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VOL. 20, NO. 10
OCTOBER 2014
CONTENTS
Hypothesis
De novo translation initiation on membrane-bound ribosomes as a mechanism for localization
of cytosolic protein mRNAs to the endoplasmic reticulum
1489
Sujatha Jagannathan, David W. Reid, Amanda H. Cox, and Christopher V. Nicchitta
Letter to the Editor
Chloroplast RNA editing going extreme: more than 3400 events of C-to-U editing in the chloroplast
transcriptome of the lycophyte Selaginella uncinata
1499
Bastian Oldenkott, Kazuo Yamaguchi, Sumika Tsuji-Tsukinoki, Nils Knie, and Volker Knoop
Bioinformatics
Detecting translational regulation by change point analysis of ribosome profiling data sets
1507OA
Anze Zupanic, Catherine Meplan, Sushma N. Grellscheid, John C. Mathers,
Tom B.L. Kirkwood, John E. Hesketh, and Daryl P. Shanley
IRBIS: a systematic search for conserved complementarity
1519OA
Dmitri D. Pervouchine
Reports
Generation of catalytic human Ago4 identifies structural elements important for RNA cleavage
1532
Judith Hauptmann, Lukas Kater, Patrick Löffler, Rainer Merkl, and Gunter Meister
Triazole-containing monophosphate mRNA cap analogs as effective translation inhibitors
1539
Karolina Piecyk, Maciej Lukaszewicz, Edward Darzynkiewicz, and Marzena Jankowska-Anyszka
Recognition of U-rich RNA by Hfq from the Gram-positive pathogen Listeria monocytogenes
1548OA
Alexander R. Kovach, Kirsten E. Hoff, John T. Canty, Jillian Orans, and Richard G. Brennan
Structure of RNA 3′ -phosphate cyclase bound to substrate RNA
1560
Kevin K. Desai, Craig A. Bingman, Chin L. Cheng, George N. Phillips Jr., and Ronald T. Raines
(continued)
Cover Illustration: Crystal structure of the A24U/U25A/A46G mutant XPT-PBUX guanine riboswitch aptamer domain in complex
with hypoxanthine (Protein Data Bank code: 4fen; Stoddard CD, Widmann J, Trausch JJ, Marcano-Velázquez JG, Knight R, Batey
RT. 2013. Nucleotides adjacent to the ligand-binding pocket are linked to activity tuning in the purine riboswitch. J Mol Biol 425:
1596–1611). Image details show riboswitch—ribbon-plate representation, base-specific coloring, A—red, U—magenta, G—green,
C—blue; hypoxanthine—spacefilling representation, gray. The image was generated with the Accelrys Discovery Studio
Visualizer. Cover image provided by the Jena Library of Biological Macromolecules—JenaLib (jenalib.fli-leibniz.de).
Published by Cold Spring Harbor Laboratory Press
Contents (continued)
Articles
Clostridium difficile Hfq can replace Escherichia coli Hfq for most of its function
1567
Joel Caillet, Céline Gracia, Fanette Fontaine, and Eliane Hajnsdorf
The interaction of cytoplasmic poly(A)-binding protein with eukaryotic initiation factor 4G suppresses
nonsense-mediated mRNA decay
1579OA
Tobias Fatscher, Volker Boehm, Benjamin Weiche, and Niels H. Gehring
Drosophila Syncrip modulates the expression of mRNAs encoding key synaptic proteins required
for morphology at the neuromuscular junction
1593OA
Suzanne M. McDermott, Lu Yang, James M. Halstead, Russell S. Hamilton, Carine Meignin, and Ilan Davis
In vivo tmRNA protection by SmpB and pre-ribosome binding conformation in solution
1607
Ehsan Ranaei-Siadat, Cécile Mérigoux, Bili Seijo, Luc Ponchon, Jean-Michel Saliou, Julie Bernauer,
Sarah Sanglier-Cianférani, Fréderic Dardel, Patrice Vachette, and Sylvie Nonin-Lecomte
Elevated SRPK1 lessens apoptosis in breast cancer cells through RBM4-regulated splicing events
1621
Jung-Chun Lin, Ching-Yu Lin, Woan-Yuh Tarn, and Fang-Yu Li
A cluster of methylations in the domain IV of 25S rRNA is required for ribosome stability
1632
Andriana Gigova, Sujitha Duggimpudi, Tim Pollex, Matthias Schaefer, and Martin Koš
Method
Determination of in vivo RNA kinetics using RATE-seq
1645OA
Benjamin Neymotin, Rodoniki Athanasiadou, and David Gresham
Erratum
1653
RNA: Instructions for contributors
1654
OA
Open Access paper