RNA preprints: W43/2018

Interplay between consensus and divergent RNA polymerase II C-terminal domain repeats in viability and targeting. Feiyue Lu, Bede Portz, David S Gilmour

mTORC1 Restricts Hepatitis C Virus Replication Through ULK1-mediated Suppression of miR-122 and Facilitates Post-replication Events. Manish Kumar Johri, Hiren Vasantrai Lashkari, Dhiviya Vedagiri, Divya Gupta, Krishnan Harshan

MicroRNA-200c suppresses epithelial-mesenchymal transition of ovarian cancer by targeting cofilin-2. Xuechen Yu, Yuanzhen Zhang, Wei Zhang, Huijun Chen

Identification and characterization of Aedes albopictus long noncoding RNAs provides insights into their roles in development and flavivirus infection. Azali Azlan, Muhammad Amir Yunus, Ghows Azzam

sRNA-target Prediction Organizing Tool (SPOT) integrates computational and experimental data to facilitate functional characterization of bacterial small RNAs. Alisa M King, Carin K Vanderpool, Patrick Degnan

A global map of RNA binding protein occupancy guides functional dissection of post-transcriptional regulation of the T cell transcriptome. Adam J Litterman, Wandi S Zhu, Robin Kageyama, Wenxue Zhao, Noah Zaitlen, David J Erle, K. Mark Ansel

Candidate Phyla Radiation Roizmanbacteria from hot springs have novel, unexpectedly abundant, and potentially alternatively functioning CRISPR-Cas systems. Lin-Xing Chen, Basem Al-Shayeb, Raphael Meheust, Wen-Jun Li, Jennifer A Doudna, Jillian F Banfield

RNA Binding Motif Protein 48 is required for U12 splicing and maize endosperm differentiation. Fang Bai, Jacob Corll, Donya N Shodja, Ruth Davenport, Guanqiao Feng, Janaki Mudunkothge, Christian J Brigolin, Federico Martin, Gertraud Spielbauer, Chi-Wah Tseung, Amy E Seibert, W. Brad Barbazuk, Shailesh Lal, A. Mark Settles

Transgenic Mice and Pluripotent Stem Cells Express EGFP under the Control of miR-302 Promoter. Karim Rahimi, Sara Parsa, Mehrnoush Nikzaban, Seyed Javad Mowla, Fardin Fathi

Re-purposing Ac/Ds transgenic system for CRISPR/dCas9 modulation of enhancers and non-coding RNAs in zebrafish. Vanessa Chong-Morrison, Filipa C. Simoes, Upeka Senanayake, Dervla S. Carroll, Paul R. Riley, Tatjana Sauka-Spengler

Arginine methylation of DDX5 RGG/RG motif by PRMT5 regulates RNA/DNA resolution. Stephane Richard, Sofiane Mersaoui, Zhenbao Yu, Yan Coulombe, Franciele Busatto, Martin Karam, Jean-Yves Masson

Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and whole rrn operon. Anna Cusco, Carlotta Catozzi, Joaquim Vines, Armand Sanchez, Olga Francino

Origins and Evolution of the Global RNA Virome. Valerian V. Dolja, Yuri I Wolf, Darius Kazlauskas, Jaime Iranzo, Adriana Lucía-Sanz, Jens H. Kuhn, Mart Krupovic, Eugene V Koonin

A small RNA controls bacterial resistance to gentamicin during iron starvation. Sylvia Chareyre, Barras Frederic, Pierre Mandin

Sendai Virus Infection Induces Expression of Novel RNAs in Human Cells. Roli Mandhana, Curt M. Horvath

Dysregulation of circular RNAs in myotonic dystrophy type 1. Christine Voellenkle, Alessandra Perfetti, Matteo Carrara, Paola Fuschi, Laura Valentina Renna, Marialucia Longo, Rosanna Cardani, Rea Valaperta, Gabriella Silvestri, Ivano Legnini, Irene Bozzoni, Denis Furling, Carlo Gaetano, Germana Falcone, Giovanni Meola, Fabio Martelli

