RNA preprints: W9/2018

Genetically regulated human NODAL splice variants are differentially post-transcriptionally processed and functionally distinct. Scott D Findlay, Olena Bilyk, Kiefer Lypka, Andrew J Waskiewicz, Lynne-Marie Postovit

A critical role for miR-142 in alveolar epithelial lineage formation. Amit Shrestha, Carraro Gianni, Nicolas Nottet, Ana Ivonne Vasquez-Armendariz, Susanne Herold, Julio Cordero, Indra Bahadur Singh, Jochen Wilhelm, Guillermo Barreto, Cho-Ming Chao, Elie El Agha, Bernard Mari, Jin-San Zhang, Saverio Bellusci

SpliceVec: distributed feature representations for splice junction prediction. Aparajita Dutta, Tushar Dubey, Kusum Kumari Singh, Ashish Anand

reactIDR: Evaluation of the statistical reproducibility of high-throughput structural analyses for a robust RNA reactivity classification. Risa Kawaguchi, Hisanori Kiryu, Junichi Iwakiri, Jun Sese

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

Differential splicing of ANP32A in birds alters its ability to stimulate RNA synthesis by restricted influenza polymerase. Steven F Baker, Mitchell P Ledwith, Andrew Mehle

Transcriptional burst initiation and polymerase pause release are key control points of transcriptional regulation. Caroline R Bartman, Cheryl A Keller, Belinda Giardine, Ross C Hardison, Gerd A Blobel, Arjun Raj

Accessibility of the Shine-Dalgarno sequence dictates N-terminal codon bias in E. coli. Sanchari Bhattacharyya, William M. Jacobs, Bharat V. Adkar, Jin Yan, Wenli Zhang, Eugene I. Shakhnovich

Molecular Genetic Analysis of Rbm45/Drbp1: Genomic Structure, Expression, and Evolution. Lauren Price, Abigail Loewen Faul, Aleksandra Vuchkovska, Kevin Lopez, Katie Fast, Andrew Eck, David Hoferer, Jeffrey O Henderson

Efficient expression of genes in the Drosophila germline using a UAS-promoter free of interference by Hsp70 piRNAs. Steven Z DeLuca, Allan C Spradling

mRNA structure dynamics identifies the embryonic RNA regulome. Jean-Denis Beaudoin, Eva Maria Novoa, Charles E Vejnar, Valeria Yartseva, Carter Takacs, Manolis Kellis, Antonio J Giraldez

The conserved phosphatase GSP-2/PP1 promotes germline immortality via small RNA-mediated genome silencing during meiosis. Katherine K Billmyre, Anna-lisa Doebley, Bree Heestand, Tony Belicard, Aya Sato-Carlton, Stephane Flibotte, Matt Simon, Megan Gnazzo, Ahna Skop, Donald Moerman, Peter Mark Carlton, Peter Sarkies, Shawn Ahmed

Repeat-specific functions for the C-terminal domain of RNA polymerase II in budding yeast. Michael Babokhov, Mohammad M Mosaheb, Richard W Baker, Stephen M Fuchs

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

miRNAs in platelet-poor blood plasma and purified RNA are highly stable: a confirmatory study. Dillon C Muth, Bonita H Powell, Zezhou Zhao, Kenneth W Witwer

RNA-directed activation of cytoplasmic dynein-1 in reconstituted transport RNPs. Mark A McClintock, Carly I Dix, Christopher M Johnson, Stephen H McLaughlin, Rory J Maizels, Ha Thi Hoang, Simon L Bullock

Evidence for a unique DNA-dependent RNA polymerase in cereal crops. Joshua T Trujillo, Arun S. Seetharam, Matthew B Hufford, Mark A Beilstein, Rebecca A Mosher

Dazl regulates germ cell survival through a network of polyA proximal mRNA interactions. Leah L Zagore, Thomas J Sweet, Molly M Hannigan, Sebastien M Weyn-Vanhentenryck, Chaolin Zhang, Donny D Licatalosi

