RNA preprints: W7/2019

An alternatively spliced zebrafish jnk1a transcript has an essential and non-redundant role in development of the first heart field derived proximal ventricular chamber. Adrian Santos-Ledo, Sam J Washer, Tamilvendhan Dhanaseelan, Paul Chrystal, Tania Papoutsi, Deborah Henderson, Bill Chaudhry

How the initiating ribosome copes with (p)ppGpp to translate mRNAs. Daria S Vinogradova, Pavel Kasatsky, Elena Maksimova, Victor Zegarra, Alena Paleskava, Andrey L Konevega, Pohl Milon

Comprehensive circular RNA expression profiles in intermuscular fat from lean and obese pigs. Zhiguo Miao, Jinzhou Zhang, Shan Wang, Panpeng Wei

Oligoribonuclease functions as a diribonucleotidase to bypass a key bottleneck in RNA degradation. Soo-Kyoung Kim, Justin D Lormand, Cordelia A Weiss, Karin A Eger, Husan Turdiev, Asan Turdiev, Wade C Winkler, Holger Sondermann, Vincent T Lee

Full-length mRNA sequencing reveals principles of poly(A) tail length control. Ivano Legnini, Jonathan Alles, Nikos Karaiskos, Salah Ayoub, Nikolaus Rajewsky

Alanine tRNAs translate environment into behavior in Caenorhabditis elegans. Diana Andrea Fernandes De Abreu, Thalia Salinas-Giege, Laurence Marechal-Drouard, Jean-Jacques Remy

lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation. Kaveh Daneshvar, M. Behfar Ardehali, Isaac A Klein, Arcadia J Kratkiewicz, Chan Zhou, Amin Mahpour, Brett M Cook, Wenyang Li, Joshua V Pondick, Sean P Moran, Richard A Young, Robert E Kingston, Alan C Mullen

Glia-derived exosomal miR-274 targets Sprouty in trachea and synaptic boutons to modulate growth and responses to hypoxia. Yi-Wei Tsai, Hsin-Ho Sung, Jian-Chiuan Li, Chun-Yen Yeh, Pei-Yi Chen, Ying-Ju Cheng, Chun-Hong Chen, Yu-Chen Tsai, Cheng-Ting Chien

Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR. Gemma Danks, Heloisa Galbiati, Martina Raasholm, Yamila N Torres Cleuren, Eivind Valen, Pavla Navratilova, Eric M Thompson

A mechanism for ligand gated strand displacement in ZTP riboswitch transcription regulation. Eric J Strobel, Luyi Cheng, Katherine E Berman, Paul D Carlson, Julius B Lucks

Structure of the Ebola virus nucleoprotein – RNA complex. Robert N Kirchdoerfer, Erica Ollmann Saphire, Andrew B Ward

Control of Shoot Meristem Size by an Aminoacyl tRNA Synthetase, OKI1, in Arabidopsis. Munenori Kitagawa, Rachappa S Balkunde, Huyen Thanh Bui, David S Jackson

MicroRNA-143 plays a protective role in ischemia-induced retinal neovascularization. Jiang-Hui Wang, Jinying Chen, Damien Ling, Leilei Tu, Vikrant Singh, Moeen Riaz, Fan Li, Selwyn M Prea, Zheng He, Bang V Bui, Alex W Hewitt, Peter van Wijngaarden, Gregory J Dusting, Guei-Sheung Liu

Decoding and recoding phase behavior of TDP43 reveals that phase separation is not required for splicing function. Hermann Broder Schmidt, Ariana Barreau, Rajat Rohatgi

MiR-590-5p sensitises pancreatic ductal adenocarcinoma cells by blocking autophagy via targeting ATG3. Leping Yang, Fazhao Li, Jun He, Susun Liu, Yawei Zhang

The Telomerase Reverse Transcriptase (TERT) and p53 Regulate Mammalian PNS and CNS Axon Regeneration downstream of c-Myc. JIn-Jin Ma, Ren-Jie Xu, Xin Ju, Wei-Hua Wang, Zong-Ping Luo, Chang-Mei Liu, Lei Yang, Bin Li, Jian-Quan Chen, Bin Meng, Hui-Lin Yang, Feng-Quan Zhou, Saijilafu

Metabolic balancing by miR-276 shapes the mosquito reproductive cycle and Plasmodium falciparum development. Lena Lampe, Marius Jentzsch, Elena A Levashina

