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Transcriptional and post-transcriptional regulation of leaf development in Arabidopsis thaliana

Frederik Coppens UGent (2011)
abstract
Plant growth follows a strict developmental program but needs to incorporate also environmental cues to adapt to the encountered conditions. This requires a complex regulatory network to ensure an appropriate response to changing conditions. We used the first leaf pair of Arabidopsis thaliana as a model system to study the regulation of organ development. Leaf growth can be divided in subsequent phases according to the major process driving it. In a young leaf primordium cells divide continuously and cell size homeostasis is ensured by matching rates of cell expansion. Next, cell division ceases and cell expansion becomes the driving force for growth. When the leaf has attained its final size, maturity is reached. In this thesis, I studied the regulation of leaf development at two regulatory levels. At the gene level, we analyzed the function of the CYCA2 core cell cycle regulatory gene family. We also studied the function of two new proliferation specific gene families putatively involved in cell cycle regulation. On the other hand, we profiled small RNA sequences during development and linked this with the occurrence of DNA methylation. The core machinery of the cell cycle in plants has been thoroughly studied, but our knowledge on how developmental and environmental signals impinge on cell division is still limited. CYCA2s are known core cell cycle regulators, involved in G2-to-M transition. Here, we studied the functional requirement of this gene family and showed that transcriptional repression is required for specific differentiation processes. Members of the CYCA2 protein family function in vascular development and differentiation of guard cells. For the latter process, we demonstrated that FOUR LIPS and MYB88, two transcription factors involved in stomatal development, directly repress CYCA2;3 expression, thus ensuring correct guard cell differentiation. Next to known ‘core’ cell cycle regulating genes, we also selected proliferation specific genes with unknown function, assuming them to be involved in the cell division process. We focused on two small gene families: three genes with four transmembrane domains (4TMs) and two genes containing three High Mobility Group (HMG) domains (3xHMG-box). Expression analysis and localization of transcriptional fusions with a fluorescent marker confirmed for both gene families the highly proliferation-specific expression pattern. Moreover, both families are highly induced in the M-phase of the cell cycle in synchronized cell cultures. The 4TMs localize to the cell plate during mitosis and we observed defects in cell plate formax tion upon overexpression and depletion of these genes. Therefore, we hypothesize that the 4TM genes are involved in formation of the cell plate. Profiling of small RNAs (sRNAs) in plants has thusfar mainly been focused on inflorescence tissue or whole seedlings. Here, we studied sRNAs during the different phases of development. Early in development, microRNAs implicated in nutrient stress response are upregulated, suggesting that at this phase nutrient availability is limiting for growth. We showed that specifically 24-nt sRNAs increase in expression during development. This class of sRNAs is known to be involved in RNA-dependent DNA methylation (RdDM) and can thus silence both transposons and genes. In general, the expression of sRNAs matching the coding sequences of protein-coding genes is positively correlated to the mRNA expression of this gene. We specifically selected genes that do not show this correlation, which were highly enriched in two categories: targets of microRNAs and trans-acting siRNAs, which generate phased sRNAs upon cleavage, and genes for which the sRNA profile is enriched for 24-nt sRNAs. This latter category is likely regulated through RdDM as this subset of genes shows increased DNA methylation in the gene body. This suggests that sRNA regulation could play an important role in regulating the leaf developmental process not only by preserving genome integrity by repressing transposon activity but also through silencing of protein-coding genes.
Please use this url to cite or link to this publication:
author
promoter
UGent
organization
year
type
dissertation (monograph)
subject
pages
XIV, 267 pages
publisher
Ghent University. Faculty of Sciences
place of publication
Ghent, Belgium
defense location
Zwijnaarde : Technologiepark (FSVM building)
defense date
2011-01-09 16:00
language
English
UGent publication?
