RNA preprints: W8/2018

CTD-dependent and -independent mechanisms govern co-transcriptional capping of Pol II transcripts. Melvin Noe Gonzalez, Shigeo Sato, Chieri Tomomori-Sato, Joan W. Conaway, Ronald C. Conaway

MCRiceRepGP: a framework for identification of sexual reproduction associated coding and lincRNA genes in rice. Agnieszka A Golicz, Prem L Bhalla, Mohan B Singh

Enhancer RNAs are necessary and sufficient for activity-dependent neuronal gene transcription. Nancy V.N. Gallus, Rhiana A. Simon, Aaron J Salisbury, Jasmin S. Revanna, Kendra D. Bunner, Katherine E. Savell, Faraz A. Sultan, Charles A. Gersbach, Jeremy J. Day

GTSF-1 is required for the formation of a functional RNA-dependent RNA Polymerase complex in C. elegans. Miguel V. Almeida, Sabrina Dietz, Stefan Redl, Emil Karaulanov, Andrea Hildebrandt, Christian Renz, Helle D. Ulrich, Julian König, Falk Butter, René F. Ketting

Sexual stage-induced long noncoding RNAs in the filamentous fungus Fusarium graminearum. Wonyong Kim, Cristina Miguel-Rojas, Jie Wang, Jeffrey P Townsend, Frances Trail

Towards comprehensive characterization of CRISPR-linked genes. Sergey A Shmakov, Kira S Makarova, Yuri I Wolf, Konstantin V Severinov, Eugene V Koonin

Intron-mediated enhancement is not limited to introns. Jenna E Gallegos, Alan B Rose

Evidence for functional and non-functional classes of peptides translated from long non-coding RNAs. Jorge Ruiz-Orera, Pol Verdaguer-Grau, José Luis Villanueva-Cañas, Xavier Messeguer, M Mar Albà

ADAR1 A-to-I RNA editing alters codon usage. Pavla Brachova, Nehemiah S Alvarez, Xiaoman Hong, Kailey A. Vincent, Keith E. Latham, Lane K. Christenson

EcRBPome: a comprehensive database of all known E. coli RNA-binding proteins. Pritha Ghosh, Niang Guita, Bernard Offmann, Ramanathan Sowdhamini

hRBPome: a central repository of all known human RNA-binding proteins. Pritha Ghosh, Pavalam Murugavel, Ramanathan Sowdhamini

MicroRNA-132 provides neuroprotection for tauopathies via multiple signaling pathways. Rachid EL Fatimy, Shaomin Li, Zhicheng Chen, Tasnim Mushannen, Sree Gongala, Zhiyun Wei, Darrick T. Balu, Rosalia Rabinovsky, Adam Cantlon, Abdallah Elkhal, Dennis J. Selkoe, Kai C. Sonntag, Dominic M. Walsh, Anna M. Krichevsky

Dual-layer transposon repression in heads of Drosophila melanogaster. Marius van den Beek, Bruno da Silva, Juliette Pouch, Mohammed el amine Ali Chaouche, Clément Carré, Christophe Antoniewski

Matrin 3-dependent neurotoxicity is modified by nucleic acid binding and nucleocytoplasmic localization. Ahmed Malik, Roberto Miguez, Xingli Li, Ye-Shih Ho, Eva Feldman, Sami Barmada

psichomics: graphical application for alternative splicing quantification and analysis. Nuno Saraiva-Agostinho, Nuno L. Barbosa-Morais

A genome-wide miRNA screen identifies regulators of tetraploid cell proliferation. Marc A Vittoria, Elizabeth M Shenk, Kevin P O’Rourke, Amanda F Bolgioni, Sanghee Lim, Victoria Kacprzak, Ryan J Quinton, Neil J Ganem

Exosomes and exosomal miRNAs from muscle-derived fibroblasts promote skeletal muscle fibrosis. Marina Mora, Simona Zanotti, Sara Gibertini, Flavia Blasevich, Cinzia Bragato, Simona Saredi, Clelia Introna, Pia Bernasconi, Lorenzo Maggi, Renato Mantegazza

Evolution of subgenomic RNA shapes dengue virus adaptation and epidemiological fitness. Esteban Finol, Eng Eong Ooi

QsRNA-seq: a method for high-throughput profiling and quantifying small RNAs. Alla Fishman, Dean Light, Ayelet T Lamm

