RNA preprints: W38/2018

Precursor microRNA Identification Using Deep Convolutional Neural Networks. Binh Thanh Do, Vladimir Golkov, Göktuğ Erce Gürel, Daniel Cremers

Pervasive selection against microRNA target sites in human populations. Andrea Hatlen, Antonio Marco

miRBaseConverter: An R/Bioconductor Package for Converting and Retrieving miRNA Name, Accession, Sequence and Family Information in Different Versions of miRbase. Taosheng Xu, Ning Su, Lin Liu, Junpeng Zhang, Hongqiang Wang, Weijia Zhang, Jie Gui, Kui Yu, Jiuyong Li, Thuc Duy Le

Improving The Performance Of The RNA Amber Force Field By Tuning The Hydrogen-Bonding Interactions. Petra Kuhrova, Vojtech Mlynsky, Marie Zgarbova, Miroslav Krepl, Giovanni Bussi, Robert B. Best, Michal Otyepka, Jiri Sponer, Pavel Banas

Over-expression of Hsp83 in grossly depleted hsrω lncRNA background causes synthetic lethality and l(2)gl phenocopy in Drosophila. Mukulika Ray, Sundaram Acharya, Sakshi Shambhavi, Subhash C Lakhotia

Olfaction regulates organismal proteostasis and longevity via microRNA-dependent signaling. Fabian Finger, Franziska Ottens, Alexander Springhorn, Tanja Drexel, Lucie Proksch, Sophia Metz, Luisa Cochella, Thorsten Hoppe

Identifying Changes in RNA Editome Unique to Major Depressive Disorder. Saam Hasan, Shahriyar Mahdi Robbani, Tamanna Afroze, Gias Uddin Ahsan, Muhammad Maqsud Hossain

lncDIFF: a novel distribution-free method for differential expression analysis of long non-coding RNA. Qian Li, Xiaoqing Yu, Ritu Chaudhary, Robbert JC Slebos, Christine H Chung, Xuefeng Wang

PolyA tracks and poly-lysine repeats are the Achilles heel of Plasmodium falciparum. Slavica Pavlovic Djuranovic, Jessey Erath, Ryan J Andrews, Peter O Bayguinov, Joyce J Chung, Douglas L Chalker, James AJ Fitzpatrick, Walter N Moss, Pawel Szczesny, Sergej Djuranovic

Transcriptome profiles and novel lncRNA identification of Aedes aegypti cells in response to dengue virus serotype 1. Azali Azlan, Sattam M. Obeidat, Muhammad Amir Yunus, Ghows Azzam

SplicedFamAlign: CDS-to-gene spliced alignment and identification of transcript orthology groups. Safa Jammali, Jean-David Aguilar, Esaie Kuitche, Aida Ouangraoua

The RNA-Binding Protein DND1 Acts Sequentially as a Negative Regulator of Pluripotency and a Positive Regulator of Epigenetic Modifiers Required for Germ Cell Reprogramming. Victor A Ruthig, Matthew B Friedersdorf, Jason A Garness, Steve C Munger, Corey Bunce, Jack D Keene, Blanche Capel

Short exon prediction based on multiscale products of a genomic-inspired multiscale bilateral filtering. Xiaolei Zhang, Weijun Pan

Unbiased screen of RNA tailing enzymes at single-nucleotide resolution reveals a poly(UG) polymerase required for genome integrity and RNA silencing. Melanie A. Preston, Douglas F. Porter, Fan Chen, Natascha Buter, Christopher P. Lapointe, Sunduz Keles, Judith Kimble, Marvin Wickens

Extrinsic Noise Suppression in Micro RNA Mediated Incoherent Feedforward Loops. Alberto Carignano, Sumit Mukherjee, Abhyudai Singh, Georg Seelig

miRNA analysis with Prost! reveals evolutionary conservation of organ-enriched expression and post-transcriptional modifications in three-spined stickleback and zebrafish. Thomas Desvignes, Peter Batzel, Jason Sydes, B. Frank Eames, John H. Postlethwait

Narrow equilibrium window for complex coacervation of tau and RNA under cellular conditions. Yanxian Lin, James McCarty, Jennifer N. Rauch, Kris T. Delaney, Kenneth S. Kosik, Glenn H. Fredrickson, Joan-Emma Shea, Songi Han

A Novel Method for the Capture-based Purification of Whole Viral Native RNA Genomes. Cedric C.S. Tan, Sebastian Maurer-Stroh, Yue Wan, October M. Sessions, Paola Florez de Sessions

