RNA preprints: W20/2019

RNA binding kinase UHMK1 regulates therapy induced metabolic adaptation in BRAFV600 melanoma. Lorey K Smith, Tiffany Parmenter, Margarete Kleinschmidt, Eric P Kusnadi, Jian Kang, Claire A Martin, Peter Lau, Teresa Ward, Aparna D Rao, Emily J Lelliott, Karen E Sheppard, Rodney J Hicks, Tony Tiganis, Kaylene J Simpson, Carleen Cullinane, Vihandha O Wickramasinghe, Richard B Pearson, Grant A McArthur

Cus2 enforces the first ATP-dependent step of splicing by binding to yeast SF3b1 through a UHM-ULM interaction. Jason Talkish, Haller Igel, Oarteze Hunter, Steven W. Horner, Nazish N. Jeffery, Justin R. Leach, Jermaine L. Jenkins, Clara L. Kielkopf, Manuel Ares Jr.

Discovery, Expression, Cellular Localization, and Molecular Properties of a Novel, Alternative Spliced HP1γ Isoform, Lacking the Chromoshadow Domain. Angela Mathison, Thiago Milech De Assuncao, Nikita R. Dsouza, Monique Williams, Michael T. Zimmermann, Gwen Lomberk, Raul Urrutia

Aberrant DNA methylation of miRNAs in Fuchs endothelial corneal dystrophy. Peipei Pan, Daniel J. Weisenberger, Siyu Zheng, Marie Wolf, David G. Hwang, Jennifer R. Rose-Nussbaumer, Ula V. Jurkunas, Matilda F. Chan

Machine learning to detect Alzheimer’s disease from circulating non-coding RNAs. Nicole Ludwig, Tobias Fehlmann, Manfred Gogol, Walter Maetzler, Stephanie Deutscher, Simone Gurlit, Claudia Schulte, Anna-Katharina von Thaler, Christian Deuschle, Florian Metzger, Daniela Berg, Ulrike Suenkel, Verena Keller, Christina Backes, Hans-Peter Lenhof, Eckart Meese, Andreas Keller

Efficient RNA-mediated reprogramming of human somatic cells to naïve pluripotency facilitated by tankyrase inhibition. Nicholas Bredenkamp, Jian Yang, James Clarke, Giuliano Giuseppe Stirparo, Ferdinand von Meyenn, Duncan Baker, Rosalind Drummond, Dongwei li, Chuman Wu, Maria Rostovskaya, Austin Smith, Ge Guo

Various components of the RNAi pathway are required for conidiation, ascosporogenesis, virulence, DON production and SIGS-mediated fungal inhibition by exogenous dsRNA in the Head Blight pathogen Fusarium graminearum. Fatima Yousif Gaffar, Jafargholi Imani, Petr Karlovsky, Aline Koch, Karl-Heinz Kogel

An intergenic non-coding RNA promoter required for histone modifications in the human β-globin chromatin domain. Emmanuel Debrand, Lyubomira Chakalova, Joanne Miles, Yan-Feng Dai, Beatriz Goyenechea, Sandra Dye, Cameron S. Osborne, Alice Horton, Susanna Harju-Baker, Ryan C. Pink, Daniel Caley, David R. F. Carter, Kenneth R. Peterson, Peter Fraser

RNA strand invasion activity of the Polycomb complex PRC2. Célia Alecki, Victoria Chiwara, Lionel A. Sanz, Daniel Grau, Osvaldo Arias Pérez, Karim-Jean Armache, Fréderic Chédin, Nicole J. Francis

SF3B1 cancer-related mutations cause vulnerability to further perturbations in the U2 snRNP complex in C. elegans. Xènia Serrat, Dmytro Kukhtar, Eric Cornes, Anna Esteve-Codina, Helena Benlloch, Germano Cecere, Julián Cerón

Updated Database and Evolutionary Dynamics of U12-Type Introns. Devlin C. Moyer, Graham E. Larue, Courtney E. Hershberger, Scott W. Roy, Richard A. Padgett

PITX1 protein interacts with ZCCHC10 to regulate hTERT mRNA transcription. Takahito Ohira, Hirotada Kojima, Yuko Kuroda, Daigo Inaoka, Mitsuhiko Osaki, Hideki Wanibuchi, Futoshi Okada, Mitsuo Oshimura, Hiroyuki Kugoh

ARGONAUTE5 Mediates Fine-Tuning of Vegetative-to-Reproductive Phase Transition Through Its Interaction with miR156 in Arabidopsis. Charles Roussin-Léveillée, Guilherme Silva-Martins, Peter Moffett

Identification of microRNA-target interactions for antioxidant defense response under drought stress by high-throughput sequencing in Zanthoxylum bungeanum Maxim. Xitong Fei, Haichao Hu, Jingmiao Li, Yulin Liu, Anzhi Wei

RNA promotes phase separation of glycolysis enzymes into yeast G bodies in hypoxia. Gregory G. Fuller, Ting Han, Mallory A. Freeberg, James J. Moresco, John R Yates III, John K. Kim

Hairpin: a tool for predicting structural non-coding RNA genes ad initio. Jakob Peder Pettersen

easyCLIP Quantifies RNA-Protein Interactions and Characterizes Recurrent PCBP1 Mutations in Cancer. Douglas F. Porter, Paul A. Khavari

Deep evolutionary origin of nematode SL2 trans-splicing revealed by genome-wide analysis of the Trichinella spiralis transcriptome. Marius Alexander Wenzel, Christopher Johnston, Berndt Müller, Jonathan Pettitt, Bernadette Connolly

