RNA preprints: Week 51 edition

“CapZyme-Seq” comprehensively defines promoter-sequence determinants for RNA 5′ capping with NAD+. Irina O Vvedenskaya, Jeremy G Bird, Yuanchao Zhang, Yu Zhang, Xinfu Jiao, Ivan Barvík, Libor Krásný, Megerditch Kiledjian, Deanne M Taylor, Richard H Ebright, Bryce E Nickels

Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes. Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Grace Tiao, Henrik Hornshøj, Julian M Hess, Randi Istrup Istrup Pedersen, Lars Feuerbach, Radhakrishnan Sabarinathan, Henrik Tobias Madsen, JAEGIL KIM, Loris Mularoni, Shimin Shuai, Andrés Arturo Lanzós Camaioni, Carl Herrmann, Yosef E Maruvka, Ciyue Shen, Samir B Amin, Johanna Bertl, Priyanka Dhingra, Klev Diamanti, Abel Gonzalez-Perez, Qianyun Guo, Nicholas J Haradhvala, Keren Isaev, Malene Juul, Jan Komorowski, sushant kumar, Donghoon Lee, Lucas Lochovsky, Eric Minwei Minwei Liu, Oriol Pich, david tamborero, Husen M. Umer, Liis Uusküla-Reimand, Claes Wadelius, Lina Wadi, Jing Zhang, Keith A Boroevich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu YW Chan, Nuno A Fonseca, Mark P Hamilton, Chen Hong, Andre Kahles, Youngwook Kim, Kjong-Van Lehmann, Todd Andrew A Johnson, Abdullah Kahraman, Keunchil Park, Gordon Saksena, Lina Sieverling, Nicholas A Sinnott-Armstrong, Peter J Campbell, Asger Hobolth, Manolis Kellis, Michael S Lawrence, Ben Raphael, Mark A Rubin, Chris Sander, Lincoln Stein, Josh Stuart, Tatsuhiko Tsunoda, David A Wheeler, Rory Johnson, Jüri Reimand, Mark B Gerstein, Ekta Khurana, Nuria Lopez-Bigas, Inigo Martincorena, Jakob Skou Skou Pedersen, Gad Getz, PCAWG Drivers and Functional Interpretation Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Net

Transcriptome dynamics describe and predict state transition from health to leukemia. Russell C. Rockne, Sergio Branciamore, Jing Qi, Guerry J. Cook, Wei-Kai Hua, Emily Carnahan, Ayelet Marom, Herman Wu, Davide Maestrini, Xiwei Wu, Chao Guo, Denis O’Meally, Yate-Ching Yuan, Zheng Liu, Nadia Carlesso, Leo D. Wang, Stephen Forman, Ya-Huei Kuo, Guido Marcucci

Multiplexed imaging of high density libraries of RNAs with MERFISH and expansion microscopy. Guiping Wang, Jeffrey R Moffitt, Xiaowei Zhuang

Pan-cancer characterisation of microRNA with hallmarks of cancer reveals role of microRNA-mediated downregulation of tumour suppressor genes. Andrew Dhawan, Jacob G Scott, Adrian L Harris, Francesca M Buffa

Analysis of RDR1/RDR2/RDR6-independent small RNAs in Arabidopsis thaliana improves MIRNA annotations and reveals novel siRNA loci. Seth Polydore, Michael Axtell

Transcription-dependent spreading of canonical yeast GATA factor across the body of highly expressed genes. Aria Ronsmans, Maxime Wery, Camille Gautier, Marc Descrimes, Evelyne Dubois, Antonin Morillon, Isabelle Georis

Comprehensive Cell Type Specific Transcriptomics of the Human Kidney. V Sivakamasundari, Mohan Bolisetty, Santhosh Sivajothi, Shannon Bessonett, Diane Ruan, Paul Robson

A memory element imposes epigenetic behavior on intrinsically labile RNAi-induced heterochromatin spread. R A Greenstein, Stephen K Jones Jr., Eric C Spivey, James R Rybarski, Ilya Finkelstein, Bassem Al-Sady

Isolation of nucleic acids from low biomass samples: detection and removal of sRNA contaminants. Anna Heintz-Buschart, Dilmurat Yusuf, Anne Kaysen, Alton Etheridge, Joelle V Fritz, Patrick May, Carine de Beaufort, Bimal Babu Upadhyaya, Anubrata Ghosal, David J Galas, Paul Wilmes

Spatial organization of single mRNPs at different stages of the gene expression pathway. Srivathsan Adivarahan, Samir Rahman, Daniel Zenklusen

