conserved in fungi. Jessica Mueller, Thomas Pohlmann, Michael Feldbruegge

RNA preprints: W44/2018

Identification of RNA-associated peptides, iRAP, defines precise sites of protein-RNA interaction. Lauri Peil, Sakharam Waghmare, Lutz Fischer, Michaela Spitzer, David Tollervey, Juri Rappsilber

Bud13 Promotes a Type I Interferon Response By Countering Intron Retention in Irf7. Luke S Frankiw, Devdoot Majumdar, Christian Burns, Logan Vlach, Annie Moradian, Michael Sweredoski, David Baltimore

Pentatricopeptide repeat poly(A) binding protein from mitochondria of trypanosomes. Mikhail V. Mesitov, Tian Yu, Takuma Suematsu, Francois Sement, Liye Zhang, Clinton Yu, Lan Huang, Inna Afasizheva

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

Functional dissection of the ARGONAUTE7 promoter. J Steen Hoyer, Jose L Pruneda-Paz, Ghislain Breton, Mariah A Hassert, Emily E Holcomb, Halley Fowler, Kaylyn M Bauer, Jacob Mreen, Steve A Kay, James C Carrington

Mapping native R-loops genome-wide using a targeted nuclease approach. Qingqing Yan, Emily J Shields, Roberto Bonasio, Kavitha Sarma

Atlas of Subcellular RNA Localization Revealed by APEX-seq. Furqan M Fazal, Shuo Han, Pornchai Kaewsapsak, Kevin R Parker, Jin Xu, Alistair N Boettiger, Howard Y Chang, Alice Y Ting

The nuclear RNAi factor, NRDE2, prevents the accumulation of DNA damage during mitosis in stressful growth conditions. Aarati Asundi, Srivats Venkataramanan, Gina Caldas Cuellar, Atsushi Suzuki, Stephen N Floor, Andrei Goga, Noelle L’Etoile

N6-methyladenosine mRNA marking promotes selective translation of regulons required for human erythropoiesis. Daniel Kuppers, Sonali Arora, Yiting Lim, Andrea Lim, Lucas Carter, Philip Corrin, Christopher Plasier, Ryan Basom, Jeffrey Delrow, Shiyan Wang, Housheng He, Beverly Torok-Storb, Andrew Hsieh, Patrick Paddison

RNA is a critical element for the sizing and the composition of phase-separated RNA-protein condensates. Marina Garcia-Jove Navarro, Shunnichi Kashida, Racha Chouaib, Sylvie Souquere, Gerard Pierron, Dominique Weil, Zoher Gueroui

Dynamics of transposable element invasions with piRNA clusters. Robert Kofler

Long Non-Coding RNA LncKdm2b Regulates Cortical Neuronal Differentiation by Cis-Activating Kdm2b. Wei Li, Wenchen Shen, Bo Zhang, Kuan Tian, Yamu Li, Lili Mu, Zhiyuan Luo, Xiaoling Zhong, Xudong Wu, Ying Liu, Yan Zhou

Genome-wide identification of alternative splicing events that regulate protein transport across the secretory pathway. Alexander Neumann, Magdalena Schindler, Didrik Olofsson, Ilka Wilhelmi, Annette Schürmann, Florian Heyd

Tensor decomposition–based unsupervised feature extraction for integrated analysis of TCGA data on microRNA expression and promoter methylation of genes in ovarian cancer. Y-h. Taguchi, Ka-Lok Ng

DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data. Albert Y Xue, Angela M Yu, Julius B Lucks, Neda Bagheri

Inferring novel lncRNA associated with Ventricular septal defect by DNA methylation interaction network. Min Zhang, Yue Gu, Mu Su, Shumei Zhang, Chuangeng Chen, Wenhua Lv, Yan Zhang

Adenosine Deaminase Acting on RNA 1 Associates with Orf Virus OV20.0 and Enhances Viral Replication. Guan-Ru Liao, Yeu-Yang Tseng, Jing-Yu Tseng, Fong-Yuan Lin, Yumiko Yamada, Hao-Ping Liu, Chih-Ying Kuan, Wei-Li Hsu

