@article{AlbrechtSharmaDittrichetal.2011,
  author    = {Albrecht, Marco and Sharma, Cynthia M. and Dittrich, Marcus T. and M{\"u}ller, Tobias and Reinhardt, Richard and Vogel, J{\"o}rg and Rudel, Thomas},
  title     = {The Transcriptional Landscape of Chlamydia pneumoniae},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-69116},
  year      = {2011},
  abstract  = {Background: Gene function analysis of the obligate intracellular bacterium Chlamydia pneumoniae is hampered by the facts that this organism is inaccessible to genetic manipulations and not cultivable outside the host. The genomes of several strains have been sequenced; however, very little information is available on the gene structure and transcriptome of C. pneumoniae. Results: Using a differential RNA-sequencing approach with specific enrichment of primary transcripts, we defined the transcriptome of purified elementary bodies and reticulate bodies of C. pneumoniae strain CWL-029; 565 transcriptional start sites of annotated genes and novel transcripts were mapped. Analysis of adjacent genes for cotranscription revealed 246 polycistronic transcripts. In total, a distinct transcription start site or an affiliation to an operon could be assigned to 862 out of 1,074 annotated protein coding genes. Semi-quantitative analysis of mapped cDNA reads revealed significant differences for 288 genes in the RNA levels of genes isolated from elementary bodies and reticulate bodies. We have identified and in part confirmed 75 novel putative non-coding RNAs. The detailed map of transcription start sites at single nucleotide resolution allowed for the first time a comprehensive and saturating analysis of promoter consensus sequences in Chlamydia. Conclusions: The precise transcriptional landscape as a complement to the genome sequence will provide new insights into the organization, control and function of genes. Novel non-coding RNAs and identified common promoter motifs will help to understand gene regulation of this important human pathogen.},
  subject      = {Chlamydia pneumoniae},
  language  = {en}
}
@article{SchmidtkeFindeissSharmaetal.2011,
  author    = {Schmidtke, Cornelius and Findeiß, Sven and Sharma, Cynthia M. and Kuhfuss, Juliane and Hoffmann, Steve and Vogel, J{\"o}rg and Stadler, Peter F. and Bonas, Ulla},
  title     = {Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions},
  series = {Nucleic Acids Research},
  volume    = {40},
  journal   = {Nucleic Acids Research},
  number    = {5},
  doi       = {10.1093/nar/gkr904},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-131781},
  pages     = {2020 -- 2031},
  year      = {2011},
  abstract  = {The Gram-negative plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria (Xcv) is an important model to elucidate the mechanisms involved in the interaction with the host. To gain insight into the transcriptome of the Xcv strain 85-10, we took a differential RNA sequencing (dRNA-seq) approach. Using a novel method to automatically generate comprehensive transcription start site (TSS) maps we report 1421 putative TSSs in the Xcv genome. Genes in Xcv exhibit a poorly conserved -10 promoter element and no consensus Shine-Dalgarno sequence. Moreover, 14\% of all mRNAs are leaderless and 13\% of them have unusually long 5'-UTRs. Northern blot analyses confirmed 16 intergenic small RNAs and seven cis-encoded antisense RNAs in Xcv. Expression of eight intergenic transcripts was controlled by HrpG and HrpX, key regulators of the Xcv type III secretion system. More detailed characterization identified sX12 as a small RNA that controls virulence of Xcv by affecting the interaction of the pathogen and its host plants. The transcriptional landscape of Xcv is unexpectedly complex, featuring abundant antisense transcripts, alternative TSSs and clade-specific small RNAs.},
  language  = {en}
}