SilentMutations (SIM): a tool for analyzing long-range RNA-RNA interactions in viral genomes and structural RNAs. Daniel Desiro, Martin Hoelzer, Bashar Ibrahim, Manja Marz

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RNA preprints: W37/2018

The biochemical basis of microRNA targeting efficacy. Sean E McGeary, Kathy S Lin, Charlie Y Shi, Namita Bisaria, David P Bartel

AptCompare: optimized de novo motif discovery of RNA aptamers via HTS-SELEX. Kevin R Shieh, Christina Kratschmer, Keith E Maier, John M Greally, Matthew Levy, Aaron Golden

Intensive and Specific Feedback Self-control of the Argonauts and MicroRNA Targeting Activity. Degeng Wang, Audrey Gill, Fangyuan Zhang

A novel interaction between Gβγ and RNA polymerase II regulates cardiac fibrosis. Shahriar M Khan, Ryan D Martin, Celia Bouazza, Jace Jones-Tabah, Andy Zhang, Sarah MacKinnon, Phan Trieu, Sarah Gora, Paul BS Clarke, Jason C Tanny, Terence E Hebert

An adaptive stress-induced tRNA depletion response mediates codon-based gene repression and growth suppression. Doowon Huh, Maria C Passarelli, Lisa Fish, Henrik Molina, Elizabeth A McMillan, Hani Goodarzi, Sohail F Tavazoie

CD95/Fas ligand mRNA is toxic to cells. William Putzbach, Ashley Haluck-Kangas, Quan Q Gao, Aishe A Sarshad, Elizabeth T Bartom, Austin M. Stults, Abdul S Qadir, Markus Hafner, Marcus E Peter

Transite: A computational motif-based analysis platform that identifies RNA-binding proteins modulating changes in gene expression. Konstantin Krismer, Shohreh Varmeh, Molly A. Bird, Anna Gattinger, Yi Wen Kong, Thomas Bernwinkler, Daniel A. Anderson, Andreas Heinzel, Brian A. Joughin, Ian G. Cannell, Michael B. Yaffe

Quantitative proteomics reveals key roles for post-transcriptional gene regulation in the molecular pathology of FSHD. Sujatha Jagannathan, Yuko Ogata, Philip Gafken, Stephen J Tapscott, Robert K Bradley

Identification of potential microRNAs associated with Herpesvirus family based on bioinformatic analysis. Kevin Lamkiewicz, Emanuel Barth, Manja Marz, Bashar Ibrahim

The key protein of endosomal mRNP transport binds translational landmark sites of cargo mRNAs.Lilli Olgeiser, Carl Haag, Susan Boerner, Jernej Ule, Anke Busch, Julian Konig, Michael Feldbrugge, KathiZarnack

Inferring Sequence-Structure Preferences of RNA-Binding Proteins with Convolutional Residual Networks. Peter K Koo, Praveen Anand, Steffan B. Paul, Sean R. Eddy

A post-transcriptional program of chemoresistance by AU-rich elements/TTP in cancer quiescence. Sooncheol Lee, Douglas Micalizzi, Samuel S Truesdell, Syed IA Bukhari, Myriam Boukhali, Jennifer Lombardi-Story, Yasutaka Kato, Ipsita Dey-Guha, Benjamin T Nicholson, Min-Kyung Choo, David T Myers, Dongjun Lee, Maria A Mazzola, Radhika Raheja, Adam Langenbucher, Nicholas J Haradhvala, Michael Lawrence, Roopali Gandhi, David A Sweetser, David Sykes, Wilhelm Haas, Daniel A Haber, Shyamala Maheswaran, Shobha Vasudevan

Evolutionary analysis of base-pairing interactions in DNA and RNA secondary structures. Michael Thomas Golden, Ben Murrell, Darren Martin, Jotun Hein

Precursor microRNA Identification Using Deep Convolutional Neural Networks. Binh Thanh Do, Vladimir Golkov, Göktuğ Erce Gürel, Daniel Cremers

Functional lability of RNA-dependent RNA polymerases in animals. Natalia Pinzón, Stéphanie Bertrand, Lucie Subirana, Isabelle Busseau, Hector Escrivá, Hervé Seitz

The interplay between small RNA pathways shapes chromatin landscape in C. elegans. Ekaterina Gushchanskaia, Ruben Esse, Qicheng Ma, Nelson Lau, Alla Grishok