Loss of Rap1 supports recombination-based telomere maintenance independent of RNA-DNA hybrids in fission yeast. Yan Hu, Henrietta W Bennett, Na Liu, Martin Moravec, Jessica F Williams, Claus M Azzalin, Megan C King

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

let-7 controls the transition to adulthood by releasing select transcriptional regulators from repression by LIN41. Florian Aeschimann, Anca Neagu, Magdalene Rausch, Helge Grosshans

Maternal Pregnancy-Associated Circulating MicroRNA predictors of infant birth outcomes are Determinants of Placental Maturation. 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

RNA preprints: W43/2018

Interplay between consensus and divergent RNA polymerase II C-terminal domain repeats in viability and targeting. Feiyue Lu, Bede Portz, David S Gilmour

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

MicroRNA-200c suppresses epithelial-mesenchymal transition of ovarian cancer by targeting cofilin-2. Xuechen Yu, Yuanzhen Zhang, Wei Zhang, Huijun Chen

Identification and characterization of Aedes albopictus long noncoding RNAs provides insights into their roles in development and flavivirus infection. Azali Azlan, Muhammad Amir Yunus, Ghows Azzam

sRNA-target Prediction Organizing Tool (SPOT) integrates computational and experimental data to facilitate functional characterization of bacterial small RNAs. Alisa M King, Carin K Vanderpool, Patrick Degnan

A global map of RNA binding protein occupancy guides functional dissection of post-transcriptional regulation of the T cell transcriptome. Adam J Litterman, Wandi S Zhu, Robin Kageyama, Wenxue Zhao, Noah Zaitlen, David J Erle, K. Mark Ansel

Candidate Phyla Radiation Roizmanbacteria from hot springs have novel, unexpectedly abundant, and potentially alternatively functioning CRISPR-Cas systems. Lin-Xing Chen, Basem Al-Shayeb, Raphael Meheust, Wen-Jun Li, Jennifer A Doudna, Jillian F Banfield

RNA Binding Motif Protein 48 is required for U12 splicing and maize endosperm differentiation. Fang Bai, Jacob Corll, Donya N Shodja, Ruth Davenport, Guanqiao Feng, Janaki Mudunkothge, Christian J Brigolin, Federico Martin, Gertraud Spielbauer, Chi-Wah Tseung, Amy E Seibert, W. Brad Barbazuk, Shailesh Lal, A. Mark Settles

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

Re-purposing Ac/Ds transgenic system for CRISPR/dCas9 modulation of enhancers and non-coding RNAs in zebrafish. Vanessa Chong-Morrison, Filipa C. Simoes, Upeka Senanayake, Dervla S. Carroll, Paul R. Riley, Tatjana Sauka-Spengler

Arginine methylation of DDX5 RGG/RG motif by PRMT5 regulates RNA/DNA resolution. Stephane Richard, Sofiane Mersaoui, Zhenbao Yu, Yan Coulombe, Franciele Busatto, Martin Karam, Jean-Yves Masson

Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and whole rrn operon. Anna Cusco, Carlotta Catozzi, Joaquim Vines, Armand Sanchez, Olga Francino

Origins and Evolution of the Global RNA Virome. Valerian V. Dolja, Yuri I Wolf, Darius Kazlauskas, Jaime Iranzo, Adriana Lucía-Sanz, Jens H. Kuhn, Mart Krupovic, Eugene V Koonin

A small RNA controls bacterial resistance to gentamicin during iron starvation. Sylvia Chareyre, Barras Frederic, Pierre Mandin

Sendai Virus Infection Induces Expression of Novel RNAs in Human Cells. Roli Mandhana, Curt M. Horvath

Dysregulation of circular RNAs in myotonic dystrophy type 1. Christine Voellenkle, Alessandra Perfetti, Matteo Carrara, Paola Fuschi, Laura Valentina Renna, Marialucia Longo, Rosanna Cardani, Rea Valaperta, Gabriella Silvestri, Ivano Legnini, Irene Bozzoni, Denis Furling, Carlo Gaetano, Germana Falcone, Giovanni Meola, Fabio Martelli

