RNA preprints: week 39 edition

Discovery of global regulators of 3’ untranslated region processing in cancers with KAPAC. Andreas J Gruber, Ralf Schmidt, Souvik Ghosh, Georges Martin, Andreas R Gruber, Erik van Nimwegen, Mihaela Zavolan

Spatial RNA proximities reveal a bipartite nuclear transcriptome and territories of differential density and transcription elongation rates. Jorg Morf, Steven W. Wingett, Irene Farabella, Jonathan Cairns, Mayra Furlan-Magaril, Xin Liu, Frank F. Craig, Simon Andrews, Marc A. Marti-Renom, Peter Fraser

MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs. Saima Shahid, Gunjune Kim, Nathan R. Johnson, Eric Wafula, Feng Wang, Ceyda Coruh, Vivian Bernal-Galeano, Tamia Phifer, Claude W. dePamphilis, James H. Westwood, Michael Axtell

Genome-Wide Characterization Of Differential Transcript Usage In Arabidopsis thaliana. Dries Vaneechoutte, April Roberts Estrada, Ying-Chen Lin, Ann Loraine, Klaas Vandepoele

MicroRNA miR-128 represses LINE-1 (L1) retrotransposition by downregulating the nuclear import factor TNPO1. Adam Idica, Evgueni Sevrioukov, Dimitri Zisoulis, Matthias Hamdorf, Iben Daugaard, Pavan Kadandale, Irene Pedersen

Interferon-inducible miR-128 modulates HIV-1 replication by targeting TNPO3 mRNA. Irene Pedersen, Aurore Bochnakiem, Dimitri Zisoulis, Adam Idica, Anjie Zhen, Vineet KewalRamani, Iben Daugaard, Matthias Hamdorf, Scott Kitchen, KyeongEun Lee

A comprehensive characterization of cis-acting splicing-associated variants in human cancer. Yuichi Shiraishi, Keisuke Kataoka, Kenichi Chiba, Ai Okada, Yasunori Kogure, Hiroko Tanaka, Seishi Ogawa, Satoru Miyano

Proto-ribosome: a theoretical approach based on RNA relics. Jacques Demongeot

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RNA in preprints: Week 38 edition

Welcome to Week 38! Here is the work on RNA that came out as a preprint over the past week. Enjoy!

miRNAgFree: prediction and profiling of novel microRNAs without genome assembly. Ernesto L. Aparicio, Antonio Rueda, Bastian Fromm, Cristina Gómez-Martin, Ricardo Lebrón, Jose L Oliver, Juan A Marchal, Michail Kotsyfakis, Michael Hackenberg

HyperTRIBE: Upgrading TRIBE with enhanced editing. Weijin Xu, Reazur Rahman, Michael Rosbash

Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome. Cai Li, Boris Lenhard, Nicholas M. Luscombe

Promoter architecture determines co-translational regulation of mRNA. Maria Lorena Espinar Calvo, Miquel Angel Schikora Tamarit, Julia Domingo Espinos, Lucas B Carey

Interaction Between Host MicroRNAs and the Gut Microbiota in Colorectal Cancer. Ce Yuan, Michael Burns, Subbaya Subramanian, Ran Blekhman

Quantitating Translational Control: mRNA Abundance-Dependent and Independent Contributions and the mRNA Sequences That Specify Them. Jingyi Jessica Li, Guo-Liang Chew, Mark D. Biggin

Updating the 97% identity threshold for 16S‌ ribosomal RNA OTUs. Robert C Edgar

Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution. Sahin Naqvi, Daniel W Bellott, Kathy S Lin, David C Page

High-Throughput Identification of Genetic Variation Impact on pre-mRNA Splicing Efficiency. Scott I Adamson, Lijun Zhan, Brenton R Graveley

A Cdk9-PP1 kinase-phosphatase switch regulates the elongation-termination transition of RNA polymerase II. Pabitra K Parua, Gregory T Booth, Miriam Sansó, Bradley Benjamin, Jason C Tanny, John T Lis, Robert P Fisher

Cdk9 regulates a promoter-proximal checkpoint to modulate RNA Polymerase II elongation rate. Gregory T Booth, Pabitra K Parua, Miriam Sanso, Robert P Fisher, John T Lis

