RNA preprints: W21/2019

Dynamic DNA structure states interact with the RNA editing enzyme ADAR1 to modulate fear extinction memory. Paul R. Marshall, Qiongyi Zhao, Xiang Li, Wei Wei, Abi Malathi, Esmi Zajaczkowski, Laura Leighton, Sachithrani Madugalle, Dean Basic, Ziqi Wang, Jiayu Yin, Wei-Siang Liau, Carl Walkley, Timothy W. Bredy

miRNA-encoded peptide, miPEP858, regulates plant growth and development in Arabidopsis. Ashish Sharma, Poorwa Kamal Badola, Chitra Bhatia, Deepika Sharma, Prabodh Kumar Trivedi

In vitro characterization of the yeast DcpS, a scavenger mRNA decapping enzyme. Madalee G. Wulf, John Buswell, Siu-Hong Chan, Nan Dai, Katherine Marks, Evan R. Martin, George Tzertzinis, Joseph M. Whipple, Ivan R. Corrêa Jr., Ira Schildkraut

Next-generation sequencing of double stranded RNA is greatly improved by treatment with the inexpensive denaturing reagent DMSO. Alexander H. Wilcox, Eric Delwart, Samuel L. Díaz Muñoz

HCMV miR-US22 down-regulation of EGR-1 regulates CD34+ hematopoietic progenitor cell proliferation and viral reactivation. Iliyana Mikell, Lindsey B. Crawford, Meaghan H. Hancock, Jennifer Mitchell, Jason Buehler, Felicia Goodrum, Jay A. Nelson

Genome-wide identification of long non-coding RNAs and their regulatory networks involved in Apis mellifera ligustica response to Nosema ceranae infection. Rui Guo, Huazhi Chen, Yu Du, Dingding Zhou, Sihai Geng, Haipeng Wang, Zhiwei Zhu, Caiyun Shi, Jieqi Wan, Cuiling Xiong, Yanzhen Zheng, Dafu Chen

Quantitative studies of an RNA duplex electrostatics by ion counting. Magdalena Gebala, Daniel Herschlag

Chromatin-enriched RNAs mark active and repressive cis-regulation: an analysis of nuclear RNA-seq. Xiangying Sun, Zhezhen Wang, Carlos Perez-Cervantes, Alex Ruthenburg, Ivan Moskowitz, Michael Gribskov, Xinan Holly Yang

Regulation of KRAS4A/B splicing in cancer stem cells by the RBM39 splicing complex. Wei-Ching Chen, Minh D. To, Peter M.K. Westcott, Reyno Delrosario, Il-Jin Kim, Mark Philips, Quan Tran, Nora Bayani, Allan Balmain

PUMILIO, but not RBMX, binding is required for regulation of genomic stability by noncoding RNA NORAD. Mahmoud M. Elguindy, Florian Kopp, Mohammad Goodarzi, Frederick Rehfeld, Anu Thomas, Tsung-Cheng Chang, Joshua T. Mendell

Nol9 is a Spatial Regulator for the Human ITS2 pre-rRNA Processing Complex. Jacob Gordon, Monica C. Pillon, Robin E. Stanley

miR-26a regulates extracellular vesicle secretion from prostate cancer cells via targeting SHC4, PFDN4 and CHORDC1. Fumihiko Urabe, Nobuyoshi Kosaka, Yurika Sawa, Tomofumi Yamamoto, Yusuke Yamamoto, Kagenori Ito, Takahiro Kimura, Shin Egawa, Takahiro Ochiya

Measuring mRNA translation in neuronal processes and somata by tRNA-FRET. Bella Koltun, Sivan Ironi, Noga Gershoni-Emek, Iliana Barrera, Mohammad Hleihil, Siddharth Nanguneri, Ranjan Sasmal, Sarit S. Agasti, Deepak Nair, Kobi Rosenblum

Transcript degradation and codon usage regulate gene expression in a lytic phage. Benjamin R. Jack, Daniel R. Boutz, Matthew L. Paff, Bartram L. Smith, Claus O. Wilke

Analysis of the expression of PIWI-interacting RNAs during cardiac differentiation of human pluripotent stem cells. Alejandro La Greca, María Agustina Scarafía, María Clara Hernández Cañás, Nelba Pérez, Sheila Castañeda, Carolina Colli, Alan Miqueas Möbbs, Natalia Lucía Santín Velazque, Gabriel Neiman, Ximena Garate, Cyntia Aban, Ariel Waisman, Lucía Moro, Gustavo Sevlever, Carlos Luzzani, Santiago Miriuka

The zinc finger proteins ZC3H20 and ZC3H21 stabilise mRNAs encoding membrane proteins and mitochondrial proteins in insect-form Trypanosoma brucei. Bin Liu, Kevin Kamanyi Marucha, Christine Clayton

The Firre locus produces a trans-acting RNA molecule that functions in hematopoiesis. Jordan P. Lewandowski, James C. Lee, Taeyoung Hwang, Hongjae Sunwoo, Jill M. Goldstein, Abigail F. Groff, Nydia Chang, William Mallard, Adam Williams, Jorge Henao-Meija, Richard A. Flavell, Jeannie T. Lee, Chiara Gerhardinger, Amy J. Wagers, John L. Rinn

Comparison of miRNA profiling methods using synthetic miRNA pools and standardized exRNA samples reveals substantial performance differences. Paula M. Godoy, Andrea J. Barczak, Peter DeHoff, Srimeenakshi Srinivasan, Saumya Das, David J. Erle, Louise C. Laurent

Scalable and cost-effective ribonuclease-based rRNA depletion for bacterial transcriptomics. Yiming Huang, Ravi U Sheth, Andrew Kaufman, Harris H Wang

Antibody cross-reactivity accounts for widespread appearance of m1A in 5’ UTRs. Anya V. Grozhik, Anthony O. Olarerin-George, Miriam Sindelar, Xing Li, Steven S. Gross, Samie R. Jaffrey

Fine chromatin-driven mechanism of transcription interference by antisense noncoding transcription. Jatinder Kaur Gill, Andrea Maffioletti, Varinia García-Molinero, Françoise Stutz, Julien Soudet

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

Long non-coding RNA GRASLND enhancets chondrogenesis via suppression of interferon type II signaling pathway. Nguyen P.T. Huynh, Catherine C. Gloss, Jeremiah Lorentz, Ruhang Tang, Jonathan M. Brunger, Audrey McAlinden, Bo Zhang, Farshid Guilak

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

Molecular detection and characterization of mutation on 23S rRNA gene associated with clarithromycin resistant in Helicobacter pylori. Sahar Obi Abd albagi, Hisham Nour aldayem Altayeb, Nadir Musa Khalil Abuzeid

Cooperativity between the 3’ untranslated region microRNA binding sites is critical for the virulence of eastern equine encephalitis virus. Derek W. Trobaugh, Chengqun Sun, Nishank Bhalla, Christina L. Gardner, Matthew Dunn, William B. Klimstra

dbMTS: a comprehensive database of putative human microRNA target site SNVs and their functional predictions. Chang Li, Michael D. Swartz, Bing Yu, Yongsheng Bai, Xiaoming Liu

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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

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