A Haploid Genetic Screening Method for Proteins Influencing Mammalian Nonsense-Mediated mRNA Decay Activity. Maximilian Popp, Lynne Maquat

Divalent cations can control a switch-like behavior in heterotypic and homotypic RNA coacervates. Paulo L Onuchic, Anthony N Milin, Ibraheem Alshareedah, Ashok A Deniz, Priya R Banerjee

Maternal and zygotic gene regulatory effects of endogenous RNAi pathways. Miguel Vasconcelos Almeida, António Miguel de Jesus Domingues, Rene F Ketting

Interplay between substrate recognition, 5′ end tRNA processing and methylation activity of human mitochondrial RNase P. Agnes Karasik, Carol Fierke, Markos Koutmos

Multiple decay events target HAC1 mRNA during splicing to regulate the unfolded protein response. Patrick D. Cherry, Sally E. Peach, Jay R. Hesselberth

Inference of splicing motifs through visualization of recurrent networks. Aparajita Dutta, Aman Dalmia, Athul R, Kusum Kumari Singh, Ashish Anand

CENP-A associated lncRNAs influence chromosome segregation in human cells. Delphine Quenet, David Sturgill, Marin Olson, Yamini Dalal

Proximity RNA labeling by APEX-Seq Reveals the Organization of Translation Initiation Complexes and Repressive RNA Granules. Alejandro Padron, Shintaro Iwasaki, Nicholas Ingolia

Structure reveals mechanism of CRISPR RNA-guided nuclease recruitment and anti-CRISPR viral mimicry. MaryClare F. Rollins, Saikat Chowdhury, Joshua Carter, Sarah M. Golden, Heini M. Miettinen, Andrew Santiago-Frangos, Dominick Faith, C. Martin Lawrence, Gabriel C. Lander, Blake Wiedenheft

Crosstalk between RNA Pol II C-Terminal Domain Acetylation and Phosphorylation via RPRD Proteins. Ibraheem Ali, Diego Garrido-Ruiz, Zuyao Ni, Jeffrey R Johnson, Heng Zhang, Pao-Chen Li, Ryan J Conrad, Xinghua Guo, Jinrong Min, Jack Greenblatt, Matthew Jacobson, Nevan J Krogan, Melanie Ott

The multi PAM2 protein Upa2 functions as novel core component of endosomal mRNA transport. Silke Jankowski, Thomas Pohlmann, Sebastian Baumann, Sabrina Zander, Senthil Kumar Devan, Michael Feldbruegge

AMPK regulates germline stem cell quiescence and integrity through an endogenous small RNA pathway. Pratik Kadekar, Richard Roy

A Biologically Motivated Asymmetric Exclusion Process: interplay of congestion in RNA polymerase traffic and slippage of nascent transcript. Soumendu Ghosh, Annwesha Dutta, Shubhadeep Patra, Jun Sato, Katsuhiro Nishinari, Debashish Chowdhury

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RNA preprints: W42/2018

The mRNA export adaptor Yra1 contributes to DNA double-strand break repair through its C-box domain. Valentina Infantino, Evelina Tutucci, Noel Yeh Martin, Audrey Zihlmann, Varinia Garcia-Molinero, Geraldine Silvano, Benoit Palancade, Francoise Stutz

Programmed Delayed Splicing: A Mechanism for Timed Inflammatory Gene Expression. Devdoot Majumdar, Luke Frankiw, Christian H. Burns, Yvette Garcia-Flores, David Baltimore

Using pan RNA-seq analysis to reveal the ubiquitous existence of 5′ end and 3′ end small RNAs. Xiaofeng Xu, Haishuo Ji, Zhi Cheng, Xiufeng Jin, Xue Yao, Yanqiang Liu, Qiang Zhao, Tao Zhang, Jishou Ruan, Wenjun Bu, Ze Chen, Gao Shan

Bud13 Promotes a Type I Interferon Response By Countering Intron Retention in Irf7. Luke S Frankiw, Devdoot Majumdar, Christian Burns, Logan Vlach, Annie Moradian, Michael Sweredoski, David Baltimore