A Haploid Genetic Screening Method for Proteins Influencing Mammalian Nonsense-Mediated mRNA Decay Activity. Maximilian Popp, Lynne Maquat

Divalent cations can control a switch-like behavior in heterotypic and homotypic RNA coacervates. Paulo L Onuchic, Anthony N Milin, Ibraheem Alshareedah, Ashok A Deniz, Priya R Banerjee

Maternal and zygotic gene regulatory effects of endogenous RNAi pathways. Miguel Vasconcelos Almeida, António Miguel de Jesus Domingues, Rene F Ketting

Interplay between substrate recognition, 5′ end tRNA processing and methylation activity of human mitochondrial RNase P. Agnes Karasik, Carol Fierke, Markos Koutmos

Multiple decay events target HAC1 mRNA during splicing to regulate the unfolded protein response. Patrick D. Cherry, Sally E. Peach, Jay R. Hesselberth

Inference of splicing motifs through visualization of recurrent networks. Aparajita Dutta, Aman Dalmia, Athul R, Kusum Kumari Singh, Ashish Anand

CENP-A associated lncRNAs influence chromosome segregation in human cells. Delphine Quenet, David Sturgill, Marin Olson, Yamini Dalal

Proximity RNA labeling by APEX-Seq Reveals the Organization of Translation Initiation Complexes and Repressive RNA Granules. Alejandro Padron, Shintaro Iwasaki, Nicholas Ingolia

Structure reveals mechanism of CRISPR RNA-guided nuclease recruitment and anti-CRISPR viral mimicry. MaryClare F. Rollins, Saikat Chowdhury, Joshua Carter, Sarah M. Golden, Heini M. Miettinen, Andrew Santiago-Frangos, Dominick Faith, C. Martin Lawrence, Gabriel C. Lander, Blake Wiedenheft

Crosstalk between RNA Pol II C-Terminal Domain Acetylation and Phosphorylation via RPRD Proteins. Ibraheem Ali, Diego Garrido-Ruiz, Zuyao Ni, Jeffrey R Johnson, Heng Zhang, Pao-Chen Li, Ryan J Conrad, Xinghua Guo, Jinrong Min, Jack Greenblatt, Matthew Jacobson, Nevan J Krogan, Melanie Ott

The multi PAM2 protein Upa2 functions as novel core component of endosomal mRNA transport. Silke Jankowski, Thomas Pohlmann, Sebastian Baumann, Sabrina Zander, Senthil Kumar Devan, Michael Feldbruegge

AMPK regulates germline stem cell quiescence and integrity through an endogenous small RNA pathway. Pratik Kadekar, Richard Roy

A Biologically Motivated Asymmetric Exclusion Process: interplay of congestion in RNA polymerase traffic and slippage of nascent transcript. Soumendu Ghosh, Annwesha Dutta, Shubhadeep Patra, Jun Sato, Katsuhiro Nishinari, Debashish Chowdhury

RNA preprints: W42/2018

The mRNA export adaptor Yra1 contributes to DNA double-strand break repair through its C-box domain. Valentina Infantino, Evelina Tutucci, Noel Yeh Martin, Audrey Zihlmann, Varinia Garcia-Molinero, Geraldine Silvano, Benoit Palancade, Francoise Stutz

Programmed Delayed Splicing: A Mechanism for Timed Inflammatory Gene Expression. Devdoot Majumdar, Luke Frankiw, Christian H. Burns, Yvette Garcia-Flores, David Baltimore

Using pan RNA-seq analysis to reveal the ubiquitous existence of 5′ end and 3′ end small RNAs. Xiaofeng Xu, Haishuo Ji, Zhi Cheng, Xiufeng Jin, Xue Yao, Yanqiang Liu, Qiang Zhao, Tao Zhang, Jishou Ruan, Wenjun Bu, Ze Chen, Gao Shan

