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Publikationen - Molekulare Signalverarbeitung

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Publikation

Acosta, I.F., Gasperini, D., Chételat, A., Stolz, S., Santuari, L. & Farmer, E.E. Role of NINJA in root jasmonate signaling. In: PNAS 110 (38), 15473-15478, (2013) DOI: 10.1073/pnas.1307910110

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Publikation

Poeschl, Y., Delker, C., Trenner, J., Ullrich, K. & Quint, M. & Grosse, I. Optimized probe masking for comparative transcriptomics of closely related species. PLOS ONE 8, e78497, (2013)

Microarrays are commonly applied to study the transcriptome of specific species. However, many available microarrays are

restricted to model organisms, and the design of custom microarrays for other species is often not feasible. Hence,

transcriptomics approaches of non-model organisms as well as comparative transcriptomics studies among two or more

species often make use of cost-intensive RNAseq studies or, alternatively, by hybridizing transcripts of a query species to a

microarray of a closely related species. When analyzing these cross-species microarray expression data, differences in the

transcriptome of the query species can cause problems, such as the following: (i) lower hybridization accuracy of probes due

to mismatches or deletions, (ii) probes binding multiple transcripts of different genes, and (iii) probes binding transcripts of

non-orthologous genes. So far, methods for (i) exist, but these neglect (ii) and (iii). Here, we propose an approach for

comparative transcriptomics addressing problems (i) to (iii), which retains only transcript-specific probes binding transcripts

of orthologous genes. We apply this approach to an Arabidopsis lyrata expression data set measured on a microarray

designed for Arabidopsis thaliana, and compare it to two alternative approaches, a sequence-based approach and a genomic

DNA hybridization-based approach. We investigate the number of retained probe sets, and we validate the resulting

expression responses by qRT-PCR. We find that the proposed approach combines the benefit of sequence-based stringency

and accuracy while allowing the expression analysis of much more genes than the alternative sequence-based approach. As

an added benefit, the proposed approach requires probes to detect transcripts of orthologous genes only, which provides asuperior base for biological interpretation of the measured expression responses.

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