Base-pair Ambiguity and the Kinetics of RNA Folding. Guangyao Zhou, Jackson Loper, Stuart Geman

Molecular anatomy and plasticity of the long noncoding RNA HOTAIR. Rachel Spokoini-Stern, Dimitar Stamov, Hadass Jessel, Lior Aharoni, Heiko Haschke, Jonathan Giron, Ron Unger, Eran Segal, Almogit Abu-Horowitz, Ido Bachele

MicroRNAs buffer genetic variation at specific temperatures during embryonic development. Christopher Amourda, Jeronica Chong, Timothy E Saunders

Structure of transcribing RNA polymerase II-nucleosome complex. Lucas Farnung, Seychelle M. Vos, Patrick Cramer

The RNA-binding ATPase, Armitage, Couples piRNA Amplification in Nuage to Phased piRNA Production on Mitochondria. Daniel Tianfang Ge, Wei Wang, Cindy Tipping, Ildar Gainetdinov, Zhiping Weng, Phillip D Zamore

Widespread RNA editing dysregulation in Autism Spectrum Disorders. Stephen Tran, Hyun-Ik Jun, Jae Hoon Bahn, Adel Azghadi, Gokul Ramaswami, Eric L. Van Nostrand, Thai B. Nguyen, Yun-Hua E. Hsiao, Changhoon Lee, Gabriel A. Pratt, Gene W. Yeo, Daniel H. Geschwind, Xinshu Xiao

Response to “No evidence of functional co-adaptation between clustered microRNAs”. Yirong Wang, Hong Zhang, Jian Lu

Nuclear actin interactome analysis links actin to KAT14 histone acetyl transferase and mRNA splicing. Tiina Viita, Salla Kyheröinen, Bina Prajapati, Jori Virtanen, Markku Varjosalo, Maria Vartiainen

Interaction of modified oligonucleotides with nuclear proteins, formation of novel nuclear structures and sequence-independent effects on RNA processing. Loren L Flynn, Ruohan Li, May T Aung-Htut, Ianthe L Pitout, Jack Cooper, Alysia Hubbard, Lisa Griffiths, Charles Bond, Steve D Wilton, Archa H Fox, Sue Fletcher

PCF11 connects alternative polyadenylation to formation and spontaneous regression of neuroblastoma. Anton Ogorodnikov, Michal Levin, Surendra Tattikota, Sergey Tokalov, Mainul Hoque, Denise Scherzinger, Federico Marini, Ansgar Poetsch, Harald Binder, Stephan Macher-Goeppinger, Bin Tian, Michael Schaefer, Karl Lackner, Frank Westermann, Sven Danckwardt

Assessing the response of small RNA populations to allopolyploidy using resynthesized Brassica napus allotetraploids. Paulina Martinez Palacios, Marie-Pierre Jacquemot, Marion Tapie, Agnes Rousselet, Mamoudou Diop, Carine Remoue, Matthieu Falque, Andrew Lloyd, Eric Jenczewski, Gilles Lassalle, Anne-Marie Chevre, Christine Lelandais, Martin Crespi, Philippe Brabant, Johann Joets, Karine Ali

The RNA-binding protein AATF coordinates rRNA maturation. Rainer Kaiser, Michael Ignarski, Eric L. Van Nostrand, Christian Frese, Manaswita Jain, Sadrija Cukoski, Heide Heinen, Melanie Schaechter, Konstantin Bunte, Peter Frommolt, Patrick Keller, Mark Helm, Katrin Bohl, Martin Höhne, Bernhard Schermer, Thomas Benzing, Katja Höpker, Christoph Dieterich, Gene W Yeo, Roman-Ulrich Mueller, Francesca Fabretti

A cell-based probabilistic approach unveils the concerted action of miRNAs. Shelly Mahlab-Aviv, Nathan Linial, Michal Linial

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

Model-based analysis of positive selection significantly expands the list of cancer driver genes, including RNA methyltransferases. Siming Zhao, Jun Liu, Pranav Nanga, Yuwen Liu, Ercument Cicek, Nicholas Knoblauch, Chuan He, Matthew Stephens, Xin He

