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