Differential Expression of Coding and Long Noncoding RNAs in Keratoconus-affected Corneas. Mariam Lofty Khaled, Yelena Bykhovskaya, Sarah ER Yablonski, Hanzhou Li, Michelle D Drewry, Inas F Aboobakar, Amy Estes, Xiaoyi Gao, W. Daniel Stamer, Hongyan Xu, R. Rand Allingham, Michael A. Hauser, Yaron S Rabinowitz, Yutao Liu

TAS3 miR390-dependent loci in non-vascular land plants: Towards a comprehensive reconstruction of the gene evolutionary history. Sergey Y. Morozov, Irina A. Milyutina, Tatiana N. Erokhina, Liudmila V. Ozerova, Alexey V. Troitsky, Andrey G. Solovyev

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RNA preprints: W7/2018

Regulation of ATR activity by the RNA polymerase II phosphatase PNUTS-PP1. Helga B. Landsverk, Lise E. Sandquist, Gro Elise Rodland, Beata Grallert, Laura Trinkle-Mulcahy, Randi G. Syljuasen

Control of mRNA decapping by autoinhibition. David R Paquette, Ryan W Tibble, Tristan S Daifuku, John D Gross

Detection and Degradation of Nonsense-mediated mRNA Decay Substrates Involve Two Distinct Upf1-bound Complexes. Marine Dehecq, Laurence Decourty, Abdelkader Namane, Caroline Proux, Joanne Kanaan, Herve Le Hir, Alain Jacquier, Cosmin Saveanu

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

Transcription initiation RNAs are associated with chromatin activation mark H3K4me3. Matthew Hobbs, Christine Ender, Gregory J. Baillie, Joanna Crawford, Kelin Ru, Ryan Taft, John S. Mattick

Mitigating the lack of knowledge about long noncoding RNA: extracting biological functions. Yagoub Ali Ibrahim Adam, Evandro Eduardo Seron Ruiz, Alessandra Alaniz Macedo

LinearFold: Linear-Time Prediction of RNA Secondary Structures. Dezhong Deng, Kai Zhao, David Hendrix, David Mathews, Liang Huang

The C. elegans heterochronic gene lin-28 coordinates the timing of hypodermal and somatic gonadal programs for hermaphrodite reproductive system morphogenesis. Sungwook Choi, Victor Ambros

mRNA expression-mediated gene repression in human cells. Ina Hollerer, Juliet Charlotte Barker, Victoria Jorgensen, Amy Tresenrider, Claire Dugast-Darzacq, Xavier Darzacq, Leon Y Chan, Robert Tjian, Elçin Ünal, Gloria A Brar

Threshold response and bistability in gene regulation by small noncoding RNA. Sutapa Mukherji

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RNA preprints: W6/2018

miRNA profiling of primate cervicovaginal lavage and extracellular vesicles reveals miR-186-5p as a potential retroviral restriction factor in macrophages. Zezhou Zhao, Dillon C Muth, Kathleen Mulka, Bonita H Powell, Grace V Hancock, Zhaohao Liao, Kelly A Metcalf Pate, Kenneth W Witwer

Effects of mRNA degradation and site-specific transcriptional pausing on protein expression noise. Sangjin Kim, Christine Jacobs-Wagner

A folded viral noncoding RNA blocks host cell exoribonucleases through programmed remodeling of RNA structure. Anna-Lena Steckelberg, Benjamin M Akiyama, David A Costantino, Tim L Sit, Jay C Nix, Jeffrey S Kieft

IFIT3 and IFIT2/3 promote IFIT1-mediated translation inhibition by enhancing binding to non-self RNA. Renata C Fleith, Harriet V Mears, Edward Emmott, Stephen C Graham, Daniel S Mansur, Trevor R Sweeney

Identification of piRNA binding sites reveals the Argonaute regulatory landscape of the C. elegans germline. En-Zhi Shen, Hao Chen, Ahmet R. Ozturk, Shikui Tu, Masaki Shirayama, Wen Tang, Yue-He Ding, Si-Yuan Dai, Zhiping Weng, Craig C. Mello

Identification and characterization of moonlighting long non-coding RNAs based on RNA and protein interactome. Lixin Cheng, Kwong-Sak Leung