RNA preprints: W41/2018

Population-scale study of eRNA transcription reveals bipartite functional enhancer architecture. Katla Kristjándsóttir, Yeonui Kwak, Nathaniel D Tippens, John T Lis, Hyun Min Kang, Hojoong Kwak

An In-Silico Mammalian Whole-Cell Model Reveals the Influence of Spatial Organization on RNA Splicing Efficiency. Zhaleh Ghaemi, Joseph Peterson, Martin Gruebele, Zaida Luthey-Schulten

The dynamic proteome of influenza A virus infection identifies M segment splicing as a host range determinant. Boris Bogdanow, Katrin Eichelbaum, Anne Sadewasser, Xi Wang, Immanuel Husic, Katharina Paki, Martha Hergeselle, Barbara Vetter, Jingyi Hou, Wei Chen, Lueder Wiebusch, Irmtraud M. Meyer, Thorsten Wolff, Matthias Selbach

A symmetric toggle switch explains the onset of random X inactivation in different mammals. Verena Mutzel, Ikuhiro Okamoto, Ilona Dunkel, Mitinori Saitou, Luca Giorgetti, Edith Heard, Edda G. Schulz

Modular modeling improves the predictions of genetic variant effects on splicing. Jun Cheng, Thi Yen Duong Nguyen, Kamil J Cygan, Muhammed Hasan Celik, William Fairbrother, Ziga Avsec, Julien Gagneur

Integrative analysis of Zika virus genome RNA structure reveals critical determinants of viral infectivity. Qiangfeng Cliff Zhang, Pan Li, Yifan Wei, Miao Mei, Lei Tang, Lei Sun, Wenze Huang, Jianyu Zhou, Chunlin Zou, Shaojun Zhang, Chengfeng Qin, Tao Jiang, Jianfeng Dai, Xu Tan

The microRNA, miR-18a, regulates NeuroD and photoreceptor differentiation in the retina of the zebrafish. Scott M Taylor, Emily Giuffre, Patience Moseley, Peter F Hitchcock

Bromodomain Protein, BRD4, Contributes to the Regulation of Alternative Splicing. Sheetal Uppal, Qingrong Chen, Daoud Meerzaman, Anne Gegonne, Dinah S Singer

Signal Transduction in Human Cell Lysate via Dynamic RNA Nanotechnology. Lisa M. Hochrein, Tianjia J. Ge, Maayan Schwarzkopf, Niles A. Pierce

The ghr-miR164 and GhNAC100 module participates in cotton plant defence against Verticillium dahlia. Jiahe Wu, Guang Hu, Yu Lei, Le Wang, Jianfen Liu, Ye Tang, Zhennan Zhang, Aiming Chen, Qingzhong Peng, Zuoren Yang

Drosophila Mutants that Are Motile but Respond Poorly to All Stimuli Tested: Mutants in RNA Splicing and RNA Helicase, Mutants in The Boss. Lar L. Vang, Julius Adler

Aminoacyl tRNA Synthetases as Malarial Drug Targets: A Comparative Bioinformatics Study. Dorothy Wavinya Nyamai, Ozlem Tastan Bishop

Specificity of RNA folding and its association with evolutionarily adaptive mRNA secondary structure. Gongwang Yu, Hanbing Zhu, Xiaoshu Chen, Jian-Rong Yang

jouvence, a new small nucleolar RNA required in the gut extends lifespan in Drosophila. Lucille Mellottee, Stephanie Soule, Abdelkrim Arab, Chongjian Chen, Jean-Rene Martin

Dynamic regulation of the Trypanosoma brucei transferrin receptor in response to iron starvation is mediated via the 3’UTR. Corinna Benz, Winston Lo, Nadin Fathallah, Ashley Connor-Guscott, Henry J Benns, Michael D. Urbaniak

A prognostic signature for lower-grade gliomas based on expression of long noncoding RNAs. Manjari Kiran, Ajay Chatrath, Xiwei Tang, Daniel Macrae Keenan, Anindya Dutta