MicroRNA miR-1002 enhances NMNAT-mediated stress response by modulating alternative splicing. Joun Park, Yi Zhu, Jennifer M. Brazill, Chong Li, Stefan Wuchty, R. Grace Zhai

Fragment-based discovery of a new class of inhibitors targeting mycobacterial tRNA modification. Sherine E. Thomas, Andrew J. Whitehouse, Karen Brown, Juan M. Belardinelli, Ramanuj Lahiri, M. Daben J. Libardo, Pooja Gupta, Sony Malhotra, Helena I. M. Boshoff, Mary Jackson, Chris Abell, Anthony G. Coyne, Tom L. Blundell, R. Andres Floto, Vítor Mendes

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RNA preprints: W19/2019

Differential effects of Doxorubicin and Actinomycin D on the stability of RNA binding proteins, RBM10 and RBM5: Actinomycin D promotes the nuclear speckles targeting of RBM10 and RBM5 through the novel structural elements. Koji Nishio, Shanlou Qiao, Kung Sang Chang

Modeling ribosome dwell times and relationships with tRNA loading and codon usage in mammals. Cédric Gobet, Benjamin Weger, Julien Marquis, Eva Martin, Frédéric Gachon, Felix Naef

Relationships between MA-RNA binding in cells and suppression of HIV-1 Gag mislocalization to intracellular membranes. Dishari Thornhill, Balaji Olety, Akira Ono

Trophoblast proliferation, migration, and invasion is regulated by the miR-195/EGFR signaling pathway in recurrent spontaneous abortion patients. Xue Bai, Chunyang Zheng, Na Ren

Non-linear sequence similarity between the Xist and Rsx long noncoding RNAs suggests shared functions of tandem repeat domains. Daniel Sprague, Shafagh A. Waters, Jessime M. Kirk, Jeremy R. Wang, Paul B. Samollow, Paul D. Waters, J. Mauro Calabrese

Discovery of interaction-related sRNAs and their targets in the Brachypodium distachyon and Magnaporthe oryzae pathosystem. Silvia Zanini, Ena Šečić, Tobias Busche, Jörn Kalinowski, Karl-Heinz Kogel

Zinc finger RNA binding protein Zn72D regulates ADAR-mediated RNA editing in neurons. Anne L. Sapiro, Emily C. Freund, Lucas Restrepo, Huan-Huan Qiao, Amruta Bhate, Qin Li, Jian-Quan Ni, Timothy J. Mosca, Jin Billy Li

Landscape and regulation of m6A and m6Am methylome across human and mouse tissues. Jun’e Liu, Kai Li, Jiabin Cai, Mingchang Zhang, Xiaoting Zhang, Xushen Xiong, Haowei Meng, Xizhan Xu, Zhibin Huang, Jia Fan, Chengqi Yi

Tissue-specific Genome Editing in vivo by MicroRNA-repressible Anti-CRISPR Proteins. Jooyoung Lee, Haiwei Mou, Raed Ibraheim, Shun-Qing Liang, Wen Xue, Erik Sontheimer

Unbiased identification of trans regulators of ADAR and A-to-I RNA editing. Emily C. Freund, Anne L. Sapiro, Qin Li, Sandra Linder, James J. Moresco, John R. Yates III, Jin Billy Li

CNOT1 mediates phosphorylation via Protein kinase A on the circadian clock. Yunfeng Zhang, Haitang Qin, Yongjie Feng, Peng Gao, Yingbin Zhong, Yicheng Tan, Han Wang, Ying Xu, Joseph S. Takahashi, Guocun Huang

A Pandas complex adapted for piRNA-guided transposon silencing. Kang Zhao, Sha Cheng, Na Miao, Ping Xu, Xiaohua Lu, Ming Wang, Yuhan Zhang, Xun Yuan, Weiwei Liu, Xin Lu, Xuan Ouyang, Peng Zhou, Jiaqi Gu, Yiqun Zhang, Ding Qiu, Shan Wang, Zhaohui Jin, Youzhong Wan, Jinbiao Ma, Hong Cheng, Ying Huang, Yang Yu

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

Multiplex RNA single molecule FISH of inducible mRNAs in single yeast cells. Guoliang Li, Gregor Neuert

MultiEditR: An easy validation method for detecting and quantifying RNA editing from Sanger sequencing. Mitchell Kluesner, Annette Arnold, Taga Lerner, Rafail Nikolaos Tasakis, Sandra Wüst, Marco Binder, Branden S. Moriarity, Riccardo Pecori

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

Post-transcriptional regulation of Nrf2-mRNA by the mRNA-binding proteins HuR and AUF1. Jesse R. Poganik, Marcus J. C. Long, Michael T. Disare, Xuyu Liu, Sung-Hee Chang, Timothy Hla, Yimon Aye

Stabilizing non-native excited states as a therapeutic strategy for targeting RNA. Laura R. Ganser, Chia-Chieh Chu, Hal P. Bogerd, Megan L. Kelly, Bryan R. Cullen, Hashim M. Al-Hashimi

Modeling of SF3B1 cancer-related missense mutations in C. elegans uncovers targets for synthetic lethal interactions. Xènia Serrat, Dmytro Kukhtar, Eric Cornes, Anna Esteve-Codina, Helena Benlloch, Germano Cecere, Julián Cerón

Predicting functional long non-coding RNAs validated by low throughput experiments. Bailing Zhou, Yuedong Yang, Jian Zhan, Xianghua Dou, Jihua Wang, Yaoqi Zhou