RNA binding and HEPN nuclease activation are decoupled in CRISPR-Cas13a. Akshay Tambe, Alexandra East-Seletsky, Gavin J Knott, Jennifer A Doudna, Mitchell R O’Connell

The ERA-related GTPase AtERG2 associated with mitochondria 18S RNA is essential for early embryo development in Arabidopsis. Pengyu Cheng, Hongjuan Li, Linlin Yuan, Huiyong Li, Lele Xi, Junjie Zhang, Jin Liu, Yingdian Wang, Heping Zhao, Huixin Zhao, Shengcheng Han

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RNA in preprints: Week 37 edition

Ancient exapted transposable elements drive nuclear localisation of lncRNAs. Joana Carlevaro-Fita, Monalisa Das, Taisia Polidori, Carmen Navarro, Rory Johnson

Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells. Yoav Lubelsky, Igor Ulitsky

EIF4A3 associated splicing and nonsense mediated decay defined by a systems analysis with novel small molecule inhibitors. Alborz Mazloomian, Shinsuke Araki, Momoko Oohori, Damian Yap, Shoichi Nakao, Atsushi Nakanishi, Sohrab Shah, Samuel Aparicio.

High-throughput identification of RNA nuclear enrichment sequences. Chinmay J Shukla, Alexandra L McCorkindale, Chiara Gerhardinger, Keegan D Korthauer, Moran N Cabili, David M Shechner, Rafael A Irizarry, Philipp G Maass, John L Rinn

Biomarker evaluation of plasma microRNA-122, high-mobility group box-1 and keratin-18 in acute gallstone disease. Francesca Th’ng, Bastiaan Vliegenthart, Jonathan D Lea, Daniel J Antoine, James W Dear, Damian James Mole

Deep learning of the splicing (epi)genetic code reveals a novel candidate mechanism linking histone modifications to ESC fate decision. Yungang Xu, Yongcui Wang, Jiesi Luo, Weiling Zhao, Xiaobo Zhou

CRISPR-based Herd Immunity Limits Phage Epidemics in Bacterial Populations. Pavel Payne, Lukas Geyrhofer, Nicholas H. Barton, Jonathan P. Bollback

Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection. Ye Jimmie Chun, Jenny Chen, Alexandra-Chloe Villani, Meena Subramaniam, Rachel E Gate, Tushar Bhangale, Mark N Lee, Towfique Raj, Raktima Raychowdhury, Weibo Li, Noga Rogel, Selina H Imboywa, Portia I Chipendo, Cristin McCabe, Michelle H Lee, Irene Y Frohlich, Barbara E Stranger, Philip L De Jager, Aviv Regev, Tim Behrens, Nir Hacohen

Motif signatures of transcribed enhancers. Dimitrios Kleftogiannis, Haitham Ashoor, Nikolaos Zarokanellos, Vladimir B. Bajic

A potential link between tuberculosis and lung cancer through non-coding RNAs. Debmalya Barh, Sandeep Tiwari, Ranjith N. Kumavath, Vasco Azevedo

Mitochondrial Dual-coding Genes in Trypanosoma brucei. Laura E. Kirby, Donna Koslowsky

The U2AF homology motif kinase 1 (UHMK1) is upregulated upon hematopoietic cell differentiation. Isabella Barbutti, Joao Agostinho Machado-Neto, Vanessa Cristina Arfelli, Paula de Melo Campos, Fabiola Traina, Sara Teresinha Olalla Saad, Leticia Froehlich Archangelo

Paupar LncRNA Promotes KAP1 Dependent Chromatin Changes And Regulates Subventricular Zone Neurogenesis. Ioanna Pavlaki, Farah Alammari, Bin Sun, Neil Clark, Tamara Sirey, Sheena Lee, Dan J. Woodcock, Chris P. Ponting, Francis G. Szele, Keith W. Vance

Antisense transcription-dependent chromatin signature modulates sense transcription and transcript dynamics. Thomas Brown, Francoise S. Howe, Struan C. Murray, Emily Seward, Scott Rata, Andrew Angel, Jane Mellor

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