Density dependent enhancement effect of Wolbachia and the host RNAi response to a densovirus in Aedes cells. Rhys Parry, Cameron Bishop, Lachlan De Hayr, Sassan Asgari

Development of a novel signature of long noncoding RNAs as a prognostic biomarker for esophageal cancer. Yan Miao, Jing Sui, Ying Zhang, Lihong Yin

DNA damage dependent hypomethylation regulates the pro-angiogenic LncRNA MEG9. Cristina Espinosa-Diez, RaeAnna Wilson, Rishima Mukherjee, Marlee Feltham, Clayton Hudson, Rebecca Ruhl, Sudarshan Anand

The influenza A virus endoribonuclease PA-X usurps host mRNA processing machinery to limit host gene expression. Lea Gaucherand, Brittany K Porter, Summer K Schmaling, Christopher Harley Rycroft, Yuzo Kevorkian, Craig McCormick, Denys A Khaperskyy, Marta Gaglia

Metatranscriptome profiling of the dynamic transcription of mRNA and sRNA of a probiotic Lactobacillus strain in human gut. Qiuwen He, zhihong sun, Jianmin Qiao, Dong Chen, Jie Huang, Xiaotian Luo, Jia Ding, Jiachao Zhang, Qiangchuan Hou, Yi Zhang, Heping Zhang

DNA and RNA binding mediate the toxicity of arginine-rich peptides encoded by C9ORF72 GGGGCC repeats. Vanesa Lafarga, Oleksandra Sirozh, Irene Diaz-Lopez, Misaru Hisaoka, Eduardo Zarzuela, Jasminka Boskovic, Bogdan Jovanovic, Rafael Fernandez-Leiro, Javier Munoz, Georg Stoecklin, Ivan Ventoso, Oscar Fernandez-Capetillo

RNA preprints: W40/2018

CRISPR Artificial Splicing Factors. Nathaniel Jillette, Albert W Cheng

PUMILIO hyperactivity drives premature aging of Norad-deficient mice. Florian Kopp, Mehmet Yalvac, Beibei Chen, He Zhang, Sungyul Lee, Frank Gillett, Mahmoud Elguindy, Sushama Sivakumar, Hongtao Yu, Yang Xie, Prashant Mishra, Zarife Sahenk, Joshua T Mendell

Mitochondrial RNA capping: highly efficient 5′-RNA capping with NAD+ and NADH by yeast and human mitochondrial RNA polymerase. Jeremy G. Bird, Urmimala Basu, David Kuster, Aparna Ramachandran, Ewa Grudzien-Nogalska, Megerditch Kiledjian, Dmitry Temiakov, Smita S. Patel, Richard H. Ebright, Bryce E. Nickels

Reversal of microRNA-blocked tumor suppressors by biphenyl- dicarboxylate impedes endotoxin-induced hepatic hyperplasia. Li-Li Tan, Dong-Mei Chen, Jian-Ping Song, Qin Xu, Chang-Qing Li, Qing-Ping Zeng

Viral RNA-dependent RNA polymerase inhibitor 7-deaza-2′-C-methyladenosine prevents death in a mouse model of West Nile virus infection. Ludek Eyer, Martina Fojtíková, Radim Nencka, Ivo Rudolf, Zdenek Hubálek, Daniel Ruzek

Epigenetic silencing of miRNA-338-5p and miRNA-421 drives SPINK1-positive prostate cancer. Vipul Bhatia, Anjali Yadav, Ritika Tiwari, Shivansh Nigam, Sakshi Goel, Shannon Carskadon, Nilesh Gupta, Apul Goel, Nallasivam Palanisamy, Bushra Ateeq

RNA polymerase I transcription fidelity, speed and processivity depend on the interplay of its lobe binding subunits. Herbert Tschochner, Philipp Emanuel Merkl, Michael Pilsl, Tobias Fremter, Gernot Längst, Philipp Milkereit, Joachim Griesenbeck