Concentration of 2’C-methyladenosine triphosphate by Leishmania guyanensis enables specific inhibition of Leishmania RNA virus 1 via its RNA polymerase. John I. Robinson, Stephen M. Beverley

psichomics: graphical application for alternative splicing quantification and analysis. Nuno Saraiva-Agostinho, Nuno L. Barbosa-Morais

Prediction of the secondary structure at the tRNASer (UCN) of Lutzomyia longipalpis (Diptera: Psychodidae). Richard Hoyos-Lopez

Mitigating the lack of knowledge about long noncoding RNA: extracting biological functions. Yagoub Ali Ibrahim Adam, Evandro Eduardo Seron Ruiz, Alessandra Alaniz Macedo

DROSHA associates to DNA damage sites and is required for DNA repair. Matteo Cabrini, Marco Roncador, Alessandro Galbiati, Lina Cipolla, Fabio Iannelli, Simone Sabbioneda, Fabrizio d’Adda di Fagagna, Sofia Francia

ASGAL: Aligning RNA-Seq Data to a Splicing Graph to Detect Novel Alternative Splicing Events. Luca Denti, Raffaella Rizzi, Stefano Beretta, Gianluca Della Vedova, Marco Previtali, Paola Bonizzoni

Blind prediction of noncanonical RNA structure at atomic accuracy. Andrew Martin Watkins, Caleb Geniesse, Wipapat Kladwang, Paul Zakrevsky, Luc Jaeger, Rhiju Das

The role of Aβ circRNA in Alzheimer’s disease. Dingding Mo

Template switching causes artificial junction formation and false identification of circular RNAs. Chong Tang, Tian Yu, Yeming Xie, Zhuqing Wang, Hayden McSwiggin, Ying Zhang, Huili Zheng, Wei Yan

MirGeneDB2.0: the curated microRNA Gene Database. Bastian Fromm, Diana Domanska, Michael Hackenberg, Anthony Mathelier, Eirik Hoye, Morten Johansen, Eivind Hovig, Kjersti Flatmark, Kevin J Peterson

The TRIM-NHL protein NHL-2 is a Novel Co-Factor of the CSR-1 and HRDE-1 22G-RNA Pathways. Peter R Boag, Gregory M Davis, Shikui Tu, Rhys N Colson, Joshua W. T. Anderson, Menachem J Gunzburg, Michelle A Francisco, Debashish Ray, Tuhin Maity, Monica Z Wu, Quaid D Morris, Timothy R Hughes, Jacqueline A Wilce, Julie Claycomb, Zhiping Weng

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RNA preprints: W5/2018

Defective RNA Polymerase III is negatively regulated by the SUMO-Ubiquitin-Cdc48 Pathway. Zheng Wang, Catherine Wu, Aaron Aslanian, Tony Hunter, John R Yates III

Xist Intron 1 Repression by TALE Transcriptional Factor Improves Somatic Cell Reprogamming in Mice. Jindun Zhang, Xuefei Gao, Jian Yang, Xiaoying Fan, Wei Wang, Yanfeng Liang, Lihong Fan, Hongmei Han, Xiaorong Xu, Fuchou Tang, Siqin Bao, Pentao Liu, Xihe Li

Genome-wide transcriptome analysis identifies alternative splicing regulatory network and key splicing factors in mouse and human psoriasis. Jin Li, Peng Yu

MiR-21 Regulates Metabolic Adaptation of TH17 Cells during Autoimmunity and Host Defence. Xiang Yu, Li Wang, Chao Yao, Rong Qiu, Yan Ge Cui, Dai Dai, Jun Deng, Guo Jun Hou, Yan Wang, Jie Qian, Ye Ouyang, Yu Ting Qin, Bo Qu, Hai Bo Zhou, You Cun Qian, Yuan Jia Tang, Nan Shen

Rbfox splicing factors maintain skeletal muscle mass by regulating calpain3 and proteostasis. Ravi K Singh, Arseniy M. Kolonin, Marta L. Fiorotto, Thomas A. Cooper

Tetracyclines Modify Translation By Targeting Key Human rRNA Substructures. Jonathan D Mortison, Monica Schenone, Jacob A Myers, Ziyang Zhang, Linfeng Chen, Christie Ciarlo, Eamon Comer, S. Kundhavai Natchiar, Steven A Carr, Bruno P Klaholz, Andrew G Myers