DOT1L suppresses nuclear RNAi originating from enhancer elements in Caenorhabditis elegans. Ruben Esse, Ekaterina Gushchanskaia, Avery Lord, Alla Grishok

RNA preprints: W36/2018

Transcripts from multicopy gene families localizing to mouse Y long arm encode piRNAs and proteins. Rachel A Jesudasan, Kankadeb Mishra, Pranatharthi Annapurna, Anurag Chaturvedi, Nissankararao M Praveena, Jomini L Alex, Sivarajan Karunanidhi, Hemakumar M Reddy

Intensive and Specific Feedback Self-control of MicroRNA Targeting Activity. Degeng Wang, Audrey Gill, Fangyuan Zhang

Musashi binding elements in Zika and related Flavivirus 3’UTRs: A comparative study in silico. Adriano de Bernardi Schneider, Michael T Wolfinger

USP21 and OTUD3 Antagonize Regulatory Ribosomal Ubiquitylation and Ribosome-Associated Quality Control. Danielle M Garshott, Elayanambi Sundaramoorthy, Marilyn Leonard, Eric J Bennett

Modeling slow-processing of toxin messenger RNAs in type-I Toxin-Antitoxin systems: post-segregational killing and noise filtering. Yusuke Himeoka, Namiko Mitarai

Deep sequencing of circulating exosomal microRNA allows non-invasive glioblastoma diagnosis. Saeideh Ebrahimkhani, Fatemeh Vafaee, Susannah Hallal, Heng Wei, Maggie Lee, Paul Young, Laveniya Satgunaseelan, Brindha Shivalingam, Catherine Suter, Michael Buckland, Kimberley Kaufman

Secondary structure of pre-mRNA introns for genes of 15q11-12 locus. Mapping of functionally significant motives of RNA binding proteins and f nucleosome positioning signals. Viya Borisovna Fedoseyeva, Irina Alexandrovna Zharinova, Alexander Anatolyevich Alexandrov

RNA-antimicrobial peptide complexes activate a self-sustaining TLR- and NETosis-mediated cycle of neutrophil activation. Franziska Herster, Zsofia Bittner, Sabine Dickhoefer, David Eisel, Tatjana Eigenbrod, Thomas Knorpp, Nicole Schneiderhan-Marra, Markus W Loeffler, Dominik Hartl, Lukas Freund, Knut Schaekel, Martin Heiser, Kamran Ghoreschi, Alexander N. R. Weber

The role of Aβ circRNA in Alzheimer′s disease: alternative mechanism of Aβ biogenesis from Aβ circRNA translation. Dingding Mo, Di Cui, Xinping Li

FUS controls the processing of snoRNAs into smaller RNA fragments that can regulate gene expression. Patrycja Plewka, Michal Szczesniak, Agata Stepien, Marek Zywicki, Andrzej Pacak, Martino Colombo, Izabela Makalowska, Marc-David Ruepp, Katarzyna Dorota Raczynska

Maternal Circulating MicroRNAs Control the Placental Response to Alcohol. Alexander M Tseng, Amanda H Mahnke, Alan B Wells, Nihal A Salem, Andrea M Allan, Victoria H.J. Roberts, Natali Newman, Nicole A.R. Walter, Christopher D Kroenke, Kathleen A Grant, Lisa K Akison, Karen M Moritz, Christina D Chambers, Rajesh C Miranda

Extracting information from RNA SHAPE data: Kalman filtering approach. Sana Vaziri, Patrice Koehl, Sharon Aviran

Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns. Alison D Tang, Cameron M Soulette, Marijke J van Baren, Kevyn Hart, Eva Hrabeta-Robinson, Catherine J Wu, Angela N Brooks

miRBaseConverter: An R/Bioconductor Package for Converting and Retrieving miRNA Name, Accession, Sequence and Family Information in Different Versions of miRbase. Taosheng Xu, Ning Su, Lin Liu, Junpeng Zhang, Hongqiang Wang, Jie Gui, Kui Yu, Jiuyong Li, Thuc Duy Le

A Novel Method for the Capture-based Purification of Whole Viral Native RNA Genomes. Cedric C.S. Tan, Sebastian Maurer-Stroh, Yue Wan, October M. Sessions, Paola Florez de Sessions

Several phased siRNA annotation methods can produce frequent false-positives for 24 nucleotide RNA-dominated loci in plants. Seth Polydore, Alice Lunardon, Michael J Axtell