yes
classification
D1
additional info
dissertation consists of copyrighted material
copyright statement
I have transferred the copyright for this publication to the publisher
id
3006330
handle
http://hdl.handle.net/1854/LU-3006330
date created
2012-10-04 12:39:53
date last changed
2012-10-05 10:42:00
@phdthesis{3006330,
  abstract     = {Plant growth follows a strict developmental program but needs to incorporate also environmental cues to adapt to the encountered conditions. This requires a complex regulatory network to ensure an appropriate response to changing conditions. We used the first leaf pair of Arabidopsis thaliana as a model system to study the regulation of organ development. Leaf growth can be divided in subsequent phases according to the major process driving it. In a young leaf primordium cells divide continuously and cell size homeostasis is ensured by matching rates of cell expansion. Next, cell division ceases and cell expansion becomes the driving force for growth. When the leaf has attained its final size, maturity is reached. In this thesis, I studied the regulation of leaf development at two regulatory levels. At the gene level, we analyzed the function of the CYCA2 core cell cycle regulatory gene family. We also studied the function of two new proliferation specific gene families putatively involved in cell cycle regulation. On the other hand, we profiled small RNA sequences during development and linked this with the occurrence of DNA methylation. The core machinery of the cell cycle in plants has been thoroughly studied, but our knowledge on how developmental and environmental signals impinge on cell division is still limited. CYCA2s are known core cell cycle regulators, involved in G2-to-M transition. Here, we studied the functional requirement of this gene family and showed that transcriptional repression is required for specific differentiation processes. Members of the CYCA2 protein family function in vascular development and differentiation of guard cells. For the latter process, we demonstrated that FOUR LIPS and MYB88, two transcription factors involved in stomatal development, directly repress CYCA2;3 expression, thus ensuring correct guard cell differentiation. Next to known {\textquoteleft}core{\textquoteright} cell cycle regulating genes, we also selected proliferation specific genes with unknown function, assuming them to be involved in the cell division process. We focused on two small gene families: three genes with four transmembrane domains (4TMs) and two genes containing three High Mobility Group (HMG) domains (3xHMG-box). Expression analysis and localization of transcriptional fusions with a fluorescent marker confirmed for both gene families the highly proliferation-specific expression pattern. Moreover, both families are highly induced in the M-phase of the cell cycle in synchronized cell cultures. The 4TMs localize to the cell plate during mitosis and we observed defects in cell plate formax tion upon overexpression and depletion of these genes. Therefore, we hypothesize that the 4TM genes are involved in formation of the cell plate. Profiling of small RNAs (sRNAs) in plants has thusfar mainly been focused on inflorescence tissue or whole seedlings. Here, we studied sRNAs during the different phases of development. Early in development, microRNAs implicated in nutrient stress response are upregulated, suggesting that at this phase nutrient availability is limiting for growth. We showed that specifically 24-nt sRNAs increase in expression during development. This class of sRNAs is known to be involved in RNA-dependent DNA methylation (RdDM) and can thus silence both transposons and genes. In general, the expression of sRNAs matching the coding sequences of protein-coding genes is positively correlated to the mRNA expression of this gene. We specifically selected genes that do not show this correlation, which were highly enriched in two categories: targets of microRNAs and trans-acting siRNAs, which generate phased sRNAs upon cleavage, and genes for which the sRNA profile is enriched for 24-nt sRNAs. This latter category is likely regulated through RdDM as this subset of genes shows increased DNA methylation in the gene body. This suggests that sRNA regulation could play an important role in regulating the leaf developmental process not only by preserving genome integrity by repressing transposon activity but also through silencing of protein-coding genes.},
  author       = {Coppens, Frederik},
  language     = {eng},
  pages        = {XIV, 267},
  publisher    = {Ghent University. Faculty of Sciences},
  school       = {Ghent University},
  title        = {Transcriptional and post-transcriptional regulation of leaf development in Arabidopsis thaliana},
  year         = {2011},
}

Chicago
Coppens, Frederik. 2011. “Transcriptional and Post-transcriptional Regulation of Leaf Development in Arabidopsis Thaliana”. Ghent, Belgium: Ghent University. Faculty of Sciences.
APA
Coppens, F. (2011). Transcriptional and post-transcriptional regulation of leaf development in Arabidopsis thaliana. Ghent University. Faculty of Sciences, Ghent, Belgium.
Vancouver
1.
Coppens F. Transcriptional and post-transcriptional regulation of leaf development in Arabidopsis thaliana. [Ghent, Belgium]: Ghent University. Faculty of Sciences; 2011.
MLA
Coppens, Frederik. “Transcriptional and Post-transcriptional Regulation of Leaf Development in Arabidopsis Thaliana.” 2011 : n. pag. Print.