Epigenetic control of root and nodule development : the role of plant-specific histone deacetylases and LHP1 in root cell reprogramming

S. Schilderink

Research output: Thesisinternal PhD, WU


In plants, unlike in animals, most organs develop post embryonically. These organs originate from clusters of undifferentiated dividing cells that form so-called meristems. Differentiated cells can be re-activated to enter the cell cycle and to ultimately give rise to new meristems. These differentiated cells reprogram to become pluripotent cells that are able to give rise to all cell types of the new organ. Examples are the formation of lateral roots from pericycle cells in Arabidopsis and the formation of root nodules from cortical cells in Medicago. In the latter organ rhizobia bacteria in symbiosis with Medicago fix atmospheric nitrogen. The reprogramming of differentiated cells is associated with large changes in gene expression. In this thesis the role of two chromatin modifiers in these reprogramming events is studied; the plant-specific histone deacetylases (HDTs) and LIKE HETEROCHROMATIN PROTEIN I (LHP1).

In Chapter 2 we show that in Arabidopsis during lateral root formation all four members of the AtHDT family are strongly induced in lateral root founder cells already before the first divisions occur. Furthermore, AtHDT1 and AtHDT2 were shown to be necessary for maintenance of the root stem cell niche and meristem.

Nodules are formed from fully differentiated root cortical cells. The reprogramming of cortical cells during the formation of nodules is unique to legumes, as cortical cells in other plants are not able to change their cell fate. In Medicago we characterized 3 HDTs and showed that these MtHDTs are involved in cell fate changes and are essential for the formation of nodules (Chapter 3). These MtHDTs are involved in early steps of reprogramming of the cortical cells in nodule initiation, since RNAi knock-down expression of all 3 MtHDTs simultaneously, strongly reduced nodule formation. Microscopic analysis of the small nodules that were still formed revealed these had a normal wt-like proximal part and a disturbed distal part.

To explain this hybrid phenotype we created a fate map of nodule development by analyzing early stages of nodule formation (Chapter 4). This analysis revealed that the proximal part of nodules contain about 8 layers of fully differentiated cells that directly originate from the nodule primordium, which is derived from the two innermost cortical layers. The nodule meristem originates from the middle cortical layer and further growth of the nodule depends of differentiation and infection of cells originating from this meristem. At the disturbed distal part of the RNAi hybrid nodules, meristem-derived cells do not properly differentiate and are not infected with rhizobia indicating a disturbed meristem function.

The second chromatin modifier we studied is LHP1, which is known to be involved in several developmental processes in plants, possibly as part of the plant analog of Polycomb Repressive Complex 1 (PRC1). We characterized the Medicago LHP1 homolog (Chapter 5) and showed that LHP1 forms euchromatic complexes that most likely regulate gene expression. MtLHP1 might be involved in proper differentiation of meristem-derived cells in the nodule since knock-down of MtLHP1 resulted in a similar phenotype as seen in MtHDT knock-down nodules.

Our findings provide new insights on the role of the chromatin modifiers HDTs and LHP1 in reprogramming events in Arabidopsis and Medicago organ development.

Original languageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Wageningen University
  • Bisseling, Ton, Promotor
  • Kulikova, Olga, Co-promotor
  • Wellink, Joan, Co-promotor
Award date11 Dec 2012
Place of PublicationS.l.
Print ISBNs9789461734259
Publication statusPublished - 11 Dec 2012


  • cells
  • epigenetics
  • roots
  • nodules
  • plant development
  • apical meristems
  • medicago
  • arabidopsis
  • root nodules
  • histones


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