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Abstract

Organismal multicellularity goes along with the determination and specialization of single cells and ultimately tissue-types, which is in turn mainly dependent on the differential regulation of gene expression. To investigate the variation between specific transcriptomes, cells or even entire tissues of interest have to be isolated from the organism under study. In contrast to the inaccessible cell types of the early Arabidopsis thaliana embryos, the majority of whole-genome expression studies were carried out with total RNA from accessible root or shoot tissue. Nuclear RNA has been neglected for a long time as not being representative for transcriptomic studies, but there is accumulating evidence for the informative value of nuclear RNA. We recently described the generation, quality assessment and analysis of nuclear transcriptomic data from Arabidopsis embryos in comparison with total RNA transcriptomic data of comparable developmental stages. We used fluorescence-activated nuclear sorting (FANS) in combination with standard DNA microarrays to generate expression profiles and validated our datasets of differentially expressed candidate genes, proving the usefulness and applicability of this method for virtually any tissue type. Currently we are extending this technique to additional cell types of the early Arabidopsis embryo with a special focus on the epidermal (outer) cell layer. For this, we make use of RNA sequencing to detect even small transcriptional or RNA accumulation differences and to cover all transcripts expressed at a given time-point.