RNA preprints: W4/2018

Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks. Kevin Walters, Radmir Sarsenov, Wen S Too, Roseanna K Hare, Ian C Paterson, Daniel W Lambert, Stephen Brown, James R Bradford

An atypical CRISPR-Cas locus in Symbiobacterium thermophilum flanked by a transposase, a reverse transcriptase, the endonuclease MutS2 and a putative Cas9-like protein. Sandeep Chakraborty

Global analysis of gene expression dynamics identifies factors required for accelerated mRNA degradation. Darach Miller, Nathan Brandt, David Gresham

Systematic meta-analyses identify differentially expressed microRNAs in Parkinson’s disease. Jessica Schulz, Petros Takousis, Inken Wohlers, Ivie Itua, Valerija Dobricic, Harald Binder, Lefkos Middleton, John Ioannidis, Robert Perneczky, Lars Bertram, Christina Lill

Assembly and validation of conserved long non-coding RNAs in the ruminant transcriptome. Stephen J Bush, Charity Muriuki, Mary E B McCulloch, Iseabail L Farquhar, Emily Louise Clark, David A Hume

Monitoring the 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) modification in eukaryotic tRNAs via the gamma-toxin endonuclease. Jenna M Lentini, Jillian Ramos, Dragony Fu

Genome-wide analysis of RNA editing levels in human blood identified interactions with mRNA processing genes and suggested correlations with biological and drug-related variables. Edoardo Giacopuzzi, Massimo Gennarelli, Chiara Sacco, Chiara Magri, Alessandro Barbon

Developmental genetics of corolla tube formation: role of the tasiRNA-ARF pathway. Baoqing Ding, Rui Xia, Vandana Gurung, Janelle M. Sagawa, Lauren E. Stanley, Matthew Strobel, Qiaoshan Lin, Pamela K. Diggle, Blake C. Meyers, Yao-Wu Yuan

Loss of mCHH islands in maize chromomethylase and DDM1-type nucleosome remodeler mutants. Fang-Fang Fu, R. Kelly Dawe, Jonathan I. Gent

Graphene-oxide quenching-based molecular beacon imaging of exosome-mediated transfer of neurogenic miR-193a on microfluidic platform. Hyun Jeong Oh, Hyejin Park, Dayoung Yoon, Seok Chung, Do Won Hwang, Dong Soo Lee

Combined analysis of genome sequencing and RNA-motifs reveals novel damaging non-coding mutations in human tumors. Babita Singh, Juan L Trincado, PJ Tatlow, Stephen R Piccolo, Eduardo Eyras

Bioinformatic analysis of endogenous and exogenous small RNAs on lipoproteins. Ryan M Allen, Shilin Zhao, Marisol A. Ramirez-Solano, Danielle L. Michell, Yuhuan Wang, Yu Shyr, Praveen Sethupathy, MacRae F Linton, Gregory A Graf, Quanhu Sheng, Kasey C Vickers

Discovering lncRNA Mediated Sponge Interactions in Breast Cancer Molecular Subtypes. Gulden Olgun, Ozgur Sahin, Oznur Tastan

Enzyme-based synthesis of single molecule RNA FISH probes. Christian Lanctôt

Large differences in small RNA composition between human biofluids. Paula Maria Godoy, Nirav R Bhakta, Andrea J Barczak, Hakan Cakmak, Susan Fisher, Tippi C Mackenzie, Tushar Patel, Richard W Price, James F Smith, Prescott G Woodruff, David J Erle

Rapid and dynamic alternative splicing impacts the Arabidopsis cold response transcriptome. Cristiane P G Calixto, Wenbin Guo, Allan B James, Nikoleta A Tzioutziou, Juan C Entizne, Paige E Panter, Heather Knight, Hugh G Nimmo, Runxuan Zhang, John Brown

The Evolutionary History and Impact of Bacterial tRNA Modifications. Gaurav D Diwan, Deepa Agashe