Reevaluation of the RNA binding properties of the Tetrahymena thermophila telomerase reverse transcriptase N-terminal domain. Christina Palka, Aishwarya P. Deshpande, Michael D. Stone, Kathleen Collins

Single mRNP analysis by super-resolution microscopy and fluorescence correlation spectroscopy reveals that small mRNP granules represent mRNA singletons. Àngels Mateu-Regué, Jan Christiansen, Frederik Otzen Bagger, Christian Hellriegel, Finn Cilius Nielsen

Native molecule sequencing by nano-ID reveals synthesis and stability of RNA isoforms. Kerstin C. Maier, Saskia Gressel, Patrick Cramer, Björn Schwalb

CROSSalive: a web server for predicting the in vivo structure of RNA molecules. Riccardo Delli Ponti, Alexandros Armaos, Gian Gaetano Tartaglia

MicroRNA Dynamics and Functions During Arabidopsis Embryogenesis. Alexandra Plotnikova, Max J. Kellner, Magdalena Mosiolek, Michael A. Schon, Michael D. Nodine

RNA preprints: W18/2019

Brain microRNAs associated with late-life depressive symptoms are also associated with cognitive trajectory and dementia. Thomas S. Wingo, Jingjing Yang, Wen Fan, Benjamin Logsdon, Se Min Canon, Bing Yao, Nicholas T. Seyfried, James J. Lah, Allan I Levey, Patricia A. Boyle, Julia A. Schneider, Philip L. De Jager, David A. Bennett, Aliza P. Wingo

Plant A20/AN1 proteins coordinate different immune responses including RNAi pathway for antiviral immunity. Li Chang, Ho-Hsiung Chang, Yi-Shu Chiu, Jui-Che Chang, Duen-Wei Hsu, Yuh Tzean, An-Po Cheng, Hsiang-Chia Lu, Hsin-Hung Yeh

Reevaluation of the RNA binding properties of the Tetrahymena thermophila telomerase reverse transcriptase N-terminal domain. Christina Palka, Aishwarya P. Deshpande, Michael D. Stone, Kathleen Collins

Intron-targeted mutagenesis reveals roles for Dscam1 RNA pairing-mediated splicing bias in neuronal wiring. Weiling Hong, Haiyang Dong, Jian Zhang, Fengyan Zhou, Yandan Wu, Yang Shi, Shuo Chen, Bingbing Xu, Wendong You, Feng Shi, Xiaofeng Yang, Zhefeng Gong, Jianhua Huang, Yongfeng Jin

Circadian regulation of microRNA-target chimeras in Drosophila. Xiju Xia, Xiaonan Fu, Binbin Wu, Jinsong Zhu, Zhangwu Zhao

Integrated analysis of the miRNA-mRNA network associated with LMP1 gene in nasopharyngeal carcinoma. Yang Yang, Wen Liu, Yan Zhang, Shuo Wu, Bing Luo

Systematic sequencing of chloroplast transcript termini from Arabidopsis thaliana reveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures. Benoît Castandet, Arnaud Germain, Amber M. Hotto, David B. Stern

Autoregulation of pre-mRNA processing for buffering noisy gene expression. Madeline Smith, Khem Raj Ghusinga, Abhyudai Singh

tRNAscan-SE 2.0: Improved Detection and Functional Classification of Transfer RNA Genes. Patricia P. Chan, Brian Y. Lin, Allysia J. Mak, Todd M. Lowe

Long noncoding RNA AVAN promotes antiviral innate immunity by interacting with TRIM25 and enhancing the transcription of FOXO3a. Chengcai Lai, Lihui Liu, Qinghua Liu, Sijie Cheng, Keyu Wang, Lingna Zhao, Min Xia, Cheng Wang, Hongjing Gu, Yueqiang Duan, Zhongpeng Zhao, Lili Zhang, Ziyang Liu, Jianjun Luo, Jianxun Song, Penghui Yang, Runsheng Chen, Xiliang Wang

Free circular introns with an unusual branchpoint in neuronal projections. Harleen Saini, Alicia A. Bicknell, Sean R. Eddy, Melissa J. Moore

C9orf72 Dipeptide Repeats Inhibit UPF1-Mediated RNA Decay Independent of Stress Granule Formation. Yu Sun, Aziz Eshov, Junjie U. Guo

More accurate transcript assembly via parameter advising. Dan DeBlasio, Kwanho Kim, Carl Kingsford

Error, noise and bias in de novo transcriptome assemblies. Adam H. Freedman, Michele Clamp, Timothy B. Sackton

The splicing factor hnRNP M is a critical regulator of innate immune gene expression in macrophages. K.O. West, H.M. Scott, S. Torres-Odio, A.P. West, K.L. Patrick, R.O. Watson

Transcriptome-wide map of m6A circRNAs identified in hypoxic pulmonary hypertension rat model. Hua Su, Lin Zhou, Na Li, Guowen Wang, Lingfang Wu, Xiuqing Ma, Kejing Ying, Ruifeng Zhang

Evolutionary analyses of base-pairing interactions in DNA and RNA secondary structures. Michael Golden, Ben Murrell, Oliver G. Pybus, Darren Martin, Jotun Hein

Significantly different expression levels of microRNAs associated with vascular invasion in hepatocellular carcinoma and their prognostic significance after surgical resection. Sung Kyu Song, Woon Yong Jung, Seung-Keun Park, Chul-Woon Chung, Yongkeun Park

