title: A new custom microarray for sRNA profiling in Escherichia coli.
abstract: Bacterial small RNAs (sRNAs) play essential roles in the post-transcriptional control of gene expression. To improve their detection by conventional microarrays, we designed a custom microarray containing a group of probes targeting known and some putative Escherichia coli sRNAs. To assess its potential in detection of sRNAs, RNA profiling experiments were performed with total RNA extracted from E. coli MG1655 cells exponentially grown in rich (Luria-Bertani) and minimal (M9/glucose) media. We found that many sRNAs could yield reasonably strong and statistically significant signals corresponding to nearly all sRNAs annotated in the EcoCyc database. Besides differential expression of two sRNAs (GcvB and RydB), expression of other sRNAs was less affected by the composition of the growth media. Other examples of the differentially expressed sRNAs were revealed by comparing gene expression of the wild-type strain and its isogenic mutant lacking functional poly(A) polymerase I (pcnB). Further, northern blot analysis was employed to validate these data and to assess the existence of new putative sRNAs. Our results suggest that the use of custom microarrays with improved capacities for detection of sRNAs can offer an attractive opportunity for efficient gene expression profiling of sRNAs and their target mRNAs at the whole transcriptome level.
authors.affiliation: Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, Leioa, Spain.
authors.forename: Olatz
authors.initials: O
authors.lastname: Ruiz-Larrabeiti
authors.affiliation: Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, Leioa, Spain.
authors.forename: Ander Hernández
authors.initials: AH
authors.lastname: Plágaro
authors.affiliation: CNRS UMR8261 (previously FRE3630), University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France.
authors.forename: Celine
authors.initials: C
authors.lastname: Gracia
authors.affiliation: Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, Leioa, Spain.
authors.forename: Elena
authors.initials: E
authors.lastname: Sevillano
authors.affiliation: Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, Leioa, Spain.
authors.forename: Lucía
authors.initials: L
authors.lastname: Gallego
authors.affiliation: CNRS UMR8261 (previously FRE3630), University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France.
authors.forename: Eliane
authors.initials: E
authors.lastname: Hajnsdorf
authors.affiliation: Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, Leioa, Spain IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain vladimir.kaberdin@ehu.eus.
authors.forename: Vladimir R
authors.initials: VR
authors.lastname: Kaberdin
mesh_terms: D004926:Escherichia coli / Q000235:genetics*; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D035001:Host Factor 1 Protein / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D012329:RNA, Bacterial; D012333:RNA, Messenger / Q000235:genetics; D058727:RNA, Small Untranslated; D059467:Transcriptome
chemical_list: D035001:Host Factor 1 Protein; D012329:RNA, Bacterial; D012333:RNA, Messenger; D058727:RNA, Small Untranslated
keywords: Custom microarrays; E. coli gene expression; pcnB mutant; riboregulators; small RNAs