HOTAIR ancient sequence suggests regulatory roles both in cis and trans. Chirag Nepal, Yavor Hadzheiv, Sachin Pundhir, Piotr Mydel, Boris Lenhard, Ferenc Mueller, Jesper B Andersen

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RNA preprints: W3/2018

Transgenerational Epigenetic Inheritance Factors Localize to Spatially and Temporally Ordered Liquid Droplet Assemblages. Gang Wan, Brandon Fields, George Spracklin, Carolyn Phillips, Scott Kennedy

Cell-type specific expression of oncogenic and tumor suppressive microRNAs in the human prostate and prostate cancer. Binod Kumar, Avi Z Rosenberg, Su Mi Choi, Karen Fox-Talbot, Angelo M De Marzo, Larisa Nonn, W. Nathaniel Brennen, Luigi Marchionni, Marc K Halushka, Shawn E Lupold

RNA polymerase II pausing regulates a quiescence-dependent transcriptional program, priming cells for cell cycle reentry. Hardik P Gala, Debarya Saha, Nisha Venugopal, Ajoy Aloysius, Jyotsna Dhawan

miRge 2.0: An updated tool to comprehensively analyze microRNA sequencing data. YIn Lu, Alexander S Baras, Marc K Halushka

Programmable RNA recognition using a CRISPR-associated Argonaute. Audrone Lapinaite, Jennifer A. Doudna, Jamie Cate

HSF2 Co-regulates Protein-coding and Long Non-coding RNA Genes Specific to Black Tissues of the Black Chicken, Yeonsan Ogye. Hyosun Hong, Han-Ha Chai, Kyoungwoo Nam, Dajeong Lim, Kyung-Tai Lee, Yoon Jung Do, Chang-Yeon Cho, Jin-Wu Nam

Conserved and ubiquitous expression of piRNAs and PIWI genes in mollusks antedates the origin of somatic PIWI/piRNA expression to the root of bilaterians. Julia Jehn, Daniel Gebert, Frank Pipilescu, Sarah Stern, Julian Simon Thilo Kiefer, Charlotte Hewel, David Rosenkranz

MicroRNA-122 supports robust innate immunity in hepatocytes by suppressing STAT3 phosphorylation. Hui Xu, Shi-Jun Xu, Shu-Juan Xie, Yin Zhang, Jian-Hua Yang, Wei-Qi Zhang, Man-Ni Zheng, Hui Zhou, Liang-Hu Qu

Genome-encoded Cytoplasmic Double-Stranded RNAs, Found in C9ORF72 ALS-FTD Brain, Provoke Propagated Neuronal Death. Steven Rodriguez, Benjamin R Schrank, Asli Sahin, Hawra Al-Lawati, Isabel Constantino, Eric Benz, Darian Fard, Alefiya D Albers, Luxiang Cao, Alexis C Gomez, Elena Ratti, Merit Cudkowicz, Matthew P Frosch, Michael Talkowski, Peter K Sorger, Bradley T Hyman, Mark W Albers

MicroRNA regulation of the MRN complex impacts DNA damage, cellular senescence and angiogenic signaling. Cristina Espinosa-Diez, RaeAnna Wilson, Namita Chatterjee, Clayton Hudson, Rebecca Ruhl, Christina Hipfinger, Erin Helms, Omar F Khan, Daniel G Anderson, Sudarshan Anand

In search of non-coding driver mutations by deep sequencing of regulatory elements in colorectal cancer. Rebecca C Poulos, Dilmi Perera, Deborah Packham, Anushi Shah, Caroline Janitz, John E Pimanda, Nicholas Hawkins, Robyn L Ward, Luke B Hesson, Jason WH Wong

miR-10b Deficiency Affords Atherosclerosis Resistance. Masako Nakahara, Norihiko Kobayashi, Masako Oka, Kenta Nakano, Tadashi Okamura, Akira Yuo, Kumiko Saeki