C1orf109L promote R-loop accumulation induced DNA damage to inhibit cell growth. Dou Peng, Li Yiqun, Xie Wanqiu, Zhang Xiaoqing, Zhang Dandan, Ci Yanpeng, Zhang Xiaohan, Qiao Shupei, Muhammad Luqman Akhtar, Han Fang, Yu Li

Mammalian NSUN2 introduces 5-methylcytidines into mitochondrial tRNAs. Saori Shinoda, Sho Kitagawa, Shinichi Nakagawa, Fan-Yan Wei, Kazuhito Tomizawa, Kimi Araki, Masatake Araki, Takeo Suzuki, Tsutomu Suzuki

The (p)ppGpp-binding GTPase Era promotes rRNA processing and cold shock survival in Staphylococcus aureus. Alison Wood, Sophie E. Irving, Daniel J. Bennison, Rebecca M. Corrigan

Precise removal of Calm1 long 3′ UTR isoform by CRISPR-Cas9 genome editing impairs dorsal root ganglion development in mice. Hannah N. Gruner, Bongmin Bae, Maebh Lynch, Daniel Oliver, Kevin So, Grant S. Mastick, Wei Yan, Pedro Miura

NSUN2 introduces 5-methylcytosines in mammalian mitochondrial tRNAs. Lindsey Van Haute, Song-Yi Lee, Beverly J McCann, Christopher A Powell, Dhiru Bansal, Caterina Garone, Sanghee Shin, Jong-Seo Kim, Michaela Frye, Joseph G Gleeson, Eric Alexander Miska, Hyun-Woo Rhee, Michal Minczuk

Two separation-of-function isoforms of human TPP1 and a novel intragenic noncoding RNA dictate telomerase regulation in somatic and germ cells. Sherilyn Grill, Kamlesh Bisht, Valerie M. Tesmer, Christopher J. Sifuentes, Jayakrishnan Nandakumar

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

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

Merits of constant expression of CRISPR loci in adaptive immunity of bacteria. Wenfa Ng

RNA preprints: W17/2019

A Simulation Study of mRNA Diffusion and Mitochondrial Localization. Paul Horton

A genetic selection reveals functional metastable structures embedded in a toxin-encoding mRNA. Sara Masachis, Nicolas J. Tourasse, Claire Lays, Marion Faucher, Sandrine Chabas, Isabelle Iost, Fabien Darfeuille

Small RNA Mcr11 regulates genes involved in the central metabolism of Mycobacterium tuberculosis and requires 3’ sequence along with the transcription factor AbmR for stable expression. Roxie C. Girardin, Kathleen A. McDonough

EternaBrain: Automated RNA design through move sets and strategies from an Internet-scale RNA videogame. Rohan V. Koodli, Benjamin Keep, Katherine R. Coppess, Fernando Portela, Eterna participants, Rhiju Das

RNA transcribed from heterochromatic simple-tandem repeats are required for male fertility and histone-protamine exchange in Drosophila melanogaster. Wilbur K Mills, Yuh Chwen G. Lee, Antje M Kochendoerfer, Elaine M Dunleavy, Gary H. Karpen

Single-cell imaging reveals unexpected heterogeneity of TERT expression across cancer cell lines. Teisha J. Rowland, Gabrijela Dumbović, Evan P. Hass, John L. Rinn, Thomas R. Cech

A network of microRNAs acts to promote cell cycle exit and differentiation of human pancreatic endocrine cells. Wen Jin, Francesca Mulas, Bjoern Gaertner, Yinghui Sui, Jinzhao Wang, Chun Zeng, Nicholas Vinckier, Allen Wang, Kim-Vy Nguyen-Ngoc, Joshua Chiou, Klaus H. Kaestner, Kelly Frazer, Andrea C. Carrano, Hung-Ping Shih, Maike Sander

O-glycosylation of SPL transcription factors regulates plant developmental transitions downstream of miR156. Krishna Vasant Mutanwad, Nicole Neumayer, Claudia Freitag, Isabella Zangl, Doris Lucyshyn

The structural basis for RNA selectivity by the IMP family of RNA binding proteins. Jeetayu Biswas, Vivek L. Patel, Varun Bhaskar, Jeffrey A. Chao, Robert H. Singer, Carolina Eliscovich

Human 28s rRNA 5’ terminal derived small RNA inhibits ribosomal protein mRNA levels. Shuai Li

Origin of a novel CYP20A1 lncRNA through 23 Alu exaptations in the human lineage creates a potential multi-miRNA sponge. Aniket Bhattacharya, Vineet Jha, Khushboo Singhal, Mahar Fatima, Dayanidhi Singh, Gaura Chaturvedi, Dhwani Dholakia, Rintu Kutum, Trygve E. Bakken, Pankaj Seth, Beena Pillai, Mitali Mukerji

Microarray screening of differentially expressed genes after up-regulating miR-205 or down-regulating miR-141 in cervical cancer cells. Xingyu Fang, Tingting Yao

RST1 and RIPR connect the cytosolic RNA exosome to the Ski complex in Arabidopsis. Heike Lange, Simon Y. A. Ndecky, Carlos Gomez-Diaz, David Pflieger, Nicolas Butel, Julie Zumsteg, Lauriane Kuhn, Christina Piermaria, Johana Chicher, Michael Christie, Ezgi S. Karaaslan, Patricia L. M. Lang, Detlef Weigel, Hervé Vaucheret, Philippe Hammann, Dominique Gagliardi

Subunit joining exposes nascent pre-40S rRNA for processing and quality control. Jay Rai, Melissa D. Parker, Homa Ghalei, Matthew C. Johnson, Katrin Karbstein, M. Elizabeth Stroupe

