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# Genome-wide transcriptional changes and chromatin modifications associated with plant stress memory

Sani, Emanuela
(2013)
*Genome-wide transcriptional changes and chromatin modifications associated with plant stress memory.*
PhD thesis, University of Glasgow.

Full text available as:

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|  | PDF   [Download (7MB)](https://theses.gla.ac.uk/4110/1/2013saniphd.pdf) |

Printed Thesis Information: <https://eleanor.lib.gla.ac.uk/record=b2983187>

## Abstract

As sessile organisms, plants had to develop various biochemical and physiological \
mechanisms to respond and adapt to abiotic stress conditions such as salt and drought and \
thus acquire stress tolerance. A particular interesting mechanism is the so called “priming \
effect”: an application of a mild short stress to plants at an early stage of development \
appears to enable them to cope better when stressed again at mature stage. However, the \
molecular effects of salt priming have not been systematically quantified and as a \
consequence the molecular basis of priming remains unknown. \
In this study an experimental procedure was established that allowed to test whether salt \
priming of young Arabidopsis thaliana plants had an effect on plants exposed to more severe \
salt stress at a later stage of development. \
To quantify how primed and non-primed plants responded to the second salt stress, global \
changes in their transcriptional expression profiles were monitored using Affymetrix \
GeneChip ATH1 microarray. Results showed that both primed and non-primed plants \
responded to the salt treatment modulating the same set of known stress responsive genes. \
However, primed plants differentially regulated a smaller set of genes. Furthermore, the vast \
majority of the stress responsive genes showed a weaker response in primed than in nonprimed plants. These results suggested that primed plants channelled the stress response \
using only selected genes. \
The next question addressed was how primed plants could “remember” the priming \
treatment after a period of extensive growth. Several studies had indicated that \
environmental stress induces changes in the chromatin structure thereby modifying the \
accessibility of the DNA for transcription factors and other regulatory proteins. This suggested \
a link between epigenetic modification and exposure of plants to stressful conditions, where \
the chromatin status might act as an epigenetic mark that could be maintained during plant \
growth and development. To investigate this hypothesis I carried out a comparative analysis \
of the epigenetic landscapes of primed and non-primed plants combining Chromatin \
Immuno-Precipitation with Illumina sequencing (ChIP-Seq). \
Genome-wide profiles of H3K4me2, H3K4me3, H3K9me2 and H3K27me3 were generated for \
roots and shoots of plants harvested immediately after the priming treatment. Roots of \
primed plants showed indeed numerous differences in their epigenetic profiles compared to \
non-primed roots, in particular at the level of H3K27me3. Therefore, I carried out an \
additional ChIP-Seq experiment before the application of the second stress to test if the \
priming induced changes in H3K27me3 were maintained over this period of extensive growth. \
Results showed that several epigenetic differences caused by priming were still maintained. \
Finally, to elucidate the relationship between epigenetic modifications and transcriptional \
responses the ChIP-Seq profiles were coupled with genome wide transcript profiles obtained \
by RNA-seq. Results shown that in the non-steady state there was no clear correlation \
between the differences detected at the transcriptional and at the epigenetic level. The \
results identified H3K27me3 as a potential mark for salt stress memory and they call for \
future studies extending both temporal and spatial resolution of epigenetic and \
transcriptional changes after salt priming.

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| Item Type: | Thesis (PhD) |
| Qualification Level: | Doctoral |
| Subjects: | [Q Science](https://theses.gla.ac.uk/view/subjects/Q.html) > [QH Natural history](https://theses.gla.ac.uk/view/subjects/QH.html) [Q Science](https://theses.gla.ac.uk/view/subjects/Q.html) > [QH Natural history](https://theses.gla.ac.uk/view/subjects/QH.html) > [QH301 Biology](https://theses.gla.ac.uk/view/subjects/QH301.html) |
| Colleges/Schools: | [College of Medical Veterinary and Life Sciences](https://theses.gla.ac.uk/view/divisions/20000000/) > [School of Life Sciences](https://theses.gla.ac.uk/view/divisions/20100000/) |
| Supervisor's Name: | Amtmann, Dr. Anna |
| Date of Award: | 2013 |
| Depositing User: | [Emanuela Sani](https://theses.gla.ac.uk/cgi/users/home?screen=User::View&userid=5429) |
| Unique ID: | glathesis:2013-4110 |
| Copyright: | Copyright of this thesis is held by the author. |
| Date Deposited: | 28 Jun 2013 07:59 |
| Last Modified: | 28 Jun 2016 09:21 |
| URI: | <https://theses.gla.ac.uk/id/eprint/4110> |

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