MicroRNA-92a negatively regulates neurofibromin 2 and inhibits its tumor suppressive function. Krizelle Mae M. Alcantara, Reynaldo L Garcia

De novo mutations involved in post-transcriptional dysregulation contribute to six neuropsychiatric disorders. Fengbiao Mao, Lu Wang, Xiaolu Zhao, Luoyuan Xiao, Xianfeng Li, Qi Liu, Xin He, Rajesh C. Rao, Jinchen Li, Huajing Teng, Yali Dou, Zhongsheng Sun

Efficient computation of co-transcriptional RNA-ligand interaction dynamics. Michael T Wolfinger, Christoph Flamm, Ivo L Hofacker

miRNAs play important roles in aroma weakening during the shelf life of ‘Nanguo’ pear after cold storage. Fei Shi, Xin Zhou, Miaomiao Yao, Zhuo Tan, Qian Zhou, Lei Zhang, Shujuan Ji

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RNA preprints: W2/2018

ZFP36 RNA-binding proteins restrain T-cell activation and anti-viral immunity. Michael J Moore, Nathalie E Blachere, John J Fak, Christopher Y Park, Kirsty Sawicka, Salina Parveen, Ilana Zucker-Scharff, Bruno Moltedo, Alexander Rudensky, Robert Darnell

Precise temporal regulation of alternative splicing during neural development. Sebastien M Weyn-Vanhentenryck, Huijuan Feng, Dmytro Ustianenko, Rachel Duffie, Qinghong Yan, Martin Jacko, Jose C Martinez, Marianne Goodwin, Xuegong Zhang, Ulrich Hengst, Stavros Lomvardas, Maurice S Swanson, Chaolin Zhang

Small interfering RNAs based on huntingtin trinucleotide repeats are highly toxic to cancer cells. Andrea E Murmann, Quan Q Gao, William Putzbach, Monal Patel, Elizabeth T Bartom, Calvin Law, Bryan Bridgeman, Siquan Chen, Kaylin M McMahon, C Shad Thaxton, Marcus Ernst Peter

Circulating small non-coding RNAs associated with age, sex, smoking, body mass and physical activity. Trine B Rounge, Sinan U Umu, Andreas Keller, Eckart Meese, Giske Ursin, Steinar Tretli, Robert Lyle, Hilde Langseth

NET-prism enables RNA polymerase-dedicated transcriptional interrogation at nucleotide resolution. Constantine Mylonas, Peter Tessarz

Bioinformatic analysis of endogenous and exogenous small RNAs on lipoproteins. Ryan M Allen, Shilin Zhao, Marisol A. Ramirez-Solano, Danielle L. Michell, Yuhuan Wang, Yu Shyr, Praveen Sethupathy, MacRae F Linton, Greg A Graf, Quanhu Sheng, Kasey C Vickers

RMalign: an RNA structural alignment tool based on a size independent scoring function. Zheng Jinfang, Juan Xie, Xu Hong, Shiyong Liu

miR-132 controls mouse pancreatic beta cell proliferation and survival through the Pten/Akt/Foxo3 signaling. Hassan Mziaut, Georg Henniger, Katharina Ganss, Sebastian Hempel, Steffen Wolk, Johanna McChord, Kamal Chowdhury Chowdhury, Klaus Peter Knoch, Jurgen Weitz, Robert Grutzmann, Christian Pilarsky, Michele Solimena, Stephan Kersting

Splice Expression Variation Analysis (SEVA) for Inter-tumor Heterogeneity of Gene Isoform Usage in Cancer. Bahman Afsari, Theresa Guo, Michael Considine, Liliana Florea, Luciane Tsukamoto Kagohara, Genevieve L Stein-O’Brien, Dylan Kelley, Emily Flam, Kristina D Zambo, Patrick Ha, Donald Geman, Michael F Ochs, Joseph A Califano, Daria A Gaykalova, Alexander V Favorov, Elana J Fertig

