Identification of pathways directly regulated by SHORT VEGETATIVE PHASE during vegetative and reproductive development in Arabidopsis.

Veronica Gregis,Federico Zambelli,Sara Simonini,Rosalinda F Guerra,Martin M Kater,Julieta L Mateos,Alice Sessa,Stefano Torti,George Coupland,Paul E Grini,Fernando Andrés,Lucia Colombo,Katrine N Bjerkan,Giulio Pavesi,Gian Marco Prazzoli

doi:10.1186/gb-2013-14-6-r56

Abstract

BackgroundMADS-domain transcription factors play important roles during plant development. The Arabidopsis MADS-box gene SHORT VEGETATIVE PHASE (SVP) is a key regulator of two developmental phases. It functions as a repressor of the floral transition during the vegetative phase and later it contributes to the specification of floral meristems. How these distinct activities are conferred by a single transcription factor is unclear, but interactions with other MADS domain proteins which specify binding to different genomic regions is likely one mechanism.ResultsTo compare the genome-wide DNA binding profile of SVP during vegetative and reproductive development we performed ChIP-seq analyses. These ChIP-seq data were combined with tiling array expression analysis, induction experiments and qRT-PCR to identify biologically relevant binding sites. In addition, we compared genome-wide target genes of SVP with those published for the MADS domain transcription factors FLC and AP1, which interact with SVP during the vegetative and reproductive phases, respectively.ConclusionsOur analyses resulted in the identification of pathways that are regulated by SVP including those controlling meristem development during vegetative growth and flower development whereas floral transition pathways and hormonal signaling were regulated predominantly during the vegetative phase. Thus, SVP regulates many developmental pathways, some of which are common to both of its developmental roles whereas others are specific to only one of them.

Highlights

MADS-domain transcription factors play important roles during plant development
Genome-wide mapping of SHORT VEGETATIVE PHASE (SVP) binding sites during vegetative and reproductive development For genome-wide identification of the in-vivo binding sites of the SVP MADS-box transcription factor chromatin immunoprecipitation (ChIP) was performed followed by single end-read sequencing with the Solexa/Illumina GA platform
Since SVP plays important roles during two distinct non-overlapping phases of development, namely the floral transition [8] and the early stages of flower development [20,24,25,39], studying the genome-wide binding sites of SVP provides an opportunity to compare the pathways directly regulated by SVP during these two developmental phases

Summary

Introduction

The Arabidopsis MADS-box gene SHORT VEGETATIVE PHASE (SVP) is a key regulator of two developmental phases. It functions as a repressor of the floral transition during the vegetative phase and later it contributes to the specification of floral meristems. How these distinct activities are conferred by a single transcription factor is unclear, but interactions with other MADS domain proteins which specify binding to different genomic regions is likely one mechanism. In plants organs are formed post-embryonically from populations of undifferentiated cells called meristems. The reprogramming of meristems is regulated by a complex gene regulatory network in which transcription factors represent important key players

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Discussion

Conclusion