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Differential RNA-Seq and transcription start site annotation in Chlamydia
Chlamydiae are obligate intracellular Gram-negative bacteria that infect a wide range of hosts. However, host specificity and virulence of the individual species differ drastically even though all members of the phylum share the majority of genes which are encoded on a much reduced genome. Striking examples of this contrast are seen in the close relatives Chlamydia (C.) psittaci and C. abortus. C. psittaci is the causative agent of psittacosis, the most widespread zoonotic chlamydiosis, while the less widespread C. abortus is still of clinical relevance because of its ability to colonize the human placenta. Other chlamydia-like organisms, such as Waddlia (W.) chondrophila, also occasionally infect humans, cause similar symptoms and exhibit the Chlamydia-specific biphasic developmental cycle. In this work, differential RNA-Sequencing (dRNA-Seq) was applied to purified infectious and non-infectious developmental forms of C. psittaci, C. abortus and W. chondrophila. The comparison revealed that both, infectious and non-infectious states contain distinct transcriptomes that match their biological functions. Furthermore, considerable differences in the expression of homologous virulence factors were found. A second focus of this work was the reliable annotation of transcription start sites (TSSs) using dRNA-Seq data. The presented approach is based on optimization and combination of three TSS annotation tools and its success was validated with data from Escherichia (E.) coli for which besides the dRNA-Seq another high throughput data set (Cappable-seq) for TSS annotation was available. In total 9,802 TSSs with high precision were identified based on data of E. coli, C. pneumoniae, C. psittaci, C. abortus and W. chondrophila. Knowing the precise TSSs positions, the corresponding 5’ untranslated regions (UTRs) and conservation among species could be analyzed. This revealed that among Chlamydia, positions of TSSs and 5’UTR sequences are evolutionary less conserved than the corresponding coding sequences. This is ...
Differential RNA-Seq and transcription start site annotation in Chlamydia
Chlamydiae are obligate intracellular Gram-negative bacteria that infect a wide range of hosts. However, host specificity and virulence of the individual species differ drastically even though all members of the phylum share the majority of genes which are encoded on a much reduced genome. Striking examples of this contrast are seen in the close relatives Chlamydia (C.) psittaci and C. abortus. C. psittaci is the causative agent of psittacosis, the most widespread zoonotic chlamydiosis, while the less widespread C. abortus is still of clinical relevance because of its ability to colonize the human placenta. Other chlamydia-like organisms, such as Waddlia (W.) chondrophila, also occasionally infect humans, cause similar symptoms and exhibit the Chlamydia-specific biphasic developmental cycle. In this work, differential RNA-Sequencing (dRNA-Seq) was applied to purified infectious and non-infectious developmental forms of C. psittaci, C. abortus and W. chondrophila. The comparison revealed that both, infectious and non-infectious states contain distinct transcriptomes that match their biological functions. Furthermore, considerable differences in the expression of homologous virulence factors were found. A second focus of this work was the reliable annotation of transcription start sites (TSSs) using dRNA-Seq data. The presented approach is based on optimization and combination of three TSS annotation tools and its success was validated with data from Escherichia (E.) coli for which besides the dRNA-Seq another high throughput data set (Cappable-seq) for TSS annotation was available. In total 9,802 TSSs with high precision were identified based on data of E. coli, C. pneumoniae, C. psittaci, C. abortus and W. chondrophila. Knowing the precise TSSs positions, the corresponding 5’ untranslated regions (UTRs) and conservation among species could be analyzed. This revealed that among Chlamydia, positions of TSSs and 5’UTR sequences are evolutionary less conserved than the corresponding coding sequences. This is ...
Differential RNA-Seq and transcription start site annotation in Chlamydia
Beder, Thomas (Autor:in) / Saluz, Hans Peter / König, Rainer / Borel, Nicole
01.01.2019
Hochschulschrift
Elektronische Ressource
Englisch
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