RNA helicase, DDX27 regulates skeletal muscle growth and regeneration by modulation of translational processes. Alexis H Bennett, Marie Francoise O’Donohue, Stacey R Gundry, Aye T Chan, Jeffery Widrick, Isabelle Draper, Anirban Chakraborty, Yi Zhou, Leonard I Zon, Pierre-Emmanuel Gleizes, Alan H Beggs, Vandana A Gupta

Identification of differentially expressed small RNAs and prediction of target genes in Italian Large White pigs with divergent backfat deposition. Roberta Davoli, Enrico Gaffo, Martina Zappaterra, Stefania Bortoluzzi, Paolo Zambonelli

Differential 3′ Processing of Specific Transcripts Expands Regulatory and Protein Diversity Across Neuronal Cell Types. Sasa Jereb, Hun-Way Hwang, Eric Van Otterloo, Eve-Ellen Govek, John J Fak, Yuan Yuan, Mary E Hatten, Robert B Darnell

Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs in Drosophila melanogaster. Michael P. Meers, Karen Adelman, Robert J. Duronio, Brian D. Strahl, Daniel J. McKay, A. Gregory Matera

Benchmark of lncRNA Quantification for RNA-Seq of Cancer Samples. Hong Zheng, Kevin Brennan, Mikel Hernaez, Olivier Gevaert

In silico design of ligand triggered RNA switches. Sven Findeiß, Stefan Hammer, Michael T. Wolfinger, Felix Kühnl, Christoph Flamm, Ivo L. Hofacker

Neuron-specific cTag-CLIP reveals cell-specific diversity of functional RNA regulation in the brain. Yuhki Saito, Yuan Yuan, Ilana Zucker-Scharff, John J Fak, Yoko Tajima, Donny D Licatalosi, Robert B Darnell

Varicella-zoster virus CNS vasculitis and RNA polymerase III gene mutation in identical twins. Madalina Carter-Timofte, Anders Fogh Hansen, Maibritt Mardahl, Sébastien Fribourg, Franck Rapaport, Shen-Ying Zhang, Jean-Laurent Casanova, Søren R Paludan, Mette Christiansen, Carsten S Larsen, Trine H Mogensen

Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons. Yuan Yuan, Shirley Xie, Jennifer C Darnell, Andrew J Darnell, Yuhki Saito, Hemali Phatnani, Elisabeth A Murphy, Chaolin Zhang, Tom Maniatis, Robert B Darnell

HOTAIR primes the Ewing sarcoma family of tumors for tumorigenesis via epigenetic dysregulation involving LSD1. Hasan Siddiqui, Julia Selich-Anderson, Joshua Felgenhauer, James Fitch, Vijay Nadella, Cenny Taslim, Laura Tomino, Emily Theisen, Satoru Otsuru, Edwin Horwitz, Stephen L Lessnick, Peter White, Nilay Shah

Fidaxomicin jams M. tuberculosis RNA polymerase motions needed for initiation via RbpA contacts. Hande Boyaci, James Chen, Mirjana Lilic, Margaret Palka, Rachel Anne Mooney, Robert Landick, Seth A Darst, Elizabeth A Campbell

Deconvolving RNA Base Pairing Signals. Torin Greenwood, Christine E. Heitsch

The effect of RNA stiffness on the self-assembly of virus particles. Siyu Li, Gonca Erdemci-Tandogan, Paul van der Schoot, Roya Zandi

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RNA preprints: W1/2018

A novel long noncoding RNA LINC00844 regulates prostate cancer cell migration and invasion through androgen receptor signaling. Shreyas Lingadahalli, Sudhir Jadhao, Ying Ying Sung, Mi Chen, Lingling Hu, Xin Chen, Edwin Cheung

Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons. Yuan Yuan, Shirley Xie, Jennifer C Darnell, Andrew J Darnell, Yuhki Saito, Hemali Phatnani, Elisabeth Murphy, Chaolin Zhang, Tom Maniatis, Robert Darnell

