RNA preprints: Week 47 edition

A Non-Classical Phase Diagram for Virus-Bacterial Co-Evolution Mediated by CRISPR. Pu Han, Michael W Deem

DDX3 is exploited by Arenaviruses to suppress type I interferons and favor their replication. Maria Eugenia Loureiro, Andre Luiz Zorzetto-Fernandes, Sheli Radoshitzky, Xiaoli Chi, Simone Dallari, Nuha Marooki, Psylvia Leger, Sabrina Foscaldi, Sonia Sharma, Nora Lopez, Juan Carlos de la Torre, Sina Bavari, Elina Zuniga

Improving bioinformatics prediction of microRNA targets by ranks aggregation. Aurélien Quillet, Chadi Saad, Gaëtan Ferry, Youssef Anouar, Nicolas Vergne, Thierry Lecroq, Christophe Dubessy

Re-arrangements in the cytoplasmic distribution of small RNAs following the maternal-to-zygotic transition in Drosophila embryos. Mehmet Ilyas Cosacak, Hatice Yigit, Bunyamin Akgul

Altered hsrω lncRNA levels in activated Ras background further enhance Ras activity in Drosophila eye and induces more R7 photoreceptors. Subhash C Lakhotia, Mukulika Ray

Chromatin-release of the long ncRNA A-ROD is required for transcriptional activation of its target gene DKK1. Evgenia Ntini, Julia Liz, Jose M Muino, Annalisa Marsico, Ulf Andersson Oerom

Non-coding Transcriptome Maps Across Twenty Tissues of the Korean Black Chicken, Yeonsan Ogye. Hyosun Hong, Han-Ha Chai, Kyoungwoo Nam, Dajeong Lim, Kyung-Tai Lee, Yoon Jung Do, Chang-Yeon Cho, Jin-Wu Nam

Spliceosome profiling visualizes the operations of a dynamic RNP in vivo at nucleotide resolution. Jordan Burke, Adam Longhurst, Daria Merkurjev, Jade Sales-Lee, Beiduo Rao, James Moresco, John Yates III, Jingyi Jessica Li, Hiten D Madhani

miR-16 suppresses growth of rhabdoid tumor cells. Emily K Stroup, Yunku Yeu, Albert Budhipramono, Tae Hyun Hwang, Dinesh Rakheja, Anat Erdreich-Epstein, Theodore W. Laetsch, James F Amatruda, Kenneth S Chen

Prediction of potential disease-associated microRNAs using structural perturbation method. Xiangxiang Zeng, Li Liu, Linyuan Lu, Quan Zou

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

Computational Design of Asymmetric Three-dimensional RNA Structures and Machines. Joseph D Yesselman, Daniel Eiler, Erik D Carlson, Alexandra N Ooms, Wipapat Kladwang, Xuesong Shi, David A Costantino, Daniel Herschlag, Michael C Jewett, Jeffrey S Kieft, Rhiju Das

Translational regulation by bacterial small RNAs via an unusual Hfq-dependent mechanism. Muhammad S. Azam, Carin K. Vanderpool

Arabidopsis U1 snRNP subunit LUC7 functions in alternative splicing and preferential removal of terminal introns. Marcella de Francisco Amorim, Eva-Maria Willing, Irina Droste-Borel, Boris Macek, Korbinian Schneeberger, Sascha Laubinger

viGEN: An open source pipeline for the detection and quantification of viral RNA in human tumors. Krithika Bhuvaneshwar, Lei Song, Subha Madhavan, Yuriy Gusev

A Rice Dual-localized Pentatricopeptide Repeat Protein is involved in Organellar RNA Editing with MORFs. Haijun Xiao, Yanghong Xu, Chenzi Ni, Qiannan Zhang, Feiya Zhong, Jishuai Huang, Yingguo Zhu, Jun Hu

A Web-resource for Nutrient Use Efficiency related Genes, QTLs, and microRNA in important cereals and model plants. Anuj Kumar, Ajay Pandeya, Girik Malik, Hima Kumari P, Anil Kumar S, Mansi Sharma, Vijay Gahlaut, Prasad MNV Gajula, Prashanth Suravajhala, Krishna Pal Singh, Harindra Singh Balyan, Pushpendra Kumar Gupta

Single-molecule fluorescent amplification of RNA using clampFISH probes. Sara H Rouhanifard, Margaret Dunagin, Ian A Mellis, Sareh Bayatpour, Orsolya Symmons, Allison Cote, Arjun Raj