Recruitment of Two Dyneins to an mRNA-Dependent Bicaudal D Transport Complex. Thomas E. Sladewski, Neil Billington, M. Yusuf Ali, Carol S. Bookwalter, Hailong Lu, Elena B. Krementsova, Trina A. Schroer, Kathleen M. Trybus

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

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

Compartmentalized RNA catalysis in membrane – free coacervate protocells. Bjoern Drobot, Juan M. Iglesias-Artola, Kris Le Vay, Viktoria Mayr, Mrityunjoy Kar, Moritz Kresying, Hannes Mutschler, T-Y. Dora Tang

MicroRNA-449 sustains cilia-related networks in the absence of transcription factor TAp73. Merit Wildung, Tilman Uli Esser, Katie Baker Grausam, Cornelia Wiedwald, Li Li, Jessica Lynn Simcox Zylla, Ann-Kathrin Günther, Magdalena Wienken, Evrim Ercetin, Felix Bremmer, Orr Shomroni, Stefan Andreas, Haotian Zhao, Muriel Lizé

Disruption in A-to-I editing levels affects C. elegans development more than a complete lack of editing. Nabeel S. Ganem, Noa Ben-Asher, Aidan C. Manning, Sarah N. Deffit, Michael C. Washburn, Emily C. Wheeler, Gene W Yeo, Orna Ben-Naim Zgayer, Einav Mantsur, Heather A. Hundley, Ayelet T Lamm

MicroRNAs as potential therapeutics to enhance chemosensitivity in advanced prostate cancer. Hui-Ming Lin, Iva Nikolic, Jessica Yang, Lesley Castillo, Niantao Deng, Chia-Ling Chan, Nicole K Yeung, Eoin Dodson, Benjamin Elsworth, Calan Spielman, Brian Lee, Zoe Boyer, Kaylene Simpson, Roger J Daly, Lisa G Horvath, Alexander Swarbrick

The yeast core spliceosome maintains genome integrity through R-loop prevention and alpha-tubulin expression. Annie S Tam, Veena Mathew, Tianna S Sihota, Anni Zhang, Peter C Stirling

Noise-induced bistability in the quasineutral coexistence of viral RNA under different replication modes. Tomas Alarcon, Josep Sardanyes, Andreu Arderiu, Santiago Elena

α-proteobacterial RNA degradosomes assemble liquid-liquid phase separated RNP bodies. Nadra Al-Husini, Dylan T Tomares, W. Seth Childers, Jared Schrader

Circular RNA expression and regulatory network prediction in posterior cingulate astrocytes in elderly subjects. Shobana Sekar, Lori Cuyugan, Jonathan Adkins, Philipp Geiger, Winnie Liang

Conserved Methyltransferase Spb1 Targets mRNAs for Regulated Modification with 2′-O-Methyl Ribose. Kristen M Bartoli, Cassandra Schaening, Thomas Carlile, Wendy V Gilbert

Differential expression of an alternative splice variant of IL-12Rβ1 impacts early dissemination in the mouse and associates with disease outcome in both mouse and humans exposed to tuberculosis. Mrinal K Das, Aurelie A Ray, Yi Cai, Akul Singhania, Christine Graham, Mingfeng Liao, Jeffrey J Fountain, John E Pearl, Manish Pareek, Pranabashis Haldar, Anne O’Garra, Xinchun Chen, Andrea M Cooper

Sex-biased long non-coding RNAs negatively correlated with sex-opposite protein coding gene co-expression networks in Diversity Outbred mouse liver. Tisha Melia, David J Waxman

bpRNA: Large-scale Automated Annotation and Analysis of RNA Secondary Structure. Padideh Danaee, Mason Rouches, Michelle Wiley, Dezhong Deng, LIang Huang, David A Hendrix

The exon junction complex regulates the release and phosphorylation of paused RNA polymerase II. Junaid Akhtar, Nastasja Kreim, Federico Marini, Giriram Kumar Mohana, Daniel Brune, Harald Binder, Jean-Yves Roignant

Multiple Small RNAs Alter Membrane Lipid Composition via Post-Transcriptional Regulation of Cyclopropane Fatty Acid Synthase. Colleen M. Bianco, Carin K. Vanderpool

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