Multi-view Co-training for microRNA Prediction. Mohsen Sheikh Hassani, James R. Green

Possible origin of the scrapie genome in small endogenous RNAs; studies on eight candidate species in 263K scrapie-infected hamster brain. Eleanor Barnard, Kathryn Estibeiro, Rory Duncan, Janet Baird, David Fettes, Jacqueline Wood, Hugh Fraser, Peter Estibeiro, Richard Lathe

Genome-wide analyses indirectly implicate miRNA regulatory mechanisms in Obsessive-compulsive Disorder psychopathology. NW McGregor, KS O’Connell, TS/ OCD PGC Workgroup, L Davis, CA Mathews, C Lochner, DJ Stein

The nascent RNA binding complex SFiNX licenses piRNA-guided heterochromatin formation. Julia Batki, Jakob Schnabl, Juncheng Wang, Dominik Handler, Veselin I. Andreev, Christian E. Stieger, Maria Novatchkova, Lisa Lampersberger, Kotryna Kauneckaite, Wei Xie, Karl Mechtler, Dinshaw J. Patel, Julius Brennecke

RNAsamba: coding potential assessment using ORF and whole transcript sequence information. Antonio P. Camargo, Vsevolod Sourkov, Marcelo F. Carazzolle

Evolving methods for rational de novo design of functional RNA molecules. Stefan Hammer, Christian Günzel, Mario Mörl, Sven Findeiß

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: W16/2019

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 G. Martinez, Karrisa Hughes, Blaine H.M. Mooers, Jorge Cruz-Reyes

Comparative transcriptomics analyses across species, organs and developmental stages reveal functionally constrained lncRNAs. Fabrice Darbellay, Anamaria Necsulea

miR-9 mediated noise optimization of the her6 oscillator is needed for cell state progression in the Zebrafish hindbrain. Ximena Soto, Veronica Biga, Jochen Kursawe, Robert Lea, Parnian Doostdar, Nancy Papalopulu

FIGARO: An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters. Michael M. Weinstein, Aishani Prem, Mingda Jin, Shuiquan Tang, Jeffrey M. Bhasin

Identification of circular RNAs in porcine sperm and their relation to sperm motility. Marta Gòdia, Anna Castelló, Martina Rocco, Betlem Cabrera, Joan E. Rodríguez-Gil, Armand Sánchez, Alex Clop

Accurate Prediction of Genome-wide RNA Secondary Structure Profile Based On Extreme Gradient Boosting. Yaobin Ke, Jiahua Rao, Huiying Zhao, Yutong Lu, Nong Xiao, Yuedong Yang

Characterization of Amino Acid Recognition in Aminoacyl-tRNA Synthetases. Florian Kaiser, Sarah Krautwurst, Sebastian Salentin, V. Joachim Haupt, Christoph Leberecht, Sebastian Bittrich, Dirk Labudde, Michael Schroeder

piRNA-guided co-transcriptional silencing coopts nuclear export factors. Martin H. Fabry, Filippo Ciabrelli, Marzia Munafò, Evelyn L. Eastwood, Emma Kneuss, Ilaria Falciatori, Federica A. Falconio, Gregory J. Hannon, Benjamin Czech

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

Distinct mechanisms of microRNA sorting into cancer cell-derived extracellular vesicle subtypes. Morayma M. Temoche-Diaz, Matthew J. Shurtleff, Ryan M. Nottingham, Jun Yao, Raj P. Fadadu, Alan M. Lambowitz, Randy Schekman

Music-listening regulates human microRNA transcriptome. Preethy S. Nair, Pirre Raijas, Minna Ahvenainen, Anju K. Philips, Liisa Ukkola-Vuoti, Irma Järvelä

Ifit1 regulates norovirus infection and enhances the interferon response in murine macrophage-like cells. Harriet V. Mears, Edward Emmott, Yasmin Chaudhry, Myra Hosmillo, Ian G. Goodfellow, Trevor R. Sweeney

piRNA-mediated silencing of an invading transposable element evolves rapidly through abundant beneficial de novo mutations. Shuo Zhang, Erin S. Kelleher

The nascent RNA binding complex SFiNX licenses piRNA-guided heterochromatin formation. Julia Batki, Jakob Schnabl, Juncheng Wang, Dominik Handler, Veselin I. Andreev, Christian E. Stieger, Maria Novatchkova, Lisa Lampersberger, Kotryna Kauneckaite, Karl Mechtler, Dinshaw J. Patel, Julius Brennecke

Long noncoding RNAs sustain high expression of exogenous Oct4 by sponging miRNA during reprogramming. Qingran Kong, Xiaolei Zhang, Jiaming Zhang, Kailun Zheng, Heng Zhang, Xixiang Pei, Zhi Yin, Duancheng Wen, Zhonghua Liu

The molecular aetiology of tRNA synthetase depletion: induction of a GCN4 amino acid starvation response despite homeostatic maintenance of charged tRNA levels. Matthew R. McFarland, Corina D. Keller, Brandon M. Childers, Holly Corrigall, Adélaïde Raguin, M. Carmen Romano, Ian Stansfield

Telomeric small RNAs in the genus Caenorhabditis. Stephen Frenk, Evan H. Lister-Shimauchi, Shawn Ahmed

Tissue and cell-type specific expression of a splice variant in the II-III cytoplasmic loop of Cacna1b. Bunda Alexandra, LaCarubba Brianna, Akiki Marie, Andrade Arturo