Bud13 Promotes a Type I Interferon Response By Countering Intron Retention in Irf7. Luke S Frankiw, Devdoot Majumdar, Christian Burns, Logan Vlach, Annie Moradian, Michael Sweredoski, David Baltimore

Base-pair Ambiguity and the Kinetics of RNA Folding. Guangyao Zhou, Jackson Loper, Stuart Geman

Molecular anatomy and plasticity of the long noncoding RNA HOTAIR. Rachel Spokoini-Stern, Dimitar Stamov, Hadass Jessel, Lior Aharoni, Heiko Haschke, Jonathan Giron, Ron Unger, Eran Segal, Almogit Abu-Horowitz, Ido Bachele

MicroRNAs buffer genetic variation at specific temperatures during embryonic development. Christopher Amourda, Jeronica Chong, Timothy E Saunders

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

The RNA-binding ATPase, Armitage, Couples piRNA Amplification in Nuage to Phased piRNA Production on Mitochondria. Daniel Tianfang Ge, Wei Wang, Cindy Tipping, Ildar Gainetdinov, Zhiping Weng, Phillip D Zamore

Widespread RNA editing dysregulation in Autism Spectrum Disorders. Stephen Tran, Hyun-Ik Jun, Jae Hoon Bahn, Adel Azghadi, Gokul Ramaswami, Eric L. Van Nostrand, Thai B. Nguyen, Yun-Hua E. Hsiao, Changhoon Lee, Gabriel A. Pratt, Gene W. Yeo, Daniel H. Geschwind, Xinshu Xiao

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

Nuclear actin interactome analysis links actin to KAT14 histone acetyl transferase and mRNA splicing. Tiina Viita, Salla Kyheröinen, Bina Prajapati, Jori Virtanen, Markku Varjosalo, Maria Vartiainen

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 Cooper, Alysia Hubbard, Lisa Griffiths, Charles Bond, Steve D Wilton, Archa H Fox, Sue Fletcher

PCF11 connects alternative polyadenylation to formation and spontaneous regression of neuroblastoma. Anton Ogorodnikov, Michal Levin, Surendra Tattikota, Sergey Tokalov, Mainul Hoque, Denise Scherzinger, Federico Marini, Ansgar Poetsch, Harald Binder, Stephan Macher-Goeppinger, Bin Tian, Michael Schaefer, Karl Lackner, Frank Westermann, Sven Danckwardt

Assessing the response of small RNA populations to allopolyploidy using resynthesized Brassica napus allotetraploids. Paulina Martinez Palacios, Marie-Pierre Jacquemot, Marion Tapie, Agnes Rousselet, Mamoudou Diop, Carine Remoue, Matthieu Falque, Andrew Lloyd, Eric Jenczewski, Gilles Lassalle, Anne-Marie Chevre, Christine Lelandais, Martin Crespi, Philippe Brabant, Johann Joets, Karine Ali

The RNA-binding protein AATF coordinates rRNA maturation. Rainer Kaiser, Michael Ignarski, Eric L. Van Nostrand, Christian Frese, Manaswita Jain, Sadrija Cukoski, Heide Heinen, Melanie Schaechter, Konstantin Bunte, Peter Frommolt, Patrick Keller, Mark Helm, Katrin Bohl, Martin Höhne, Bernhard Schermer, Thomas Benzing, Katja Höpker, Christoph Dieterich, Gene W Yeo, Roman-Ulrich Mueller, Francesca Fabretti

A cell-based probabilistic approach unveils the concerted action of miRNAs. Shelly Mahlab-Aviv, Nathan Linial, Michal Linial

Disruption in A-to-I editing levels affects C. elegans development more than a complete lack of editing. Nabeel S. Ganem, Noa Ben-Asher, Aidan C. Manning, Sarah N. Deffit, Michael C. Washburn, Emily C. Wheeler, Gene W Yeo, Orna Ben-Naim Zgayer, Einav Mantsur, Heather A. Hundley, Ayelet T Lamm

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

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