Deep sequencing reveals two Jurkat subpopulations with distinct miRNA profiles during camptothecin-induced apoptosis. Ipek Erdogan, Mehmet Ilyas Ilyas Cosacak, Ayten Nalbant Aldanmaz, Bunyamin Akgul

The primary transcriptome, small RNAs, and regulation of antimicrobial resistance in Acinetobacter baumannii. Carsten Kröger, Keith D. MacKenzie, Ebtihal Y. Al-Shabib, Morgan W. B. Kirzinger, Danae M. Suchan, Tzu-Chiao Chao, Valentyna Akulova, Alesksandra A. Miranda-CasoLuengo, Vivian A. Monzon, Tyrrell Conway, Sathesh K. Sivasankaran, Jay C. D. Hinton, Karsten Hokamp, Andrew D. S. Cameron

Terminal uridylyltransferases target RNA viruses as part of the innate immune system in animals. Jeremie Le Pen, Hongbing Jiang, Tomas Di Domenico, Emma Kneuss, Joanna Kosalka, Marcos Morgan, Christian Much, Konrad L. M. Rudolph, Anton J. Enright, Donal O’Carroll, David Wang, Eric A. Miska

ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2. Devanshi Jain, M. Rhyan Puno, Cem Meydan, Nathalie Lailler, Christopher E. Mason, Christopher D Lima, Kathryn V. Anderson, Scott Keeney

The detection of covariation of mRNA levels of large sets of genes across multiple human populations. Yu Quan, Chao Xie, Rohan B. H. Williams, Peter Little

Long-read sequencing of nascent RNA in S. pombe reveals coupling among RNA processing events. Lydia Herzel, Korinna Straube, Karla M. Neugebauer

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

Mutations alter RNA-mediated conversion of human prions. Erik J Alred, Izra Lodangco, Jennifer Gallaher, Ulrich Hansmann

Universal Alternative Splicing Of Noncoding Exons. Ira W. Deveson, Marion E. Brunck, James Blackburn, Elizabeth Tseng, Ting Hon, Tyson A. Clark, Michael B. Clark, Joanna Crawford, Marcel E. Dinger, Lars K. Nielsen, John S. Mattick, Tim R. Mercer

Multiplexed targeted resequencing identifies coding and regulatory variation underlying phenotypic extremes of HDL-cholesterol in humans. Sumeet A. Khetarpal, Paul L. Babb, Wei Zhao, William F. Hancock-Cerutti, Christopher D. Brown, Daniel J. Rader, Benjamin F. Voight

Diverse spatial expression patterns emerge from common transcription bursting kinetics. Benjamin Zoller, Shawn C. Little, Thomas Gregor

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RNA preprints: Week 50 edition

A cytoplasmic Argonaute protein promotes the inheritance of RNAi. Fei Xu, Xuezhu Feng, Xiangyang Chen, Chenchun Weng, Qi Yan, Ting Xu, Minjie Hong, Shouhong Guang

Genome-wide post-transcriptional dysregulation by microRNAs in human asthma as revealed by Frac-seq. Rocio Teresa Martinez-Nunez, Hitasha Rupani, Manuela Plate, Mahesan Niranjan, Rachel C Chambers, Peter H Howarth, Tilman Sanchez-Elsner

An antisense RNA capable of modulating the expression of the tumour suppressor microRNA-34a. Jason T Serviss, Felix Clemens Richter, Jimmy Van den Eynden, Nathanael Andrews, Miranda Houtman, Mattias Vesterlund, Laura Schwarzmueller, Per Johnsson, Erik Larsson Lekholm, Dan Grandér, Katja Pokrovskaja Tamm

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

Transcription establishes microenvironments that organize euchromatin. Lennart Hilbert, Yuko Sato, Hiroshi Kimura, Frank Jülicher, Alf Honigmann, Vasily Zaburdaev, Nadine Vastenhouw

CLAN: the CrossLinked reads ANalysis tool. Cuncong Zhong, Shaojie Zhang

mRNA structure determines specificity of a polyQ-driven phase separation. Erin M Langdon, Peggy Billingsly, Amirhossein Ghanbari Niaki, Grace McLaughlin, Chase Weidmann, Therese Gerbich, Christina M Termini, Kevin M Weeks, Sua Myong, Amy Gladfelter

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

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

Complemented palindrome small RNAs first discovered from SARS coronavirus. Chang Liu, Ze Chen, Wenyuan Shen, Deshui Yu, Siyu Li, Yue Hu, Haishuo Ji, Wenjun Bu, Qingsong Wang, Shan Gao