Endogenous RNAi pathway evolutionarily shapes the destiny of the antisense lncRNAs transcriptome. Ugo Szachnowski, Sara Andus, Dominika Foretek, Antonin Morillon, Maxime Wery

PopTargs: A database for studying population evolutionary genetics of human microRNA target sites. Andrea Hatlen, Mohab Helmy, Antonio Marco

The impact of population variation in the analysis of microRNA target sites. Mohab Helmy, Andrea Hatlen, Antonio Marco

baerhunter: An R package for the discovery and analysis of expressed non-coding regions in bacterial RNA-seq data. A. Ozuna, D. Liberto, R. M. Joyce, K.B. Arnvig, I. Nobeli

Discovery of functional alternatively spliced PKM transcripts in human cancers. Xiangyu Li, Cheng Zhang, Woonghee Kim, Muhammad Arif, Chunxia Gao, Andreas Hober, David Kotol, Linnéa Strandberg, Björn Forsström, Åsa Sivertsson, Per Oksvold, Morten Grøtli, Yusuke Sato, Haruki Kume, Seishi Ogawa, Jan Boren, Jens Nielsen, Mathias Uhlen, Adil Mardinoglu

Hallmarks of slow translation initiation revealed in mitochondrially localizing mRNA sequences. Thomas M. Poulsen, Kenichiro Imai, Martin C. Frith, Paul Horton

Comprehensive Classification of the RNaseH-like domain-containing Proteins in Plants. Shuai Li, Kunpeng Liu, Qianwen Sun

Targeted mRNA demethylation using an engineered dCas13b-ALKBH5 fusion protein. Jiexin Li, Zhuojia Chen, Feng Chen, Yuyi Ling, Yanxi Peng, Nan Luo, Hongsheng Wang

RNA preprints: W15/2019

Native molecule sequencing by nano-ID reveals synthesis and stability of RNA isoforms. Kerstin C. Maier, Saskia Gressel, Patrick Cramer, Björn Schwalb

Sex-related perturbations in schizophrenia and bipolar disorder brains reflect microRNA-mediated cholinergic/neurokine interactions. Sebastian Lobentanzer, Geula Hanin, Jochen Klein, Hermona Soreq

Splice junction-centric approach to identify translated noncanonical isoforms in the human proteome. Edward Lau, Yu Han, Damon R. Williams, Rajani Shrestha, Joseph C. Wu, Maggie P. Y. Lam

In-Silico Analysis of nsSNPs Associated with CYP11B2 Gene. Anam Arooj, Muhammad Tariq Pervez, Zeeshan Gillani, Tahir Ali Chohan, M. Tayyab Chaudhry, Masroor Ellahi Babar, Asma Tufail Shah

RNA polymerase II plays an active role in the formation of gene loops through the Rpb4 subunit. Paula Allepuz-Fuster, Michael J. O’Brien, Noelia González-Polo, Bianca Pereira, Zuzer Dhoondia, Athar Ansari, Olga Calvo

The receptor-like kinases BAM1 and BAM2 promote the cell-to-cell movement of miRNA in the root stele to regulate xylem patterning. Pengfei Fan, Hua Wang, Hao Xue, Tabata Rosas-Diaz, Weihua Tang, Heng Zhang, Lin Xu, Rosa Lozano-Duran

Fidelity of Prespacer Capture and Processing is Governed by the PAM Mediated Interaction of Cas1-2 Adaptation complex in Escherichia coli. K.N.R. Yoganand, Manasasri Muralidharan, B. Anand

Tissue-specific changes in the RNA structurome mediate salinity response in Arabidopsis. David C. Tack, Zhao Su, Yunqing Yu, Philip C. Bevilacqua, Sarah M. Assmann

Crowder-induced Conformational Ensemble Shift in Escherichia Coli Prolyl-tRNA Synthetase. L. M. Adams, R. J. Andrews, Q. H. Hu, H. L. Schmit, S. Hati, S. Bhattacharyya

Focused screening reveals functional effects of microRNAs differentially expressed in colorectal cancer. Danuta Sastre, João Baiochi, Ildercilio Mota de Souza Lima, Josiane Lilian dos Santos Schiavinato, Dimas Tadeu Covas, Rodrigo Alexandre Panepucci

AGO1x prevents dsRNA-induced interferon signaling to promote breast cancer cell proliferation. Souvik Ghosh, Joao C Guimaraes, Manuela Lanzafame, Alexander Schmidt, Afzal Pasha Syed, Beatrice Dimitriades, Anastasiya Börsch, Shreemoyee Ghosh, Ana Luisa Correia, Johannes Danner, Gunter Meister, Luigi M. Terracciano, Salvatore Piscuoglio, Mihaela Zavolan

Endogenous TDP-43 prevents retrotransposons activation through Dicer-2 activity and the RNA silencing machinery in Drosophila neurons. Giulia Romano, Raffaella Klima, Fabian Feiguin

The Israeli Acute Paralysis Virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs. Francisco Acosta-Reyes, Ritam Neupane, Joachim Frank, Israel S. Fernández

CD4 T-cell transcriptome expression reversal of the lncRNA-mRNA co-expression network in elite controller vs. normal-process HIV patients. Chaoyu Chen, Xiangyun Lu, Nanping Wu

tRNA dissociation from EF-Tu after GTP hydrolysis and Pi release: primary steps and antibiotic inhibition. Malte Warias, Helmut Grubmüller, Lars V. Bock

