RNA preprints: W12/2018

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

Y chromosomal noncoding RNA regulates autosomal gene expression via piRNAs in mouse testis. Hemakumar M Reddy, Rupa Bhattacharya, Zeenath Jehan, Kankadeb Mishra, Pranatharthi Annapurna, Shrish Tiwari, Nissankararao Mary Praveena, Jomini Liza Alex, Vishnu M Dhople, Lalji Singh, Mahadevan Sivaramakrishnan, Anurag Chaturvedi, Nandini Rangaraj, Shiju Michael Thomas, Badanapuram Sridevi, Sachin Kumar, Ram Reddy Dereddi, Sunayana Rayabandla, Rachel A Jesudasan

SSMART: Sequence-structure motif identification for RNA-binding proteins. Alina Munteanu, Neelanjan Mukherjee, Uwe Ohler

The U1 snRNP subunit LUC7 controls plant development and stress response through alternative splicing regulation. Marcella de Francisco Amorim, Eva-Maria Willing, Anchilie G. Francisco-Mangilet, Irina Droste-Borel, Boris Macek, Korbinian Schneeberger, Sascha Laubinger

Dynamic temperature-sensitive A-to-I RNA editing in the brain of a heterothermic mammal during hibernation. Kent A Riemondy Jr., Austin Gillen, Emily A White, Lori K Bogren, Jay R

Selective maintenance of multiple CRISPR arrays across prokaryotes. Jake L. Weissman, William F. Fagan, Philip L. F. Johnson

Hydrophobicity drives the systemic distribution of lipid-conjugated siRNAs via lipid transport pathways. Maire F. Osborn, Andrew H Coles, Annabelle Biscans, Reka A Haraszti, Loic Roux, Sarah Davis, Socheata Ly, Dimas Echeverria, Matthew R. Hassler, Bruno M.D.C. Godinho, Mehran Nikan, Anastasia Khvorova

An unexpected contribution of lincRNA splicing to enhancer function. Jennifer Y Tan, Adriano Biasini, Robert S Young, Ana Marques

Lipid utilization in skeletal muscle cells is modulated in vitro and in vivo by specific miRNAs. Francesco Chemello, Francesca Grespi, Alessandra Zulian, Pasqua Cancellara, Etienne Hebert-Chatelain, Paolo Martini, Camilla Bean, Enrico Alessio, Riggero Ferrazza, Paolo Laveder, Graziano Guella, Carlo Reggiani, Chiara Romualdi, Paolo Bernardi, Luca Scorrano, Stefano Cagnin, Gerolamo Lanfranchi

Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation. Peter Kindgren, Ryan Ard, Maxim Ivanov, Sebastian Marquardt

N6-methyladenosine modification and the YTHDF2 reader protein play cell type specific roles in lytic viral gene expression during Kaposi’s sarcoma-associated herpesvirus infection. Charles Hesser, John Karijolich, Dan Dominissini, Chuan He, Britt A. Glaunsinger

MicroRNA-202 (miR-202) controls female fecundity by regulating medaka oogenesis. Stephanie Gay, Jerome Bugeon, Amine Bouchareb, Laure Henry, Jerome Montfort, Aurelie Le Cam, Julien Bobe, Violette Thermes

Crystallographic observation of nonenzymatic RNA primer extension. Jack W Szostak, Wen Zhang, Travis Walton, Li Li

Intronic miRNA Mediated Gene Expression Regulation Controls Protein Crowding Inside the Cell. Prashant Sinha, Pragya Jaiswal, Ashwin Kumar Jainarayanan, Samir Kumar Brahmachari

Preclinical Study: Sunitinib-suppressed MiR-452-5p Facilitates Renal Cancer Cell Invasion and Metastasis Through Modulating SMAD4/SMAD7/EMT Signals. Wei Zhai, Saiyang Li, Jin Zhang, Yonghui Chen, Junjie Ma, Wen Kong, Dongkui Gong, Junhua Zheng, Wei Xue, Yunfei Xu

Evidence for a potential role of miR-1908-5p and miR-3614-5p in autoimmune disease risk using genome-wide analyses. Inken Wohlers, Lars Bertram, Christina Lill

RppH can faithfully replace TAP to allow cloning of 5′-triphosphate carrying small RNAs. Miguel V. Vasconcelos Almeida, António Miguel de Jesus Domingues, Hanna Lukas, Maria Mendez-Lago, René F. Ketting

MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions. Alexander Roman Gawronski, Michael Uhl, Yajia Zhang, Yen-Yi Lin, Yashar Niknafs, Varune Ramnarine, Rohit Malik, Felix Feng, Arul Chinnaiyan, Colin Collins, Cenk Sahinalp, Rolf Backofen

Down-regulated Long Noncoding RNA HOXA11-AS affects trophoblast cell proliferation and migration by regulating RND3 and HOXA7 expression in preeclampsia. Lizhou Sun, Yetao Xu, Dan Wu, Jie Liu, Zhonghua Ma, Bingqing Hui, Jing Wang, Yanzi Chen, Sailan Wang, Yifan Lian

Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes. Fergal M Waldron, Graham N Stone, Darren J Obbard

Transcriptome-wide interrogation of the functional intronome by spliceosome profiling. Weijun Chen, Jill Moore, Hakan Ozadam, Hennady P Shulha, Nicholas Rhind, Zhiping Weng, Melissa J. Moore

LncRNA OIP5-AS1 is overexpressed in undifferentiated oral tumors and integrated analysis identifies as a downstream effector of stemness-associated transcription factors. Ganesan Arunkumar, Shankar Anand, Partha Raksha, Shankar Dhamodharan, Harikrishnan Prasanna Srinivasa Rao, Shanmugam Subbiah, Avaniyapuram Kannan Murugan, Arasambattu Kannan Munirajan

Premature termination codons signal targeted gene repair by nonsense mRNA-mediated gene editing in E. coli. Xiaolong Wang, Haibo Peng, Chunyan Li, Xuxiang Wang, Yalei Wang, Gang Chen, Jianye Zhang, Michael Lynch

6mer Seed Toxicity Determines Strand Selection in miRNAs. Quan Q Gao, William E Putzbach, Andrea E Murmann, Siquan Chen, Giovanna Ambrosini, Johannes M Peter, Elizabeth T Bartom, Marcus Peter

Diverse RNA interference strategies in early-branching metazoans. Andrew D Calcino, Selene L Fernandez-Valverde, Ryan J Taft, Bernard M Degnan

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