A SKI subcomplex specifically required for the degradation of ribosome-free RNA regions. Elodie Zhang, Varun Khanna, Abdelkader Namane, Antonia Doyen, Estelle Dacheux, Bernard Turcotte, Alain Jacquier, Micheline Fromont-Racine

Dimerisation of APOBEC1 is dispensable for its RNA editing activity. Martina Chieca, Marco D Montini, Francesco Severi, Riccardo Pecori, Silvestro G Conticello

Identification of miRNAs and associated pathways regulated by Leukemia Inhibitory Factor in trophoblastic cell lines. Diana M. Morales-Prieto, Emanuel Barth, Ruby N. Gutièrrez-Samudio, Wittaya Chaiwangyen, Stephanie Ospina-Prieto, Bernd Gruhn, Ekkehard Schleußner, Manja Marz, Udo R. Markert

Active site closure stabilizes the backtracked state of RNA polymerase. Matti Turtola, Janne Makinen, Georgiy A Belogurov

Comparative analysis of miR-155 tissue expression profiles of different breeds of chicken. Chaolai Man, Sifan Xu, Yang Chang, Guanxian Wu, Wangting Zhang

The functional circular RNA, ciRS-7 (CDR1as), is biosynthesized using back-splicing promoted by inverted mammalian-wide MIRs but not primate-specific Alus. Rei Yoshimoto, Karim Rahimi, Karoline K Ebbesen, Thomas Hansen, Jorgen Kjems, Akila Mayeda

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, Raul Jobava, Maria Hatzoglou, Chaolin Zhang, Donny D Licatalosi

Transcriptomic analyses reveal groups of co-expressed, syntenic lncRNAs in four species of the genus Caenorhabditis. Cinta Pegueroles, Susana Iraola-Guzman, Uciel P Chorostecki, Ewa Ksiezopolska, Ester Saus, Toni Gabaldon

The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders. Cheen Euong Ang, Qing Ma, Orly Wapinski, ShengHua Fan, Ryan A Flynn, Bradley Coe, Masahiro Onoguchi, Victor H Olmos, Brian T Do, Lynn Dukes-Rimsky, Jin Xu, Qian Yi Lee, Koji Tanabe, LiangJiang Wang, Ulrich Elling, Josef Penninger, Kun Qu, Evan E Eichler, Anand Srivastava, Marius Wernig, Howard Chang

MiR-16-1* and miR-16-2* possess strong tumor suppressive and anti-metastatic properties in osteosarcoma. Vadim V. Maximov, Saleh Khawaled, Zaidoun Salah, Lina Jaber, Nataly Bengaiev, Ahlam Barhoum, Marco Galasso, Eylon Yavin, Rami I. Aqeilan

Regulation of Cell-Type-Specific Transcriptomes by miRNA Networks During Human Brain Development. Tomasz J Nowakowski, Neha Rani, Mahdi Golkaram, Hongjun R Zhou, Beatriz Alvarado, Kylie Huch, Jay West, Anne Leyrat, Alex A Pollen, Arnold R Kriegstein, Linda R Petzold, Kenneth S Kosik

RNA preprints: W35/2018

The RNA helicase UPF1 associates with mRNAs co-transcriptionally and is required for the release of mRNAs from transcription sites. Anand Kumar Singh, Subhendu Roy Choudhury, Sandip De, Jie Zhang, Stephen Kissane, Vibha Dwivedi, Preethi Ramanathan, Luisa Orsini, Daniel Hebenstreit, Saverio Brogna

PARylation regulates stress granule dynamics, phase separation, and neurotoxicity of disease-related RNA-binding proteins. Yongjia Duan, Aiying Du, Jinge Gu, Gang Duan, Chen Wang, Zhiwei Ma, Le Sun, Beituo Qian, Xue Deng, Kai Zhang, Kuili Tian, Yaoyang Zhang, Hong Jiang, Cong Liu, Yanshan Fang

DSCAM-AS1 promotes tumor growth of breast cancer by reducing miR-204-5p and upregulating RRM2. Wen-Hui Liang, Na Li, Zhi-Qing Yuan, Xin-Lai Qian, Zhi-Hui Wang

Engineered transfer RNAs for suppression of premature termination codons. John D Lueck, Jae Seok Yoon, Alfredo Perales-Puchalt, Adam L Mackey, Daniel T Infield, Mark A Behlke, Marshall R Pope, David B Weiner, William R Skach, Paul B McCray, Christopher A Ahern