Interplay between gene nucleotide composition bias and splicing. Sébastien Lemaire, Nicolas Fontrodona, Jean-Baptiste Claude, Hélène Polvèche, Fabien Aubé, Laurent Modolo, Cyril F. Bourgeois, Franck Mortreux, Didier Auboeuf

Comparison of different extraction kits to isolate microRNA from Galleria mellonella (wax moth) larvae infected with Metarhizium brunneum (ARSEF4556). Muneefah A. Alenezi, Tariq M. Butt, Daniel C. Eastwood

Extensive post-transcriptional buffering of gene expression in the response to oxidative stress in baker’s yeast. William R. Blevins, Teresa Tavella, Simone G. Moro, Bernat Blasco-Moreno, Adrià Closa-Mosquera, Juana Díez, Lucas B. Carey, M. Mar Albà

Exon-mediated activation of transcription starts. Ana Fiszbein, Keegan S. Krick, Christopher B. Burge

Inhibition of the Dead Box RNA Helicase 3 prevents HIV-1 Tat and cocaine-induced neurotoxicity by targeting microglia activation. Marina Aksenova, Justin Sybrandt, Biyun Cui, Vitali Sikirzhytski, Hao Ji, Diana Odhiambo, Matthew D. Lucius, Jill R. Turner, Eugenia Broude, Edsel Peña, Sofia Lizarraga, Jun Zhu, Ilya Safro, Michael D Wyatt, Michael Shtutman

In silico analysis of coding SNPs and 3′-UTR associated miRNAs in DCAF17 gene that may affect the regulation and pathogenesis of Woodhouse-Sakati Syndrome. Abdelrahman H. Abdelmoneim, Asia M. Elrashied, Alaa I. Mohammed, Sara A. Mirghani, Rania E. Osman, Esraa O. Gadim, Mohamed A. Hassan

Developmentally regulated tcf7l2 splice variants mediate transcriptional repressor functions during eye formation. Rodrigo M. Young, Kenneth B. Ewan, Veronica P. Ferrer, Miguel L. Allende, Trevor C. Dale, Stephen W. Wilson

Comparative transcriptomics analyses across species, organs and developmental stages reveal functionally constrained lncRNAs. Fabrice Darbellay, Anamaria Necsulea

Nuclear RNA export factor variant initiates piRNA-guided co-transcriptional silencing. Kensaku Murano, Yuka W. Iwasaki, Hirotsugu Ishizu, Akane Mashiko, Aoi Shibuya, Shu Kondo, Shungo Adachi, Saori Suzuki, Kuniaki Saito, Tohru Natsume, Mikiko C. Siomi, Haruhiko Siomi

MiR-219 deficiency in Alzheimer’s disease contributes to neurodegeneration and memory dysfunction through post-transcriptional regulation of tau-kinase network. Mercedes Arnes, Yoon A. Kim, Jerome Lannes, Maria E. Alaniz, Joshua D. Cho, Brian D. McCabe, Ismael Santa-Maria

Global analyses of the dynamics of mammalian microRNA metabolism. Elena R. Kingston, David P. Bartel

Posttranscriptional regulation of ribosomal and multiresistance genes by the bacterial leader peptide peTrpL. Hendrik Melior, Siqi Li, Maximilian Stötzel, Konrad U. Förstner, Sandra Maaß, Rubina Schütz, Saina Azarderakhsh, Susanne Barth-Weber, Aleksei Shevkoplias, Kathrin Baumgardt, Zoe Chervontseva, John Ziebuhr, Christian H. Ahrens, Elena Evguenieva-Hackenberg

Altered levels of hsromega lncRNAs further enhance Ras signaling during ectopically activated Ras induced R7 differentiation in Drosophila. Mukulika Ray, Gunjan Singh, Subhash C. Lakhotia

A novel retroviral vector system to analyze expression from mRNA with retained introns using fluorescent proteins and flow cytometry. Patrick E.H. Jackson, Jing Huang, Monika Sharma, Sara K. Rasmussen, Marie-Louise Hammarskjold, David Rekosh

Daedalus and Gasz recruit Armitage to mitochondria, bringing piRNA precursors to the biogenesis machinery. Marzia Munafò, Vera Manelli, Federica A. Falconio, Ashley Sawle, Emma Kneuss, Evelyn L. Eastwood, Jun Wen Eugene Seah, Benjamin Czech, Gregory J. Hannon

Atrx deletion in neurons leads to sexually-dimorphic dysregulation of miR-137 and spatial learning and memory deficits. Renee J. Tamming, Vanessa Dumeaux, Luana Langlois, Jacob Ellegood, Lily R. Qiu, Yan Jiang, Jason P. Lerch, Nathalie G. Bérubé

In situ structure of rotavirus VP1 RNA-dependent RNA polymerase. Simon Jenni, Eric N. Salgado, Tobias Herrmann, Zongli Li, Timothy Grant, Nikolaus Grigorieff, Stefano Trapani, Leandro F. Estrozi, Stephen C. Harrison

A Pandas complex adapted for piRNA-guided transposon silencing. Kang Zhao, Sha Cheng, Na Miao, Ping Xu, Xiaohua Lu, Ming Wang, Yuhan Zhang, Xun Yuan, Weiwei Liu, Xin Lu, Xuan Ouyang, Peng Zhou, Jiaqi Gu, Yiqun Zhang, Ding Qiu, Shan Wang, Zhaohui Jin, Youzhong Wan, Jinbiao Ma, Ying Huang, Yang Yu

RNA preprints: W14/2019

Circular RNA circGTIC1 drives gastric TIC self-renewal to initiate gastric tumorigenesis and metastasis. Liyan Wang, Bin Li, Xuhua Xiao, Xiaoyuan Yi, Feifei He