The basis of accumulation differences in plant 21-nt reproductive phasiRNAs, and their cis-directed activity. Saleh Tamim, Zhaoxia Cai, Sandra Mathioni, Jixian Zhai, Chong Teng, Qifa Zhang, Blake C. Meyers

Reproductive phasiRNAs in grasses are compositionally distinct from other classes of small RNAs. Parth Patel, Sandra Mathioni, Atul Kakrana, Hagit Shatkay, Blake C. Meyers

Long Noncoding RNA-Maternally Expressed Gene 3 Contributes to Hypoxic Pulmonary Hypertension. Daling Zhu, Yan Xing, Xiaodong Zheng, Yao Fu, Jing Qi, Minghui Li, Haisheng Peng, Mingfei Ma, Shuang Wang, Shuzhen Li

RNA-binding proteins with mixed charge domains self-assemble and aggregate in Alzheimer’s Disease. Isaac Bishof, Eric B Dammer, Duc M Duong, Marla Gearing, James J Lah, Allan I Levey, Nicholas T Seyfried

Targeting the DNM3OS / miR-199a~214 cluster for the treatment of fibroproliferative diseases. Gregoire Savary, Matthieu Buscot, Edmone Dewaeles, Serena Diazzi, Nicolas Nottet, Elisabeth Courcot, Julien Fassy, Kevin Lebrigand, Imene Sarah Henaoui, Nihal Martis, Cynthia Van der Hauwaert, Sylvie Leroy, Laurent Plantier, Agnes Paquet, Christian L Lino Cardenas, Georges Vassaux, Bruno Crestani, Benoit Wallaert, Roger Rezzonico, Thierry Brousseau, Francois Glowacki, Saverio Bellusci, Michael Perrais, Franck Broly, Pascal Barbry, Charles-Hugo Marquette, Christelle Cauffiez, Nicolas Pottier, Bernard Mari

Transient N-6-methyladensosine Transcriptome sequencing reveals a regulatory role of m6A in splicing efficiency. Annita Louloupi, Evgenia Ntini, Thomas Conrad, Ulf Andersson Orom

The Tudor protein Veneno assembles the ping-pong amplification complex that produces viral piRNAs in Aedes mosquitoes. Joep Joosten, Pascal Miesen, Bas Pennings, Pascal W. Jansen, Martijn A. Huynen, Michiel Vermeulen, Ronald P. Van Rij

The extent of B-form structure in a 6S RNA variant that mimics DNA to bind to the Escherichia coli RNA Polymerase. Nilesh Kishor Banavali

Differential regulation of microRNA-15a by radiation affects angiogenesis and tumor growth via modulation of acid sphingomyelinase. Shushan Rana, Cristina Espinosa-Diez, Rebecca Ruhl, Charles R Thomas Jr., Sudarshan Anand

Gemin4 is an essential gene in mice, and its overexpression in human cells causes relocalization of the SMN complex to the nucleoplasm. Ingo D. Meier, Michael P. Walker, A. Gregory Matera

Benchmark of lncRNA Quantification for RNA-Seq of Cancer Samples. Hong Zheng, Kevin Brennan, Mikel Hernaez, Olivier Gevaert

HMGA1 zebrafish co-orthologue hmga1b can modulate p53-dependent cellular responses but is unable to control the alternative splicing of psen1. Seyyed Hani Moussavi Nik, Morgan Newman, Amanda Lumsden, Tanya Jayne, Michael Lardelli

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RNA preprints: Week 52 edition

Happy New year everyone, and congratulations to labs that managed to submit manuscripts on the last week of the year!

Revisiting criteria for plant miRNA annotation in the era of big data. Michael J. Axtell, Blake C. Meyers

Murine polyomavirus microRNAs promote viuria during the acute phase of infection. James M Burke, Clovis R Bass, Emin T Ulug, Christopher S Sullivan

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