Differential amplicons for the evaluation of RNA integrity extracted from complex environmental samples. Fabien Cholet, Umer Zeeshan Ijaz, Cindy Jane Smith

CLIP-Seq and massively parallel functional analysis of the CELF6 RNA binding protein reveals a role in destabilizing synaptic gene mRNAs through interaction with 3’UTR elements in vivo. Michael A Rieger, Dana M King, Barak A Cohen, Joseph D. Dougherty

UNCROSS2: identification of cross-talk in 16S rRNA OTU tables. Robert Edgar

The RNA-Binding Protein DND1 Acts Sequentially as a Negative Regulator of Pluripotency and a Positive Regulator of Epigenetic Modifiers Required for Germ Cell Reprogramming. Victor A Ruthig, Matthew B Friedersdorf, Jason A Garness, Steve C Munger, Corey Bunce, Jack D Keene, Blanche Capel

IsoformSwitchAnalyzeR: Analysis of changes in genome-wide patterns of alternative splicing and its functional consequences. Kristoffer Vitting-Seerup, Albin Sandelin

MiR-505-3p is a Repressor of the Puberty Onset in Female Mice. Yuxun Zhou, li tong, maochun wang, xueying chang, sijia wang, kai li, Junhua Xiao

A quantitative and predictive model for RNA binding by human Pumilio proteins. Inga Jarmoskaite, Sarah K. Denny, Pavanapuresan P. Vaidyanathan, Winston R. Becker, Johan O.L. Andreasson, Curtis J. Layton, Kalli Kappel, Varun Shivashankar, Raashi Sreenivasan, Rhiju Das, William J. Greenleaf, Daniel Herschlag

CTP synthase regulation by miR-975 controls cell proliferation and differentiation in Drosophila melanogaster. Wai-Kan Woo, Najat Dzaki, Ghows Azzam

Staufen2 mediated RNA recognition and localization requires combinatorial action of multiple domains. Simone Heber, Imre Gaspar, Jan-Niklas Tants, Johannes Günther, Sandra M Fernández Moya, Robert Janowski, Anne Ephrussi, Michael Sattler, Dierk Niessing

An homeotic post-transcriptional network controlled by the RNA-binding protein RBMX. Paola Zuccotti, Daniele Peroni, Valentina Potrich, Alessandro Quattrone, Erik Dassi

Pat1 promotes processing body assembly by enhancing the phase separation of the DEAD-box ATPase Dhh1 and RNA. Ruchika Sachdev, Maria Hondele, Miriam Linsenmeier, Pascal Vallotton, Christopher F Mugler, Paolo Arosio, Karsten Weis

MicroRNAs reinforce repression of PRC2 transcriptional targets independently and through a feed-forward regulatory network with PRC2. Haridha Shivram, Steven V Le, Vishwanath R Iyer

Pathogenicity and selective constraint on variation near splice sites. Jenny Lord, Giuseppe Gallone, Patrick J. Short, Jeremy F. McRae, Holly Ironfield, Elizabeth H. Wynn, Sebastian S. Gerety, Liu He, Bronwyn Kerr, Diana S. Johnson, Emma McCann, Esther Kinning, Frances Flinter, I. Karen Temple, Jill Clayton-Smith, Meriel McEntagart, Sally Ann Lynch, Shelagh Joss, Sofia Douzgou, Tabib Dabir, Virginia Clowes, Vivienne P. M. McConnell, Wayne Lam, Caroline F. Wright, David R. FitzPatrick, Helen V. Firth, Jeffrey C. Barrett, Matthew E. Hurles, on behalf of the Deciphering Developmental Disorders study

β-actin mRNA interactome mapping by proximity biotinylation. Joyita Mukherjee, Orit Hermesh, Nicolas Nalpas, Mirita Franz-Wachtel, Boris Macek, Ralf-Peter Jansen

miPIE: NGS-based Prediction of miRNA Using Integrated Evidence. Robert J Peace, Mohsen Sheikh Hassani, James R Green

Anti-microRNA screen uncovers miR-17 family within miR-17~92 cluster as the primary driver of kidney cyst growth. Matanel Yheskel, Ronak Lakhia, Andrea Flaten, Vishal Patel

Identification of microRNA-27a as a key regulator of cholesterol homeostasis. Abrar Ali Khan, Vinayak Gupta, Ananthamohan Kalyani, Vikas Arige, Santosh Reddy, Manoj Kumar Barthwal, Madhu Dikshit, Bhanuprakash Reddy, Nitish Ranjan Mahapatra