ArticleNucleic acids research2014
Large-scale mapping of sequence-function relations in small regulatory RNAs reveals plasticity and modularity.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 39 citations in OpenAlex.
- Distribution of prophage-encoded Pas sRNAs across pathogenicbioRxiv : the preprint server for biology · 2026Article
- What makes a small RNA work?Nucleic acids research · 2025Review
- Diversity of Transcriptional Regulatory Adaptation in E. coli.Molecular biology and evolution · 2024Article
- Transcriptome fine-mapping inmBio · 2024Article
- Deep-learning-assisted Sort-Seq enables high-throughput profiling of gene expression characteristics with high precision.Science advances · 2023Article
- Deep Mutational Scanning of an Oxygen-Independent Fluorescent Protein CreiLOV for Comprehensive Profiling of Mutational and Epistatic Effects.ACS synthetic biology · 2023Article
- Effective design and inference for cell sorting and sequencing based massively parallel reporter assays.Bioinformatics (Oxford, England) · 2023Article
- Design and Analysis of Massively Parallel Reporter Assays Using FORECAST.Methods in molecular biology (Clifton, N.J.) · 2023Article
- A Sort-Seq Approach to the Development of Single Fluorescent Protein Biosensors.ACS chemical biology · 2021Article
- Effects of individual base-pairs on in vivo target search and destruction kinetics of bacterial small RNA.Nature communications · 2021Article
- Poly(A) polymerase is required for RyhB sRNA stability and function inRNA (New York, N.Y.) · 2018Article
- Origin, Evolution, and Loss of Bacterial Small RNAs.Microbiology spectrum · 2018Review
- Contrasting silencing mechanisms of the same target mRNA by two regulatory RNAs in Escherichia coli.Nucleic acids research · 2018Article
- Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq.Scientific reports · 2017Article
- Divergence of functional effects among bacterial sRNA paralogs.BMC evolutionary biology · 2017Article
- Sort-seq under the hood: implications of design choices on large-scale characterization of sequence-function relations.BMC genomics · 2016Article
- Towards the complete small RNome ofMicrobial genomics · 2016Article
- Comprehensive analysis reveals how single nucleotides contribute to noncoding RNA function in bacterial quorum sensing.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Quantification of the gene silencing performances of rationally-designed synthetic small RNAs.Systems and synthetic biology · 2015Article
- How do base-pairing small RNAs evolve?FEMS microbiology reviews · 2015Review
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Two decades into the genomics era the question of mapping sequence to function has evolved from identifying functional elements to characterizing their quantitative properties including, in particular, their specificity and efficiency. Here, we use a large-scale approach to establish a quantitative map between the sequence of a bacterial regulatory RNA and its efficiency in modulating the expression of its targets. Our approach generalizes the sort-seq method, introduced recently to analyze promoter sequences, in order to accurately quantify the efficiency of a large library of sequence variants. We focus on two small RNAs (sRNAs) in E. coli, DsrA and RyhB, and their regulation of both repressed and activated targets. In addition to precisely identifying functional elements in the sRNAs, our data establish quantitative relationships between structural and energetic features of the sRNAs and their regulatory activity, and characterize a large set of direct and indirect interactions between nucleotides. A core of these interactions supports a model where specificity can be enhanced by a rigid molecular structure. Both sRNAs exhibit a modular design with limited cross-interactions, dividing the requirements for structural stability and target binding among modules.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.