Pervasiveness of exoribonuclease-resistant RNAs in plant viruses suggests new roles for these conserved RNA structures. Anna-Lena Steckelberg, Quentin Vicens, Jeffrey Scott Kieft

RNA polymerases display collaborative and antagonistic group behaviors over long distances through DNA supercoiling. Sangjin Kim, Bruno Beltran, Irnov Irnov, Christine Jacobs-Wagner

A high-throughput screen identifies small molecule modulators of alternative splicing by targeting RNA G-quadruplexes. Jing Zhang, Samuel E. Harvey, Chonghui Cheng

The cellular NMD pathway restricts Zika virus infection and is targeted by the viral capsid protein. Krystal A Fontaine, Kristoffer E Leon, Mir Mubashir Khalid, Sakshi Tomar, David Jimenez-Morales, Mariah Dunlap, Julia A Kaye, Priya S Shah, Steve Finkbeiner, Nevan J Krogan, Melanie Ott

Dynamic G-quadruplexes on the surface of the human ribosome. Santi Mestre-Fos, Petar I. Penev, Suttipong Suttapitugsakul, Chieri Ito, Anton S. Petrov, Roger M. Wartell, Ronghu Wu, Loren Dean Williams

Defining the RNA Interactome by Total RNA-Associated Protein Purification. Vadim Shchepachev, Stefan Bresson, Christos Spanos, Elisabeth Petfalski, Lutz Fischer, Juri Rappsilber, David Tollervey

Insights into the structure-driven protein interactivity of RNA molecules. Natalia Sanchez de Groot, Alexandros Armaos, Ricardo Grana-Montes, Marion Alriquet, Giulia Calloni, Martin Vabulas, Gian Gaetano Tartagli

RegTools: Integrated analysis of genomic and transcriptomic data for discovery of splicing variants in cancer. Yang-Yang Feng, Avinash Ramu, Kelsy C Cotto, Zachary L Skidmore, Jason Kunisaki, Donald F Conrad, Yiing Lin, William Chapman, Ravindra Uppaulri, Ramaswamy Govindan, Obi L Griffith, Malachi Griffith

A Large-Scale Binding and Functional Map of Human RNA Binding Proteins. Eric L Van Nostrand, Peter Freese, Gabriel A Pratt, Xiaofeng Wang, Xintao Wei, Steven M Blue, Daniel Dominguez, Neal A L Cody, Sara Olson, Balaji Sundararaman, Rui Xiao, Lijun Zhan, Cassandra Bazile, Louis Philip Benoit Bouvrette, Jiayu Chen, Michael O Duff, Keri Garcia, Chelsea Gelboin-Burkhart, Myles Hochman, Nicole J Lambert, Hairi Li, Thai B Nguyen, Tsultrim Palden, Ines Rabano, Shashank Sathe, Rebecca Stanton, Ashley L Louie, Stefan Aigner, Julie Bergalet, Bing Zhou, Amanda Su, Ruth Wang, Brian A Yee, Xiang-Dong Fu, Eric Lecuyer, Christopher B Burge, Brenton Graveley, Gene W Yeo

Evidence for an Integrated Gene Repression Mechanism based on mRNA Isoform Toggling in Human Cells. Ina Hollerer, Juliet C Barker, Victoria Jorgensen, Amy Tresenrider, Claire Dugast-Darzacq, Xavier Darzacq, Leon Y Chan, Robert Tjian, Elcin Unal, Gloria A Brar

Deciphering the rules of mRNA structure differentiation in vivo and in vitro with deep neural networks in Saccharomyces cerevisiae. Haopeng Yu, Wenjing Meng, Yuanhui Mao, Yi Zhang, Qing Sun, Shiheng Tao

Structure of transcribing RNA polymerase II-nucleosome complex. Lucas Farnung, Seychelle M. Vos, Patrick Cramer

Cold denaturation of RNA secondary structures with loop entropy and quenched disorder. Flavio Iannelli, Yevgeni Mamasakhlisov, Roland R. Netz