Cytoplasmic import and processing of mRNA amplify transcriptional bursts accounting for the majority of cellular noise. Maike M. K. Hansen, Ravi V. Desai, Michael L. Simpson, Leor S. Weinberger

Interplay of target site architecture and miRNA abundance determine miRNA activity and specificity. Giovanna Brancati, Sarah H Carl, Helge Grosshans

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RNA preprints: Week 46 edition

Methylation guide RNA evolution in archaea: structure, function, and genomic organization of 110 C/D box sRNA families across six Pyrobaculum species. Lauren M Lui, Andrew V Uzilov, David L Bernick, Andrea Corredor, Todd M Lowe, Patrick P Dennis

Determinants of target prioritization and regulatory hierarchy for the bacterial small RNA SgrS. Maksym Bobrovskyy, Jane Frandsen, Jichuan Zhang, Anustup Poddar, Muhammad S. Azam, Tina M. Henkin, Taekjip Ha, Carin K Vanderpool

Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter encoded enhancer activities. Sarah Rennie, Maria Dalby, Marta Lloret-Llinares, Stylianos Bakoulis, Christian Dalager Vaagenso, Torben Heick Jensen, Robin Andersson

Synaptic m6A Epitranscriptome Reveals Functional Partitioning of Localized Transcripts for Dynamic Tripartite Synapse Modulation. Daria Merkurjev, Wan-Ting Hong, Kei Iida, Belinda Goldie, Hitoshi Yamaguti, Ikumi Oomoto, Takayuki Ohara, Shin-ya Kawaguchi, Tomoo Hirano, Kelsey C Martin, Matteo Pellegrini, Dan O Wang

Cross-Site Comparison of Ribosomal Depletion Kits for Illumina RNAseq Library Construction. Zachary T Herbert, Jamie P Kershner, Vincent L Butty, Jyothi Thimmapuram, Sulbha Choudhari, Yuriy O Alekseyev, Jun Fan, Jessica W Podnar, Edward Wilcox, Jenny Gipson, Allison Gillaspy, Kristen Jepsen, Sandra Splinter BonDurant, Krystalynne Morris, Maura Berkeley, Ashley LeClerc, Stephen D. Simpson, Gary Sommerville, Leslie Grimmett, Marie Adams, Stuart S. Levine

Antisense lncRNAs expression correlates with attenuation of highly transcribed genes in fission yeast. Maxime Wery, Camille Gautier, Marc Descrimes, Mayuko Yoda, Valerie Migeot, Damien Hermand, Antonin Morillon

miRAW: A deep learning approach to predict miRNA targets by analyzing whole miRNA transcripts. Albert Pla Planas, Xiangfu Zhong, Simon Rayn

Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA–sequencing data. Alemu Takele Assefa, Katrijn De Paepe, Celine Everaert, Pieter Mestdagh, Olivier Thas, Jo Vandesompele

Embryonic circular RNAs at tandem duplicated genes in zebrafish present new paradigm in gene expression. Vanessa Chong-Morrison, Tatjana Sauka-Spengler

Nuclear Abl Drives miR-34c Transfer by Extracellular Vesicles to Induce Radiation Bystander Effects. Shubhra Rastogi, Amini Hwang, Josolyn Chan, Jean YJ Wang

Optimizing gene expression by adapting splicing. Idan Frumkin, Ido Yofe, Raz Bar-Ziv, Yoav Voichek, Yitzhak Pilpel

The necessary emergence of structural complexity in self-replicating RNA populations. Carlos G. Oliver, Vladimir Reinharz, Jérôme Waldispühl

Histone deacetylation promotes transcriptional silencing at facultative heterochromatin. Beth Rosina Watts, Sina Wittmann, Maxime Wery, Camille Gautier, Krzysztof Kus, Dong-Hyuk Heo, Cornelia Kilchert, Antonin Morillon, Lidia Vasiljeva

Smg5 is required for multiple nonsense-mediated mRNA decay pathways in Drosophila. Jonathan O. Nelson, Dominique Foerster, Kimberly Frizzell, Stefan Luschnig, Mark M. Metzstein

Evidence of non-tandemly repeated rDNAs and their intragenomic heterogeneity in Rhizophagus irregularis. Taro Maeda, Yuuki Kobayashi, Hiromu Kameoka, Nao Okuma, Naoya Takeda, Katsushi Yamaguchi, Takahiro Bino, Shuji Shigenobu, Masayoshi Kawaguchi