Combination of mitochondrial tRNA and OXPHOS mutation reduces lifespan and physical condition in aged mice. Gesine Reichart, Johannes Mayer, Tursonjan Tokay, Falko Lange, Cindy Johne, Simone Baltrusch, Markus Tiedge, Georg Fuellen, Saleh Ibrahim, Rudiger Kohling

Structurally conserved primate lncRNAs are transiently expressed during human cortical differentiation and influence cell type specific genes. Andrew R. Field, Frank M.J. Jacobs, Ian T. Fiddes, Alex P.R. Phillips, Andrea M. Reyes-Ortiz, Erin LaMontagne, Lila Whitehead, Vincent Meng, Jimi L. Rosenkrantz, Maximillian Haeussler, Sol Katzman, Sofie R. Salama, David Haussler

Mir-132 controls beta cell proliferation and survival in mouse model through the PTEN/AKT/FOXO3 signaling. Hassan Mziaut, Georg Henniger, Katharina Ganss, Sebastian Hempel, Steffen Wolk, Johanna McChord, Kamal Chowdhury Chowdhury, Klaus Peter Knoch, Jurgen Weitz, Michele Solimena, Stephan Kersting

Characterizing highly dynamic conformational states: the transcription bubble in RNAP-promoter open complex as an example. Eitan Lerner, Antonino Ingargiola, Shimon Weiss

Human iPSC-derived RPE and retinal organoids reveal impaired alternative splicing of genes involved in pre-mRNA splicing in PRPF31 autosomal dominant retinitis pigmentosa. Adriana Buskin, Lili Zhu, Valeria Chichagova, Basudha Basu, Sina Mozaffari-Jovin, David Dolan, Alastair Droop, Joseph Collin, Revital Bronstein, Sudeep Mehrotra, Michael Farkas, Gerrit Hilgen, Kathryn White, Dean Hallam, Katarzyna Bialas, Git Chung, Carla Mellough, Yuchun Ding, Natalio Krasnogor, Stefan Przyborski, Jumana Al-Aama, Sameer Alharthi, Yaobo Xu, Gabrielle Wheway, Katarzyna Szymanska, Martin McKibbin, Chris F Inglehearn, David J Elliott, Susan Lindsay, Robin R Ali, David H Steel, Lyle Armstrong, Evelyne Sernagor, Eric Pierce, Reinhard Luehrmann, Sushma-Nagaraja Grellscheid, Colin A Johnson, Majlinda Lako

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA, and mRNA data in GDC. Ruidong Li, Han Qu, Shibo Wang, Julong Wei, Le Zhang, Renyuan Ma, Jianming Lu, Jianguo Zhu, Wei-De Zhong, Zhenyu Jia

Cell-wall synthesis and ribosome maturation are co-regulated by an RNA switch in Mycobacterium tuberculosis. Stefan Schwenk, Alexandra Moores, Irene Nobeli, Timothy D McHugh, Kristine Bourke Arnvig

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RNA preprints: Week 49 edition

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

Antisense transcriptional interference mediates condition-specific gene repression in budding yeast. Alicia Nevers, Antonia Doyen, Christophe Malabat, Bertrand Neron, Thomas Kergrohen, Alain Jacquier, Gwenael Badis

Dual tRNA mimicry in the Cricket Paralysis Virus IRES uncovers an unexpected similarity with the Hepatitis C Virus IRES. Israel S Fernández, Vera P Pisareva, Andrey V Pisarev

Conformational Ensemble of RNA Oligonucleotides from Reweighted Molecular Simulations. Sandro Bottaro, Giovanni Bussi, Scott D Kennedy, Douglas H Turner, Kresten Lindorff-Larsen

Transfer RNA genes experience exceptionally elevated mutation rates. Bryan Thornlow, Josh Hough, Jackie Roger, Henry Gong, Todd Lowe, Russell Corbett-Detig

pysster: Learning Sequence and Structure Motifs in DNA and RNA Sequences using Convolutional Neural Networks. Stefan Budach, Annalisa Marsico

Allosteric effector ppGpp potentiates the inhibition of transcript initiation by DksA. Vadim Molodtsov, Elena Sineva, Lu Zhang, Xuhui Huang, Michael Cashel, Sarah E. Ades, Katsuhiko Murakami

Development of an in vitro pre-mRNA splicing assay using plant nuclear extract. Mohammed Albaqami, Anireddy Reddy

