Genome-wide transcriptional responses to shade: Linking shade avoidance and auxin


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PhD thesis: a PhD thesis.
Genome-wide transcriptional responses to shade: Linking shade avoidance and auxin
Kohnen M. V.
Fankhauser C.
Xenarios I.
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Université de Lausanne, Faculté de biologie et médecine
Center for Integrative Genomics Genopode Building University of Lausanne CH-1015 Lausanne, Switzerland
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Plants have the ability to use the composition of incident light as a cue to adapt development
and growth to their environment. Arabidopsis thaliana as well as many crops are best adapted
to sunny habitats. When subjected to shade, these plants exhibit a variety of physiological
responses collectively called shade avoidance syndrome (SAS). It includes increased growth of
hypocotyl and petioles, decreased growth rate of cotyledons and reduced branching and crop
These responses are mainly mediated by phytochrome photoreceptors, which exist either in
an active, far-red light (FR) absorbing or an inactive, red light (R) absorbing isoform. In direct
sunlight, the R to FR light (R/FR) ratio is high and converts the phytochromes into their
physiologically active state. The phytochromes interact with downstream transcription factors
such as PHYTOCHROME INTERACTING FACTOR (PIF), which are subsequently degraded.
Light filtered through a canopy is strongly depleted in R, which result in a low R/FR ratio
and renders the phytochromes inactive. Protein levels of downstream transcription factors are
stabilized, which initiates the expression of shade-induced genes such as HFR1, PIL1 or ATHB-2.
In my thesis, I investigated transcriptional responses mediated by the SAS in whole Arabidopsis
seedlings. Using microarray and chromatin immunoprecipitation data, we identified genome-wide
PIF4 and PIF5 dependent shade regulated gene as well as putative direct target genes of PIF5.
This revealed evidence for a direct regulatory link between phytochrome signaling and the growth
promoting phytohormone auxin (IAA) at the level of biosynthesis, transport and signaling.
Subsequently, it was shown, that free-IAA levels are upregulated in response to shade. It
is assumed that shade-induced auxin production takes predominantly place in cotyledons of
seedlings. This implies, that IAA is subsequently transported basipetally to the hypocotyl and
enhances elongation growth. The importance of auxin transport for growth responses has been
established by chemical and genetic approaches.
To gain a better understanding of spatio-temporal transcriptional regulation of shade-induce
auxin, I generated in a second project, an organ specific high throughput data focusing on cotyledon and hypocotyl of young Arabidopsis seedlings. Interestingly, both organs show an opposite
growth regulation by shade. I first investigated the spatio-transcriptional regulation of auxin re-
sponsive gene, in order to determine how broad gene expression pattern can be explained by the
hypothesized movement of auxin from cotyledons to hypocotyls in shade. The analysis suggests,
that several genes are indeed regulated according to our prediction and others are regulated in a
more complex manner. In addition, analysis of gene families of auxin biosynthetic and transport
components, lead to the identification of essential family members for shade-induced growth re-
sponses, which were subsequently experimentally confirmed. Finally, the analysis of expression
pattern identified several candidate genes, which possibly explain aspects of the opposite growth
response of the different organs.
Arabidopsis, shade, shade avoidance, neighbor detection, phytochrome interacting factor, PIF4, PIF5, ChIP sequencing, RNA sequencing, auxin, DNA binding motif
Create date
09/03/2015 15:19
Last modification date
20/08/2019 14:30
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