High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites
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Title
High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites
Authors
Keywords
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Journal
Nature Communications
Volume 9, Issue 1, Pages -
Publisher
Springer Nature America, Inc
Online
2018-09-29
DOI
10.1038/s41467-018-06207-z
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Note: Only part of the references are listed.- Hfq chaperone brings speed dating to bacterial sRNA
- (2018) Andrew Santiago-Frangos et al. Wiley Interdisciplinary Reviews-RNA
- Optimization of a novel biophysical model using large scale in vivo antisense hybridization data displays improved prediction capabilities of structurally accessible RNA regions
- (2017) Jorge Vazquez-Anderson et al. NUCLEIC ACIDS RESEARCH
- Rational Modular RNA Engineering Based on In Vivo Profiling of Structural Accessibility
- (2017) Abigail N. Leistra et al. ACS Synthetic Biology
- RNA systems biology: uniting functional discoveries and structural tools to understand global roles of RNAs
- (2016) Eric J Strobel et al. CURRENT OPINION IN BIOTECHNOLOGY
- Hfq: the flexible RNA matchmaker
- (2016) Taylor B Updegrove et al. CURRENT OPINION IN MICROBIOLOGY
- Fresh layers of RNA-mediated regulation in Gram-positive bacteria
- (2016) Philippe Bouloc et al. CURRENT OPINION IN MICROBIOLOGY
- Translation regulation via nascent polypeptide-mediated ribosome stalling
- (2016) Daniel N Wilson et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Small RNA interactome of pathogenic E. coli revealed through crosslinking of RNase E
- (2016) Shafagh A Waters et al. EMBO JOURNAL
- Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinkingin vivo
- (2016) Erik Holmqvist et al. EMBO JOURNAL
- Global Mapping of Small RNA-Target Interactions in Bacteria
- (2016) Sahar Melamed et al. MOLECULAR CELL
- Competing endogenous RNAs: a target-centric view of small RNA regulation in bacteria
- (2016) Lionello Bossi et al. NATURE REVIEWS MICROBIOLOGY
- UniProt: the universal protein knowledgebase
- (2016) NUCLEIC ACIDS RESEARCH
- Grad-seq guides the discovery of ProQ as a major small RNA-binding protein
- (2016) Alexandre Smirnov et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Mapping RNA–RNA interactome and RNA structure in vivo by MARIO
- (2016) Tri C. Nguyen et al. Nature Communications
- AccessFold: predicting RNA–RNA interactions with consideration for competing self-structure
- (2015) Laura DiChiacchio et al. BIOINFORMATICS
- Alternative Hfq-sRNA interaction modes dictate alternative mRNA recognition
- (2015) D. J. Schu et al. EMBO JOURNAL
- Global Analysis of Posttranscriptional Regulation by GlmY and GlmZ in Enterohemorrhagic Escherichia coli O157:H7
- (2015) Charley C. Gruber et al. INFECTION AND IMMUNITY
- sRNATarBase 3.0: an updated database for sRNA-target interactions in bacteria
- (2015) Jiang Wang et al. NUCLEIC ACIDS RESEARCH
- An assessment of bacterial small RNA target prediction programs
- (2015) Adrien Pain et al. RNA Biology
- Toehold Switches: De-Novo-Designed Regulators of Gene Expression
- (2014) Alexander A. Green et al. CELL
- Exploiting post-transcriptional regulation to probe RNA structures in vivo via fluorescence
- (2014) Steven W. Sowa et al. NUCLEIC ACIDS RESEARCH
- Recognition of the small regulatory RNA RydC by the bacterial Hfq protein
- (2014) Daniela Dimastrogiovanni et al. eLife
- Small RNAs in mycobacteria: an unfolding story
- (2014) Katie Haning et al. Frontiers in Cellular and Infection Microbiology
- Genome-wide Mapping of Cellular Protein–RNA Interactions Enabled by Chemical Crosslinking
- (2014) Xiaoyu Li et al. GENOMICS PROTEOMICS & BIOINFORMATICS
- Identification of Novel sRNAs in Mycobacterial Species
- (2013) Chen-Hsun Tsai et al. PLoS One
- Hfq binding changes the structure of Escherichia coli small noncoding RNAs OxyS and RprA, which are involved in the riboregulation of rpoS
- (2013) C. A. Henderson et al. RNA
- Mechanism of Eukaryotic RNA Polymerase III Transcription Termination
- (2013) S. Nielsen et al. SCIENCE
- Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
- (2012) H. Thorvaldsdottir et al. BRIEFINGS IN BIOINFORMATICS
- Targeting of csgD by the small regulatory RNA RprA links stationary phase, biofilm formation and cell envelope stress in Escherichia coli
- (2012) Franziska Mika et al. MOLECULAR MICROBIOLOGY
- An adaptor from translational to transcriptional control enables predictable assembly of complex regulation
- (2012) Chang C Liu et al. NATURE METHODS
- BSRD: a repository for bacterial small regulatory RNA
- (2012) Lei Li et al. NUCLEIC ACIDS RESEARCH
- Small RNA binding to the lateral surface of Hfq hexamers and structural rearrangements upon mRNA target recognition
- (2012) E. Sauer et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The functional Hfq-binding module of bacterial sRNAs consists of a double or single hairpin preceded by a U-rich sequence and followed by a 3' poly(U) tail
- (2012) H. Ishikawa et al. RNA
- FIMO: scanning for occurrences of a given motif
- (2011) Charles E. Grant et al. BIOINFORMATICS
- Accessibility and Evolutionary Conservation Mark Bacterial Small-RNA Target-Binding Regions
- (2011) A. Peer et al. JOURNAL OF BACTERIOLOGY
- Regulation by Small RNAs in Bacteria: Expanding Frontiers
- (2011) Gisela Storz et al. MOLECULAR CELL
- Pervasive post-transcriptional control of genes involved in amino acid metabolism by the Hfq-dependent GcvB small RNA
- (2011) Cynthia M. Sharma et al. MOLECULAR MICROBIOLOGY
- Dynamic competition of DsrA and rpoS fragments for the proximal binding site of Hfq as a means for efficient annealing
- (2011) Wonseok Hwang et al. NUCLEIC ACIDS RESEARCH
- Major role for mRNA binding and restructuring in sRNA recruitment by Hfq
- (2011) T. J. Soper et al. RNA
- BEDTools: a flexible suite of utilities for comparing genomic features
- (2010) Aaron R. Quinlan et al. BIOINFORMATICS
- RNAstructure: software for RNA secondary structure prediction and analysis
- (2010) Jessica S Reuter et al. BMC BIOINFORMATICS
- NUPACK: Analysis and design of nucleic acid systems
- (2010) Joseph N. Zadeh et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Evidence for an autonomous 5' target recognition domain in an Hfq-associated small RNA
- (2010) K. Papenfort et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- Small noncoding RNA GcvB is a novel regulator of acid resistance in Escherichia coli
- (2009) Ye Jin et al. BMC GENOMICS
- Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target
- (2009) N. Figueroa-Bossi et al. GENES & DEVELOPMENT
- SHAPE Analysis of Long-Range Interactions Reveals Extensive and Thermodynamically Preferred Misfolding in a Fragile Group I Intron RNA†
- (2008) Caia D. S. Duncan et al. BIOCHEMISTRY
- IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
- (2008) Anke Busch et al. BIOINFORMATICS
- Conserved Residues Asp16 and Pro24 of TnaC-tRNAPro Participate in Tryptophan Induction of tna Operon Expression
- (2008) L. R. Cruz-Vera et al. JOURNAL OF BACTERIOLOGY
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