Barley Long Non-Coding RNAs and Their Tissue-Specific Co-expression Pattern with Coding-Transcripts. Gokhan Karakulah, Turgay Unver

Engineering a promiscuous pyrrolysyl-tRNA synthetase by a high throughput FACS screen. Adrian Hohl, Ram Karan, Anstassja Akal, Dominik Renn, Xuechao Liu, Alaguraj Dharamarajnadar, Seema Arun Ghoprade, Michael Groll, Magnus Rueping, Jörg Eppinger

A-to-I RNA editing uncovers hidden signals of adaptive genome evolution in animals. Niko Popitsch, Christian D. Huber, Ilana Buchumenski, Eli Eisenberg, Michael Jantsch, Arndt von Haeseler, Miguel Gallach

Transcription activation domains of the yeast factors Met4 and Ino2: tandem activation domains with properties similar to the yeast Gcn4 activator. Derek Pacheco, linda warfield, michelle brajcich, hannah robbins, jie luo, jeff ranish, Steven Hahn

Targeted RNA knockdown by crRNA guided Csm in zebrafish. Thomas Fricke, Gintautas Tamulaitis, Dalia Smalakyte, Michal Pastor, Agnieszka Kolano, Virginijus Siksnys, Matthias Bochtler

Attention based convolutional neural network for predicting RNA-protein binding sites. Xiaoyong Pan, Junchi Yan

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RNA preprints: Week 48 edition

Spatial organization and dynamics of RNase E and ribosomes in Caulobacter crescentus. Camille A Bayas, Jiarui Wang, Marissa K Lee, Jared M Schrader, Lucy Shapiro, W.E. Moerner

Exploring Drivers of Gene Expression in The Cancer Genome Atlas. Andrea Rau, Michael J Flister, Hallgeir Rui, Paul Livermore Auer

Prospects for recurrent neural network models to learn RNA biophysics from high-throughput data. Michelle J Wu, Johan OL Andreasson, Wipapat Kladwang, William J Greenleaf, Eterna players, Rhiju Das

Aberrant splicing in B-cell acute lymphoblastic leukemia. Kathryn L. Black, Ammar S. Naqvi, Katharina E. Hayer, Scarlett Y. Yang, Elisabeth Gillespie, Asen Bagashev, Vinodh Pillai, Sarah Tasian, Matthew R. Gazzara, Martin Carroll, Deanne Taylor, Kristen W. Lynch, Yoseph Barash, Andrei Thomas-Tikhonenko

Engineering a Functional small RNA Negative Autoregulation Network with Model-guided Design. Chelsea Hu, Melissa Takahashi, Yan Zhang, Julius Lucks

Discovery of physiological and cancer-related regulators of 3′ UTR processing with KAPAC. Andreas J Gruber, Ralf Schmidt, Souvik Ghosh, Georges Martin, Andreas R Gruber, Erik van Nimwegen, Mihaela Zavolan

Gene regulatory network rewiring by an adaptively evolving microRNA cluster in Drosophila. Yang Lyu, Zhongqi Liufu, Juan Xiao, Yuxin Chen, Chung-I Wu, Tian Tang

An Essential Role for Argonaute 2 in EGFR-KRAS Signaling in Pancreatic Cancer Development. Sunita Shankar, Jean Tien, Ronald F Siebenaler, Vijaya L Dommeti, Sylvia Zelenka-Wang, Kristin M Juckette, Alice Xu, Malay Mody, Andrew Goodrum, Grace Tsaloff, Ingrid J Apel, Lisha Wang, Javed Siddiqui, Jiaqi Shi, Chandan Kumar-Sinha, Arul M Chinnaiyan

CRISPR-Cas12a target binding unleashes single-stranded DNase activity. Janice S Chen, Enbo Ma, Lucas B Harrington, Xinran Tian, Jennifer A Doudna

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

The miR-96/RARγ signaling axis governs androgen signaling and prostate cancer progression. Mark D. Long, Prashant K. Singh, James R. Russell, Gerard Llimos, Spencer Rosario, Abbas Rizvi, Henry Withers, Patrick R. van den Berg, Jason Kirk, Lara E. Sucheston-Campbell, Dominic J. Smiraglia, Moray J. Campbell

Diminishing returns of inoculum size on the rate of a plant RNA virus evolution. Rebeca Navarro, Silvia Ambros, Fernando Martinez, Santiago F Elena

Producing Hfq/Sm Proteins and sRNAs for Structural and Biophysical Studies of Ribonucleoprotein Assembly. Kimberly A. Stanek, Cameron Mura

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