Prospects for recurrent neural network models to learn RNA biophysics from high-throughput data. Michelle J Wu, Johan OL Andreasson, Wipapat Kladwang, William J Greenleaf, Eterna participants, Rhiju Das

Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases. Florian Kaiser, Sebastian Bittrich, Sebastian Salentin, Christoph Leberecht, V. Joachim Haupt, Sarah Krautwurst, Michael Schroeder, Dirk Labudde

The evolutionary dynamics of microRNAs in domestic mammals. Luca Penso Dolfin, Simon Moxon, Wilfried Haerty, Federica Di Palma

DNA Topoisomerase I differentially modulates R-loops across the human genome. Stefano Manzo, Stella Regina Hartono, Lionel Sanz, Sara De Biasi, Andrea Cossarizza, Giovanni Capranico, Frederic Chedin

The plasma miR-122 basal levels respond to circulating catecholamine in rats. Xu Peng, Qiao Li, Song Lu, Xueling He, Sisi Yu, Zhihui Zhang, Guohui Xu, Lu Li, Tinghan Yang, Jiang Zhu, Wenli Zhu, Zhigang Wu, Delun Luo, Jue Zhu, Binghe Xu, Jian Huang, Hailin Yin, Kai Xu

A stable mode of bookmarking by TBP recruits RNA Polymerase II to mitotic chromosomes. Sheila S Teves, Luye An, Aarohi Bhargava-Shah, Liangqi Xie, Xavier Darzacq, Robert Tjian

Association of a lincRNA postmortem with suicide by violent means and in vivo with aggressive phenotypes. Giovanna Punzi, Gianluca Ursini, Giovanna Viscanti, Eugenia Radulescu, Joo Heon Shin, Tiziana Quarto, Roberto Catanesi, Giuseppe Blasi, Andrew Jaffe, Amy Deep-Soboslay, Thomas Hyde, Joel Kleinman, Alessandro Bertolino, Daniel Weinberger

N6-methyladenosine Binding Proteins Negatively Regulate HIV-1 Infectivity and Viral Production. Wuxun Lu, Nagaraja Tirumuru, Pratibha C. Koneru, Chang Liu, Mamuka Kvaratskhelia, Chuan He, Li Wu

Intron-mediated enhancement boosts Rtn4 circRNA expression: A robust method for exploring circRNA function. Dingding Mo, Xinping Li

Determining rewiring effects of alternatively spliced isoforms on protein-protein interactions using a computational approach. Oleksandr Narykov, Nathan Johnson, Dmitry Korkin

Cryo-EM structure of Escherichia coli σ70 RNAP and promoter DNA complex revealed a role of σ nonconserved region during the open complex formation. Anoop Narayanan, Frank S. Vago, Kungpeng Li, M. Zuhaib Qayyum, Dinesh Yernool, Wen Jiang, Katsuhiko Murakami

The contribution of non-canonical splicing mutations to severe dominant developmental disorders. Jenny Lord, Giuseppe Gallone, Patrick J. Short, Jeremy F. McRae, Holly Ironfield, Elizabeth H. Wynn, Sebastian S. Gerety, Liu He, Bronwyn Kerr, Diana S. Johnson, Emma McCann, Esther Kinning, Frances Flinter, I. Karen Temple, Jill Clayton-Smith, Meriel McEntagart, Sally Ann Lynch, Shelagh Joss, Sofia Douzgou, Tabib Dabir, Virginia Clowes, Vivienne P. M. McConnell, Wayne Lam, Caroline F. Wright, David R. FitzPatrick, Helen V. Firth, Jeffrey C. Barrett, Matthew E. Hurles, on behalf of the DDD study

A role for RNA and DNA:RNA hybrids in the modulation of DNA repair by homologous recombination. Giuseppina D’Alessandro, Marek Adamowicz, Donna Whelan, Sean Michael Howard, Corey Winston Jones-Weinert, Valentina Matti, Eli Rothenberg, Petr Cejka, Fabrizio d’Adda di Fagagna

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

COSSMO: Predicting Competitive Alternative Splice Site Selection using Deep Learning. Hannes Bretschneider, Shreshth Gandhi, Khalid Zuberi, Amit G Deshwar, Brendan J Frey

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