Data driven approach to auxin transcriptomic response of Arabidopsis thaliana root cells

da | Giu 4, 2018 | Biologia Molecolare

Auxin is a phytohormone essential for the plant survival and its development. Indeed mutants defective in auxin production are not viable. It regulates processes as growth, cell division, tropisms, fruit development, apical dominance, buds tissue morphogenesis and adventitious root elongation. [1] N. A. Omelyanchuk et al. treated root tissue of Arabidopsis thaliana with a 1µM auxin solution for 6 hours to induce the transcriptomic response in root cells [2].
They analysed the transcriptomic pattern with RNAseq and ePCR. The  genome of Arabidopsis thaliana is well by all plant scientists thanks to an important article published in Nature in 2000 [3].  The Arabidopsis thaliana genome  let the author of this work to study, using bioinformatics tools, the specific enrichment of gene transcripts. By Gene Ontology (GO) they  obtained a

Figure 1 AUXIN INDUCED TRANSCRIPTOMIC RESPONSE

bigger and comprehensive map of auxin-dependent  upregulated and downregulated functions. Furthermore, following the cellular component ontology they described the auxin spatial modulation response inside the cell. The transcription of each gene group is finely regulated in a so-called fold-change-specific manner. By these analyses, they underlined three bottlenecks in the gene expression pathways under  auxin treatment. These bottlenecks (histone modification, RNA methylation and translation) represent different steps in cell metabolism, which are finely regulated by this hormone. Studying the 5’-upstream regions of the same fold-change-specific expression genes, they identified specific regulative hexamers sequences, called cis-regulatory elements that modulate, through yet unknown factors, gene expression in the same fold-change-specific manner.

As shown in Figure 1, thanks to high throughput data crossed with GO terms is possible to have a complete profile map of the metabolic behaviour of the cell responding to auxin and the amplitude of down- or up-regulation of the  genes. Furthermore, the transcriptional map allows visualizing which processes are regulated and the amplitude of cellular response. The fold-change-specific expression information of some genes, correlated with specific cis-regulatory elements (Figure 2), could suggest the promoter strength when induced by auxin.

Conclusions. The experiments shown in this report are relatively  simple . The strength of their approach lies in the bioinformatics and in the analysis in the aftermath that could allow scientists to a more comprehensive knowledge of the transcriptomic response. In silico analysis is fundamental to approach data produced form experimental science and allow scientists to extract much information depending how, the data, is treated.

Figure 2 CIS-REGULATORY ELEMENTS

A weak point of the work is that in this case root cells have been used as a population without type cell distinctions. However, this analysis, made on animal or prokaryote cells, could help to better understand specific cell response patterns and let us to identify new genetic regulatory elements with specific response amplitude under exogenous stimuli.   The new acquired information could be used to design new plasmid promoters and find pharmacological targets to inhibit specific pathways in abnormal cell behaviour.

References

  1. L. Taiz, E. Zeiger. Plant Physiology, 5th edition, Sinauer Associates Inc. Ch. 19, pg. 545-573. ISBN-10: 1605352551.
  2. N.A. Omelyanchuk, D.S. Wiebe, D.D. Novikova, V.G. Levitsky, N. Klimova, V. Gorelova, C. Weinholdt, G.V: Vasiliev, E.V. Zemlyanskaya, N.A. Kolchanov, A.V. Kochetov, I. Grosse & V.V. Mironova. Auxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots. Scientific Reports | 7: 2489 | DOI:10.1038/s41598-017-02476-8, pg. 1-11, 2017
  3. The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. Vol 408, december 2000.

Carlotta Brino

Master Industrial Biotechnology student

Giorgio Gabrielli

Master Industrial Biotechnology student