RNA polymerase interactions and elongation rate. V. Belitsky, G. M. Schütz

RNA preprints: W39/2018

Interaction paths promote spliceosome module integration and network-level robustness to cascading effects. Paulo R Guimaraes Jr., Mathias M Pires, Mauricio Cantor, Patricia P Coltri

Excised linear introns regulate growth in yeast. Jeffrey T Morgan, Gerald R Fink, David P Bartel

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

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

Nuclear export of chimeric mRNAs depends on an lncRNA-triggered autoregulatory loop. Zhen-Hua Chen, Zhancheng Zen, Tian-Qi Chen, Cai Han, Yu-Meng Sun, Wei Huang, Lin-Yu Sun, Ke Fang, Xue-Qun Luo, Wen-Tao Wang, Michelle YQ Chen

Changes in mRNA abundance drive differential shuttling of RNA binding proteins, linking cytoplasmic RNA degradation to transcription. Sarah Gilbertson, Joel D Federspiel, Ella Hartenian, Ileana M Cristea, Britt Glaunsinger

Isolation of cancer stem cells by selection for miR-302 expressing cells. Karim Rahimi, Annette Christine Fuchtbauer, Fardin Fathi, Seyed Javad Mowla, Ernst-Martin Fuchtbauer

Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes. Boas Pucker, Samuel Fraser Brockington

Population-scale study of eRNA transcription reveals bipartite functional enhancer architecture. Katla Kristjándsóttir, Yeonui Kwak, Nathaniel D Tippens, John T Lis, Hyun Min Kang, Hojoong Kwak

Modeling RNA-binding protein specificity in vivo by precisely registering protein-RNA crosslink sites. Huijuan Feng, Suying Bao, Sebastien M Weyn-Vanhentenryck, Aziz Khan, Justin Wong, Ankeeta Shah, Elise D Flynn, Chaolin Zhang

MiR-146a-dependent regulation of CD24/AKT/β-catenin axis drives stem cell phenotype in oral cancer. Susanta Roychoudhury, Sangeeta Ghuwalewala, Dishari Ghatak, Sumit Das, Pijush Das, Ramesh Butti, Mahadeo Gorain, Gopal C Kundu

On the optimal design of metabolic RNA labeling experiments. Alexey Uvarovskii, Isabel Naarmann-de Vries, Christoph Dieterich

Alternative splicing of bicistronic MOCS1 defines a novel mitochondrial protein maturation mechanism. Simon Julius Mayr, Juliane Roeper, Guenter Schwarz

Widespread gene duplication and adaptive evolution in the RNA interference pathways of the Drosophila obscura group. Danang Crysnanto, Darren Obbard

A mouse tissue atlas of small non-coding RNA. Alina Isakova, Stephen Quake

LTMG (Left truncated mixture Gaussian) based modeling of transcriptional regulatory heterogeneities in single cell RNA-seq data – a perspective from the kinetics of mRNA metabolism. Changlin Wan, Wennan Chang, Yu Zhang, Fenil Shah, Sha Cao, Xin Chen, Melissa Fishel, Qin Ma, Chi Zhang

Single-cell microRNA/mRNA co-sequencing reveals non-genetic heterogeneity and novel regulatory mechanisms. Nayi Wang, Ji Zheng, Zhuo Chen, Yang Liu, Burak Dura, Minsuk Kwak, Juliana Xavier-Ferrucio, Yi-Chien Lu, Miaomiao Zhang, Christine Roden, Jijun Cheng, Diane Krauss, Ye Ding, Rong Fan, Jun Lu

MicroRNA-223 protects neurons from degeneration in Experimental Autoimmune Encephalomyelitis. Barbara Morquette, Camille A. Juzwik, Sienna S. Drake, Marc Charabati, Julia Zhang, Marc-Andre Lecuyer, Dylan Galloway, Aline Dumas, Omar de Faria Junior, Mardja Bueno, Isabel Rambaldi, Craig Moore, Amit Bar-Or, Luc Vallieres, Alexander Prat, Alyson Fournier

Quantifying Local Randomness in Human DNA and RNA Sequences Using Erdos Motifs. Wentian Li, Dimitrios Thanos, Astero Provata