title: Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor.
abstract: Streptomyces coelicolor is considered the model organism among Gram positive, GC rich bacteria. Its genome has been sequenced but little is known about the occurrence and distribution of small non-coding RNAs in this biotechnologically relevant organism. Using deep sequencing we analyzed the transcriptome at the end of exponential growth, which corresponds to the onset of secondary metabolism. We mapped 193 transcriptional start sites of mRNA genes and identified putative new and alternative open reading frames. We identified 63 non-coding RNAs including 29 cis encoded antisense RNAs, and confirmed expression for 11, most of them being growth-phase dependent. A comparison between the sequencing results and bioinformatic sRNA predictions using Dynalign and RNAz revealed only a small overlap between the different approaches.
authors.affiliation: Institut für Molekulare Biowissenschaften, Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt, Germany.
authors.forename: Michael-Paul
authors.initials: MP
authors.lastname: Vockenhuber
authors.forename: Cynthia M
authors.initials: CM
authors.lastname: Sharma
authors.forename: Michaela G
authors.initials: MG
authors.lastname: Statt
authors.forename: Denis
authors.initials: D
authors.lastname: Schmidt
authors.forename: Zhenjiang
authors.initials: Z
authors.lastname: Xu
authors.forename: Sascha
authors.initials: S
authors.lastname: Dietrich
authors.forename: Heiko
authors.initials: H
authors.lastname: Liesegang
authors.forename: David H
authors.initials: DH
authors.lastname: Mathews
authors.forename: Beatrix
authors.initials: B
authors.lastname: Suess
mesh_terms: D001483:Base Sequence; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D016366:Open Reading Frames; D016372:RNA, Antisense / Q000737:chemistry; D012329:RNA, Bacterial / Q000737:chemistry*; D058727:RNA, Small Untranslated / Q000737:chemistry*; D048372:Streptomyces coelicolor / Q000235:genetics* / Q000378:metabolism
chemical_list: D016372:RNA, Antisense; D012329:RNA, Bacterial; D058727:RNA, Small Untranslated