A Deep Recurrent Neural Network Discovers Complex Biological Rules to Decipher RNA Protein-Coding Potential. Steven T Hill, Rachael C Kuintzle, Amy Teegarden, Erich Merrill III, Padideh Danaee, David A Hendrix

Transcriptional landscape and regulatory roles of small non-coding RNAs in the oxidative stress response of the haloarchaeon Haloferax volcanii. Diego R. Gelsinger, Jocelyne DiRuggiero

MicroRNA-21 Regulates Metabolic Adaptation of Pathogenic TH17 cells and Controls Autoimmune Inflammation. Xiang Yu, Li Wang, Chao Yao, Rong Qiu, Yang Ge Cui, Dai Dai, Jun Deng, Guo Jun Hou, Yan Wang, Jie Qian, Yang Ye Ou, Yu Ting Qin, Hai Bo Zhou, You Cun Qian, Yuan Jia Tang, Nan Shen

Comparing miRNA structure of mirtrons and non-mirtrons. Igor I. Titov, Pavel S. Vorozheykin

LINE-2 transposable elements shape post-transcriptional gene regulation in the human brain. Rebecca Petri, Per Ludvik Brattås, Marie E. Jönsson, Karolina Pircs, Johan Bengzon, Johan Jakobsson

The role of m6A-RNA methylation in stress response regulation. Mareen Engel, Simone Roeh, Carola Eggert, Paul M. Kaplick, Lisa Tietze, Janine Arloth, Peter Weber, Monika Rex-Haffner, Mira Jakovcevski, Manfred Uhr, Matthias Eder, Carsten T. Wotjak, Mathias V. Schmidt, Jan M. Deussing, Elisabeth B. Binder, Alon Chen

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RNA preprints: Week 45 edition

The effect of macromolecular crowding on single-round transcription by E. coli RNA polymerase. SangYoon Chung, Eitan Lerner, Yan Jin, Soohong Kim, Yazan Alhadid, Logan Wilson Grimaud, Irina X. Zhang, Charles M. Knobler, William M. Gelbart, Shimon Weiss

Role of SCN5A coding and non-coding sequences in Brugada syndrome onset. What’s behind the scenes? Houria Daimi, Amel Haj Khelil, Ali Neji, Khaldoun Ben Hamda, Sabri Maaoui, Amelia Aranega, Jemni Be Chibani, Diego Franco Jaime

Polymerase pausing induced by sequence-specific RNA binding protein drives heterochromatin assembly. Jahan-Yar Parsa, Selim Boudoukha, Jordan Burke, Christina Homer, Hiten Madhani

Phytophthora methylomes modulated by expanded 6mA methyltransferases are associated with adaptive genome regions. Han Chen, Haidong Shu, Liyuan Wang, Fan Zhang, Xi Li, Sylvans Ochola, Fei Mao, Hongyu Ma, Wenwu Ye, Tingting Gu, Lubing Jiang, Yufeng Wu, Yuanchao Wang, Sophien Kamoun, Suomeng Dong

Nuclear Abl Drives Extracellular-Vesicle Transfer of miR-34c to Induce Bystander Effects of Radiation. Shubhra Rastogi, Amini Hwang, Josolyn Chan, Jean YJ Wang

Dynamics of human telomerase recruitment depend on template-telomere base-pairing. Jens Christopher Schmidt, Arthur J. Zaug, Regina Kufer, Thomas R. Cech

Tn5Prime, a Tn5 based 5′ Capture Method for Single Cell RNA-seq. Charles Cole, Ashley Byrne, Anna E. Beaudin, E. Camilla Forsberg, Christopher Vollmers

Efficient and accurate detection of splice junctions from RNAseq with Portcullis. Daniel Mapleson, Luca Venturini, Gemy Kaithakottil, David Swarbreck

Structural basis for terminal loop recognition and processing of pri-miRNA-18a by hnRNP A1. Hamed Kooshapur, Nila Roy Choudhury, Bernd Simon, Max Muehlbauer, Alexander Jussupow, Noemi Fernandez, Andre Dallmann, Frank Gabel, Carlo Camilloni, Gracjan Michlewski, Javier F. Caceres, Michael Sattler

The affinity of the S9.6 antibody for double-stranded RNAs impacts the mapping of R-loops in fission yeast. Stella R. Hartono, Amélie Malapert, Pénélope Legros, Pascal Bernard, Frédéric Chédin, Vincent Vanoosthuyse

