RNA preprints: W10/2019

Small RNA expression pattern in multiply inbred lines and their hybrids of maize embryo. Yong-Xin Liu

Nanopore sequencing of full-length circRNAs in human and mouse brains reveals circRNA-specific exon usage and intron retention. Karim Rahimi, Morten T. Venø, Daniel M. Dupont, Jørgen Kjems

Functional RNA Structures in the 3’UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses. Roman Ochsenreiter, Ivo L. Hofacker, Michael T. Wolfinger

FUS ALS-causative mutations impact FUS autoregulation and the processing of RNA-binding proteins through intron retention. Jack Humphrey, Nicol Birsa, Carmelo Milioto, David Robaldo, Matthew Bentham, Seth Jarvis, Cristian Bodo, Maria Giovanna Garone, Anny Devoy, Alessandro Rosa, Irene Bozzoni, Elizabeth Fisher, Marc-David Ruepp, Giampietro Schiavo, Adrian Isaacs, Vincent Plagnol, Pietro Fratta

Interaction of modified oligonucleotides with nuclear proteins, formation of novel nuclear structures and sequence-independent effects on RNA processing. Loren L Flynn, Ruohan Li, May T Aung-Htut, Ianthe L Pitout, Jack A L Cooper, Alysia Hubbard, Lisa Griffiths, Charlie Bond, Steve D Wilton, Archa H Fox, Sue Fletcher

Identification of RBPMS as a smooth muscle master splicing regulator via proximity of its gene with super-enhancers. Erick E. Nakagaki-Silva, Clare Gooding, Miriam Llorian, Aishwarya Griselda Jacob, Frederick Richards, Adrian Buckroyd, Sanjay Sinha, Christopher W.J. Smith

Base pairing interactions between substrate RNA and H/ACA guide RNA modulate the kinetics of pseudouridylation, but not the affinity of substrate binding by H/ACA small nucleolar Ribonucleoproteins. Erin Katelyn Kelly, Ute Kothe

Mechanistic characterization of RASGRP1 variants identifies an hnRNP K-regulated transcriptional enhancer contributing to SLE susceptibility. Julio E Molineros, Bhupinder Singh, Chikashi Terao, Yukinori Okada, Jakub Kaplan, Barbara McDaniel, Shuji Akizuki, Celi Sun, Carol Webb, Loren L Looger, Swapan K Nath

Unearthing Regulatory Axes of Breast Cancer circRNAs Networks to Find Novel Targets and Fathom Pivotal Mechanisms. Farzaneh Afzali, Mahdieh Salimi

Extracellular vesicle-mediated RNA release in Histoplasma capsulatum. Lysangela R Alves, Roberta Peres da Silva, David A Sanchez, Daniel Zamith-Miranda, Marcio L Rodrigues, Samuel Goldenberg, Rosana Puccia, Joshua D Nosanchuk

Sterol-O acyltransferase 1 is inhibited by gga-miR-181a-5p and gga-miR-429-3p through the TGFβ pathway in endodermal epithelial cells of Japanese quail. Han-Jen Lin, Chiao-Wei Lin, Harry J Mersmann, Shih-Torng Ding

HRPK-1, a conserved KH-domain protein, modulates microRNA activity during Caenorhabditis elegans development. Anna Zinovyeva, Li Li, Isana Veksler-Lublinsky

Widespread gene duplication and adaptive evolution in the RNA interference pathways of the Drosophila obscura group. Danang Crysnanto, Darren Obbard

The Gag Protein PEG10 Binds to RNA and Regulates Trophoblast Stem Cell Lineage Specification. Mona Abed, Erik Verschueren, Hanna Budayeva, Peter Liu, Donald Kirkpatrick, Rohit Reja, Sarah Kummerfeld, Joshua Webster, Sarah Gierke, Mike Reichelt, Keith Anderson, Robert Newman, Merone Roose-Girma, Zora Modrusan, Hazal Pektas, Emin Maltepe, Kim Newton, Vishva Dixit

Quantitative high-throughput tests of ubiquitous RNA secondary structure prediction algorithms via RNA/protein binding. Winston R Becker, Inga Jarmoskaite, Kalli Kappel, Pavanapuresan P Vaidyanathan, Sarah K Denny, Rhiju Das, William J Greenleaf, Daniel Herschlag

Deciphering the ‘m6A code’ via quantitative profiling of m6A at single-nucleotide resolution. Miguel Angel Garcia-Campos, Sarit Edelheit, Ursula Toth, Ran Shachar, Ronit Nir, Lior Lasman, Alexander Brandis, Jacob H. Hanna, Walter Rossmanith, Schraga Schwartz

The solution structure of Dead End bound to AU-rich RNA reveals an unprecedented mode of tandem RRM-RNA recognition required for mRNA repression. Malgorzata M Duszczyk, Harry Wischnewski, Tamara Kazeeva, Fionna E Loughlin, Christine von Schroetter, Ugo Pradère, Jonathan Hall, Constance Ciaudo, Frédéric H.-T. Allain

Bid as a novel interacting partner of IRE1 differentially regulating its RNAse activity. Samirul Bashir, Khalid Majid Fazili

The evolution of the 9aaTAD domain in Sp2 proteins: inactivation with valines and intron reservoirs. Martin Piskacek, Marek Havelka, Kristina Jendruchova, Andrea Knight, Liam Peter Keegan

Transcriptome-wide dynamics of extensive m6A mRNA methylation during Plasmodium falciparum blood-stage development. Sebastian Baumgarten, Jessica M. Bryant, Ameya Sinha, Thibaud Reyser, Peter R. Preiser, Peter C. Dedon, Artur Scherf

SF3B1ness score: screening SF3B1 mutation status from over 60,000 transcriptomes based on a machine learning approach. Yuichi Shiraishi, Kenichi Chiba, Ai Okada

The mechanism of RNA base fraying: molecular dynamics simulations analyzed with core-set Markov state models. Giovanni Pinamonti, Fabian Paul, Frank Noé, Alex Rodriguez, Giovanni Bussi

SentRNA: Improving computational RNA design by incorporating a prior of human design strategies. Jade Shi, Rhiju Das, Vijay S. Pande

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