Exosome-mediated MIR211 modulates tumor microenvironment via the DUSP6-ERK5 axis and contributes to BRAFV600E inhibitor resistance in melanoma. Bongyong Lee, Anupama Sahoo, John Marchica, Junko Sawada, Sanjay Sahoo, Fabiana I. A. L. Layng, Darren Finlay, Joseph Mazar, Piyush Joshi, Masanobu Komatsu, Kristiina Vuori, Garth Powis, Petrus R. de Jong, Animesh Ray, Ranajan J. Perera

mRNA structure regulates protein expression through changes in functional half-life. David M. Mauger, B. Joseph Cabral, Vladimir Presnyak, Stephen V. Su, David W. Reid, Brooke Goodman, Kristian Link, Nikhil Khatwani, John Reynders, Melissa J. Moore, Iain J. McFadyen

Comprehensive network analysis reveals alternative splicing-related lncRNAs in hepatocellular carcinoma. Junqing Wang, Yixin Chen, Keli Xu, Yin-yuan Mo, Yunyun Zhou

Expression changes confirm predicted single nucleotide variants affecting mRNA splicing. Eliseos J Mucaki, Peter K Rogan

Changes in Ovary Transcriptome and Alternative Splicing at Estrus from Xiang Pigs with Large and Small Litter Size. Fu P Zhang, Xue Q Ran

The length of the expressed 3′ UTR is an intermediate molecular phenotype linking genetic variants to complex diseases. Elisa Mariella, Federico Marotta, Elena Grassi, Stefano Gilotto, Paolo Provero

Arenaviridae exoribonuclease presents genomic RNA edition capacity. Elsie Yekwa, Chutima Aphibanthammakit, Xavier Carnec, Caroline Picard, Bruno Canard, Sylvain Baize, François Ferron

Analysis of genetically driven alternative splicing identifies FBXO38 as a novel COPD susceptibility gene. Aabida Saferali, Jeong H Yun, Margaret M Parker, Phuwanat Sakornsakolpat, Robert P Chase, Andrew Lamb, Brian D Hobbs, Marike H Boezen, Xiangpeng Dai, Kim de Jong, Terri H Beaty, Wenyi Wei, Xiaobo Zhou, Edwin K Silverman, Michael H Cho, Peter J Castaldi, Craig P Hersh, COPDGene Investigators, and the International COPD Genetics Consortium Investigators

SCANVIS: a tool for SCoring, ANnotating and VISualing splice junctions. Phaedra Agius, Heather Geiger, Nicolas Robine

Egalitarian binding partners, Dynein Light Chain and Bicaudal-D, act sequentially to link mRNA to the Dynein motor. Chandler H. Goldman, Rajalakshmi Veeranan-Karmegam, Hannah Neiswender, Graydon B. Gonsalvez

A universal fluorescence-based toolkit for real-time quantification of DNA and RNA nuclease activity. Emily C Sheppard, Sally Rogers, Nicholas J Harmer, Richard Chahwan

Genome-wide identification and analysis of A-to-I RNA editing events in the malignantly transformed cell lines from BEP2D induced by α-particles radiation. Qiaowei Liu, Hao Li, Lukuan You, Tao Li, Lingling Li, Pingkun Zhou, Xiaochen Bo, Hebing Chen, Xiaohua Chen, Yi Hu

Evaluations of short telomere risk-associated single nucleotide polymorphisms in telomerase reverse transcriptase gene on telomere length maintenance. Jialin Xu, Matthew A Trudeau, Andrew J Sandford, Judy MY Wong

Identification of lncRNAs associated with early stage breast cancer and their prognostic implications. Deva Magendhra Rao Arunagiri Kuha, Krishna Patel, Sunitha Korivi Jyothi, Meenakumari Balaiah, Shirley Sundersingh, Sridevi Velusami, Rajkumar Thangarajan, Akhilesh Pandey, Aditi Chatterjee, Harsha Gowda, Samson Mani

Environmental pheromone and endocrine signals correct heterochronic developmental phenotypes caused by insufficient expression of let-7 family microRNAs in C. elegans. Orkan Ilbay, Victor Ambros

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

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

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

PLIT: An alignment-free computational tool for identification of long non-coding RNAs in plant transcriptomic datasets. S. Deshpande, J. Shuttleworth, J. Yang, S. Taramonli, M. England

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