A hyperthermophilic phage decoration protein suggests common evolutionary origin with Herpesvirus Triplex proteins and an anti-CRISPR protein. Nicholas P. Stone, Brendan J. Hilbert, Daniel Hidalgo, Kevin T. Halloran, Brian A. Kelch

Structure of the eukaryotic cytoplasmic pre-40S ribosomal subunit. Alain Scaiola, Cohue Pena, Melanie Weisser, Daniel Boehringer, Marc Leibundgut, Purnima Klingauf-Nerurkar, Stefan Gerhardy, Vikram Panse, Nenad Ban

AptaBlocks: Accelerating the Design of RNA-based Drug Delivery Systems. Yijie Wang, Jan Hoinka, Piotr Swiderski, Teresa Przytycka

Deimination of arginine at the C-terminal domain favors RNA polymerase II pause release. Priyanka Sharma, Antonios Lioutas, Javier Quilez, Roni H. G. Wright, Chiara Di Vona, Francois Le Dily, Roland Schuller, Dirk Eick, Miguel Beato

DHX36 binding at G-rich sites in mRNA untranslated regions promotes translation. Markus Sauer, Stefan A. Juranek, Hinke G. Kazemier, Daniel Benhalevy, Xiantao Wang, Markus Hafner, Katrin Paeschke

Non-invasive measurement of mRNA decay reveals translation initiation as the major determinant of mRNA stability. Leon Y. Chan, Christopher F. Mugler, Stephanie Heinrich, Pascal Vallotton, Karsten Weis

A bacterial GW-effector targets Arabidopsis AGO1 to promote pathogenicity and induces Effector-triggered immunity by disrupting AGO1 homeostasis. Odon Thiebeauld, Magali Charvin, Meenu Singla Rastogi, Fan Yang, Dominique Pontier, Cecile Pouzet, Laure Bapaume, Guangyong Li, Laurent Deslandes, Thierry Lagrange, James R. Alfano, Lionel Navarro

Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos. Vikas Trivedi, Harry M. T. Choi, Scott E. Fraser, Niles A. Pierce

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RNA preprints: Week 44 edition

Subtle alteration in microRNA dynamics accounts for differential nature of cellular proliferation. Dola Sengupta, Vinodhini Govindaraj, Sandip Kar

Distinct types of short open reading frames are translated in plant cells. Igor Fesenko, Ilya Kirov, Andrey Kniazev, Regina Khazigaleeva, Vassili Lazarev, Daria Kharlampieva, Ekaterina Grafskaia, Viktor Zgoda, Ivan Butenko, Georgy Arapidi, Anna Mamaeva, Vadim Ivanov, Vadim Govorun

Multi-state design of kinetically-controlled RNA aptamer ribosensors. Cassandra R. Burke, David Sparkman-Yager, James M. Carothers

Revisiting criteria for plant miRNA annotation in the era of big data. Michael J. Axtell, Blake C. Meyers

Genome-Wide Mining, Characterization and Development of miRNA-SSRs in Arabidopsis thaliana. Anuj Kumar, Aditi Chauhan, Mansi Sharma, Sai Kumar Kompelli, Vijay Gahlaut, Johny Ijaq, Krishna Pal Singh, M. N. V. Prasad Gajula, Prashanth Suravajhala, Harindra Singh Balyan, Pushpendra Kumar Gupta

Gene network analysis identifies a central post-transcriptional regulator of cellular stress survival. Matthew Z. Tien, Aretha Fiebig, Sean Crosson

Post-catalytic spliceosome structure reveals mechanism of 3′-splice site selection. Max E Wilkinson, Sebastian M Fica, Wojciech P Galej, Chritine M Norman, Andrew J Newman, Kiyoshi NAGAI

The mechano-chemistry of a monomeric reverse transcriptase. Omri Malik, Hadeel Khamis, Sergei Rudnizky, Ariel Kaplan

Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection. Chun Jimmie Ye, 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

INFERNO – INFERring the molecular mechanisms of NOncoding genetic variants. Alexandre Amlie-Wolf, Mitchell Tang, Elisabeth E. Mlynarski, Pavel P. Kuksa, Otto Valladares, Zivadin Katanic, Debby Tsuang, Christopher D. Brown, Gerard D. Schellenberg, Li-San Wang

A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs. Simón Poblete, Sandro Bottaro, Giovanni Bussi

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