Conserved Epigenetic Mechanisms Could Play a Key Role in Regulation of Photosynthesis and Development-Related Genes during Needle Development of Pinus radiata.

Luis Valledor,Mónica Meijón,Mónica Escandón,Jesús Pascual,María Jesús Cañal

doi:10.1371/journal.pone.0126405

Abstract

Needle maturation is a complex process that involves cell growth, differentiation and tissue remodelling towards the acquisition of full physiological competence. Leaf induction mechanisms are well known; however, those underlying the acquisition of physiological competence are still poorly understood, especially in conifers. We studied the specific epigenetic regulation of genes defining organ function (PrRBCS and PrRBCA) and competence and stress response (PrCSDP2 and PrSHMT4) during three stages of needle development and one de-differentiated control. Gene-specific changes in DNA methylation and histone were analysed by bisulfite sequencing and chromatin immunoprecipitation (ChIP). The expression of PrRBCA and PrRBCS increased during needle maturation and was associated with the progressive loss of H3K9me3, H3K27me3 and the increase in AcH4. The maturation-related silencing of PrSHMT4 was correlated with increased H3K9me3 levels, and the repression of PrCSDP2, to the interplay between AcH4, H3K27me3, H3K9me3 and specific DNA methylation. The employ of HAT and HDAC inhibitors led to a further determination of the role of histone acetylation in the regulation of our target genes. The integration of these results with high-throughput analyses in Arabidopsis thaliana and Populus trichocarpa suggests that the specific epigenetic mechanisms that regulate photosynthetic genes are conserved between the analysed species.

Highlights

Leaf development is a complex process that involves many cell and tissue differentiation and remodelling processes [1]
We selected two genes closely related to leaf maturation; PrRBCA, PrRBCS, and two genes related to immature tissues PrSHMT4 and PrCSDP2, for which partial sequences were available
The expression levels of PrRBCA, PrRBCS, PrCSDP2, and PrSHMT4 can be used to distinguish between needle maturation stages

Summary

Introduction

Leaf development is a complex process that involves many cell and tissue differentiation and remodelling processes [1]. Efforts towards the characterisation of the epigenetic role of tree cell plasticity and in growth and development processes have been focused on global epigenetic dynamics for defining phase change, maturation stage, bud set and burst, and production hallmarks (see Bräutigam et al [21] for a review), with no record to our knowledge, of any study dealing with gene-specific epigenetic dynamics during leaf maturation To fill this gap we have studied four genes that had demonstrated a differential accumulation of its products during needle development [12] and have a major function in needle. Development and plant growth covering photosynthesis (RUBISCO ACTIVASE, PrRBCA; RUBISCO SMALL SUBUNIT, PrRBCS), one carbon metabolism (SERINE HYDROXYMETHYL TRANSFERASE 4, PrSHMT4) [35], and developmental control and stress response (COLD SHOCK DOMAIN PROTEIN 2, PrCSDP2) [36] We cloned these genes and investigated their transcription levels in three needle developmental stages and a de-differentiated tissue (white, non photosynthetic, calli derived from needles which is showing active growth) used as control. These results provide new insights over how the epigenetic mechanisms regulate key metabolic pathways during needle maturation

Materials and Methods

Results

Discussion