title: Massive functional mapping of a 5'-UTR by saturation mutagenesis, phenotypic sorting and deep sequencing.
abstract: We present here a method that enables functional screening of large number of mutations in a single experiment through the combination of random mutagenesis, phenotypic cell sorting and high-throughput sequencing. As a test case, we studied post-transcriptional gene regulation of the bacterial csgD messenger RNA, which is regulated by a small RNA (sRNA). A 109 bp sequence within the csgD 5'-UTR, containing all elements for expression and sRNA-dependent control, was mutagenized close to saturation. We monitored expression from a translational gfp fusion and collected fractions of cells with distinct expression levels by fluorescence-activated cell sorting. Deep sequencing of mutant plasmids from cells in different activity-sorted fractions identified functionally important positions in the messenger RNA that impact on intrinsic (translational activity per se) and extrinsic (sRNA-based) gene regulation. The results obtained corroborate previously published data. In addition to pinpointing nucleotide positions that change expression levels, our approach also reveals mutations that are silent in terms of gene expression and/or regulation. This method provides a simple and informative tool for studies of regulatory sequences in RNA, in particular addressing RNA structure-function relationships (e.g. sRNA-mediated control, riboswitch elements). However, slight protocol modifications also permit mapping of functional DNA elements and functionally important regions in proteins.
authors.affiliation: Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SciLifeLab Uppsala, Box 596, S-75124 Uppsala, Sweden.
authors.forename: Erik
authors.initials: E
authors.lastname: Holmqvist
authors.forename: Johan
authors.initials: J
authors.lastname: Reimegård
authors.forename: E Gerhart H
authors.initials: EG
authors.lastname: Wagner
mesh_terms: D020121:5' Untranslated Regions; D029968:Escherichia coli Proteins / Q000235:genetics; D005434:Flow Cytometry; D015964:Gene Expression Regulation, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D016296:Mutagenesis; D009690:Nucleic Acid Conformation; D010641:Phenotype; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000737:chemistry; D058727:RNA, Small Untranslated / Q000378:metabolism; D038621:Regulatory Sequences, Ribonucleic Acid; D017422:Sequence Analysis, DNA; D015534:Trans-Activators / Q000235:genetics
chemical_list: D020121:5' Untranslated Regions; C499694:CsgD protein, E coli; D029968:Escherichia coli Proteins; D012333:RNA, Messenger; D058727:RNA, Small Untranslated; D038621:Regulatory Sequences, Ribonucleic Acid; D015534:Trans-Activators