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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That’s a wrap. Did we miss something? Let us know!

 

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