Risk variant in miR-544a binding site in CCDC170 is associated with osteoporosis. Xinhong Liu, Yang Wang, Qin Tan, Yunqi He, Xin Zhao

mRNA Degradation Rates Are Coupled to Metabolic Status in Mycobacteria. Diego A. Vargas-Blanco, Ying Zhou, Luis Gutierrez Zamalloa, Tim Antonelli, Scarlet S. Shell

FilTar: Using RNA-Seq data to improve microRNA target prediction accuracy in animals. Thomas Bradley, Simon Moxon

A heterochromatin-specific RNA export pathway facilitates piRNA production. Mostafa F. ElMaghraby, Peter Refsing Andersen, Florian Pühringer, Katharina Meixner, Thomas Lendl, Laszlo Tirian, Julius Brennecke

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

Molecular determinants of metazoan tricRNA biogenesis. Casey A. Schmidt, Joseph D. Giusto, Alicia Bao, Anita K. Hopper, A. Gregory Matera

RNA base pairing complexity in living cells visualized by correlated chemical probing. Anthony M. Mustoe, Nicole Lama, Patrick S. Irving, Samuel W. Olson, Kevin M. Weeks

dSreg: A bayesian model to integrate changes in splicing and RNA binding protein activity. Carlos Martí-Gómez, Enrique Lara-Pezzi, Fátima Sánchez-Cabo

MicroRNAs expressed from FSHR and aromatase genes target important ovarian functions. Ilmatar Rooda, Birgitta Kaselt, Andres Salumets, Agne Velthut-Meikas

Fast and unbiased purification of RNA-protein complexes after UV cross-linking. Erika C Urdaneta, Benedikt M Beckmann

Codon Bias Confers Stability to mRNAs via ILF2 in Humans. Fabian Hia, Sheng Fan Yang, Yuichi Shichino, Masanori Yoshinaga, Yasuhiro Murakawa, Alexis Vandenbon, Akira Fukao, Toshinobu Fujiwara, Markus Landthaler, Tohru Natsume, Shungo Adachi, Shintaro Iwasaki, Osamu Takeuchi

Quantitative Principles of cis-translational control by general mRNA sequence features in eukaryotes. Jingyi Jessica Li, Guo-Liang Chew, Mark D. Biggin

TDP-43 proteinopathy impairs neuronal mRNP granule mediated postsynaptic local translation and mRNA metabolism. Chia-En Wong, Kuen-Jer Tsai

The RNA binding protein DAZL functions as repressor and activator of maternal mRNA translation during oocyte maturation. Cai-Rong Yang, Gabriel Rajkovic, Enrico Maria Daldello, Xuan G. Luong, Jing Chen, Marco Conti

The rs6505162 C>A polymorphism in the miRNA-423 gene exhibits a protective element of coronary artery in a southern Chinese population with Kawasaki disease. Jiawen Li, Jinxin Wang, Xiaoping Su, Zhiyong Jiang, Xing Rong, Xueping Gu, Huixian Qiu, Lanlan Zeng, Hao Zheng, Xiaoqiong Gu, Maoping Chu

SSD1 suppresses phenotypes induced by the lack of Elongator-dependent tRNA modifications. Fu Xu, Anders Bystrom, Marcus Johansson

The piRNA Response to Retroviral Invasion of the Koala Genome. Tianxiong Yu, Birgit S. Koppetsch, Keith Chappell, Sara Pagliarani, Stephen Johnston, Zhiping Weng, William E. Theurkauf

Drosophila ribosomal protein S5b is essential for oogenesis and interacts with distinct RNAs. Jian Kong, Hong Han, Julie Bergalet, Louis Philip Benoit Bouvrette, Greco Hernández, Nam Sung Moon, Hojatollah Vali, Éric Lécuyer, Paul Lasko

Interplay Between Short-range Attraction and Long-range Repulsion Controls Reentrant Liquid Condensation of Ribonucleoprotein-RNA Complexes. Ibraheem Alshareedah, Taranpreet Kaur, Jason Ngo, Hannah Seppala, Liz-Audrey Djomnang Kounatse, Wei Wang, Mahdi Muhammad Moosa, Priya R Banerjee

Translation and Transforming Activity of a Circular RNA from Human Papillomavirus. Jiawei Zhao, Eunice E Lee, Jiwoong Kim, Bahir Chamseddin, Rong Yang, Yang Xie, Xiaowei Zhan, Richard Wang

3′-UTR shortening disrupts ceRNA crosstalk of housekeeping genes resulting in subtype-specific breast cancer development. Fan Zhenjiang, Soyeon Kim, Brenda Diergaarde, Hyun Jung Park

In silico analysis of coding SNPs and 3′-UTR associated miRNAs in DCAF17 gene that may affect the regulation and pathogenesis of Woodhouse-Sakati Syndrome. abdelrahman hamza abdelmoneim Sr., Asia M Elrashied, Alaa I Mohammed, Sara A Mirghani, Rania E Osman, Esraa O Gadim, Mohamed A Salih

Alternative Polyadenylation Modifies Target Sites of MicroRNAs with Clinical Potential for Breast Cancer Progression. Soyeon Kim, Yulong Bai, Brenda Diergaarde, George C. Tseng, Hyun Jung Park

BPPart and BPMax: RNA-RNA Interaction Partition Function and Structure Prediction for the Base Pair Counting Model. Ali Ebrahimpour-Boroojeny, Sanjay Rajopadhye, Hamidreza Chitsaz