Role of Polycomb repressive complex 2 (PRC2) during early seedling establishment in Arabidopsis thaliana

Naseem SAMO

Doctoral thesis

Role of Polycomb repression during seedling establishment in \kur{Arabidopsis thaliana}

Abstract:

Annotation The Polycomb Repressive Complex 2 (PRC2) is an epigenetic regulator that is highly conserved across eukaryotes. It catalyses the trimethylation of lysine 27 on histone H3 (H3K27me3), a well-known chromatin mark associated with gene repression. PRC2 plays a crucial role in regulating developmental transitions in plants, including the seed-to-seedling transition, one of the most important developmental transitions in the plant life cycle. The seed-to-seedling transition involves both a developmental and metabolic switch. Seed germination and early seedling establishment is a heterotrophic process that relies exclusively on the catabolism of reverse seed storage until the emerging seedling switches to photoautotrophy and initiates vegetative growth. The transition to the vegetative state involves an extensive reprogramming of gene expression, which is accompanied by a redistribution of various histone modifications and a reorganisation of chromatin. It is known that PRC2 is involved in the transition from seed to seedling. However, it is not yet known how the activity of PRC2 and the downstream reprogramming of H3K27me3 during seedling development alters gene expression to achieve a stable developmental and metabolic transition in the developing seedling. In this study, I analysed the global reprogramming of H3K27me3 and the associated changes in gene expression during the transition from the heterotrophic to the photoautotrophic state in the developing seedling. Subsequently, the global reprogramming of H3K27me3 was linked to the dysregulated pathways in PRC2 mutants (clf29/- swn3/-) to understand how PRC2 activity influences the developmental and metabolic defects observed in these mutants. Our analysis revealed that the transition from the heterotrophic to the photoautotrophic state in emerging seedling relies on concerted repression of several key metabolic pathway genes, which are upregulated in plants where functional PRC2 is missing. To investigate whether repression of these pathways may condition the entry of the developing seedling into the vegetative phase, I used a reverse genetic approach to select candidate genes and generate CRISPR/Cas9 knockout plants in the PRC2-depleted background. Although analyses of CRISPR mutant lines are still ongoing, our first results from CRISPR Ccss icl have shown that PRC2-mediated repression of key metabolic genes promotes the vegetative transition in developing seedling. Additionally, to dissect the individual contributions of PRC2 catalytic subunits during the seed-to-seedling transition, I generated hypomorphic CLF and SWN mutant lines. These mutant lines are valuable tools to further explore the role of PRC2 catalytic subunits in regulating the seed-to-seedling transition.

Abstract:

Annotation The Polycomb Repressive Complex 2 (PRC2) is an epigenetic regulator that is highly conserved across eukaryotes. It catalyses the trimethylation of lysine 27 on histone H3 (H3K27me3), a well-known chromatin mark associated with gene repression. PRC2 plays a crucial role in regulating developmental transitions in plants, including the seed-to-seedling transition, one of the most important developmental transitions in the plant life cycle. The seed-to-seedling transition involves both a developmental and metabolic switch. Seed germination and early seedling establishment is a heterotrophic process that relies exclusively on the catabolism of reverse seed storage until the emerging seedling switches to photoautotrophy and initiates vegetative growth. The transition to the vegetative state involves an extensive reprogramming of gene expression, which is accompanied by a redistribution of various histone modifications and a reorganisation of chromatin. It is known that PRC2 is involved in the transition from seed to seedling. However, it is not yet known how the activity of PRC2 and the downstream reprogramming of H3K27me3 during seedling development alters gene expression to achieve a stable developmental and metabolic transition in the developing seedling. In this study, I analysed the global reprogramming of H3K27me3 and the associated changes in gene expression during the transition from the heterotrophic to the photoautotrophic state in the developing seedling. Subsequently, the global reprogramming of H3K27me3 was linked to the dysregulated pathways in PRC2 mutants (clf29/- swn3/-) to understand how PRC2 activity influences the developmental and metabolic defects observed in these mutants. Our analysis revealed that the transition from the heterotrophic to the photoautotrophic state in emerging seedling relies on concerted repression of several key metabolic pathway genes, which are upregulated in plants where functional PRC2 is missing. To investigate whether repression of these pathways may condition the entry of the developing seedling into the vegetative phase, I used a reverse genetic approach to select candidate genes and generate CRISPR/Cas9 knockout plants in the PRC2-depleted background. Although analyses of CRISPR mutant lines are still ongoing, our first results from CRISPR Ccss icl have shown that PRC2-mediated repression of key metabolic genes promotes the vegetative transition in developing seedling. Additionally, to dissect the individual contributions of PRC2 catalytic subunits during the seed-to-seedling transition, I generated hypomorphic CLF and SWN mutant lines. These mutant lines are valuable tools to further explore the role of PRC2 catalytic subunits in regulating the seed-to-seedling transition.

Language used: English

Date on which the thesis was submitted / produced: 14. 1. 2025

Thesis defence

• Supervisor: Mgr. Iva Mozgová, Ph.D.

UNIVERSITY OF SOUTH BOHEMIA IN ČESKÉ BUDĚJOVICE

Faculty of Science

Doctoral programme / field:
Integrative biology / Integrative biology