MADS box transcription factor SHORT VEGETATIVE PHASE, understanding the molecular mechanism and involvement in sense and antisense transcript regulation

This research project will focus on the development of inflorescence and flower meristems. MADS-domain transcription factors (TFs) are key regulators of these processes and the project will especially focus on how these TFs control the regulatory network leading to reproductive meristem formation in the model plant Arabidopsis thaliana. An excellent starting point for this research project is the large amount of information and tools that we and other groups have already generated for one of the key players in both vegetative and reproductive meristem development: the MADS-domain TF SHORT VEGETATIVE PHASE (SVP). SVP acts as a repressor of the floral transition in the vegetative meristem and later as a key factor floral meristem identity factor. This project will study two important interconnected research lines that are related to the regulatory mechanisms that underlay reproductive meristem formation: (i) the regulatory function of SVP through the control of long non-coding RNAs, and (ii) the mechanistic molecular aspects of target gene regulation by SVP and its interacting partners. Recently, we have analysed the genome wide targets of SVP in floral meristems by a ChIP-seq approach (Gregis et al., 2013). Interestingly, this analysis showed that SVP (but also some its interacting partners, e.g. the MADS-domain factor AP1) bind a subset of target genes in both the 5¿ and 3¿ regions. Interestingly, for many of these genes noncoding sense or antisense RNAs have been annotated. Therefore, this binding pattern indicates the involvement of SVP (and interacting MADS TFs) in the regulation of noncoding RNAs, suggesting a completely unexplored and conserved mechanism by which MADS domain TFs could control the regulation of their targets. Non-coding RNAs are involved in transcriptional interference, genomic imprinting, X inactivation, RNA editing, translational regulation, RNA export, DNA methylation, histone modifications, and so on. Antisense transcripts regulate gene expression through direct interaction with the sense transcripts or indirect interaction with other targets, such as DNA methyltransferases, histone acetylases and deacetylases. Through formation of sense¿antisense duplex structures, antisense RNA exert a widespread impact on conventional gene expression at the mRNA and/or protein level and regulate sense transcripts in a concordant or discordant manner. The project will analyse this exciting feature in detail and will explore the biological role of SVP in the regulation of non-coding RNA expression. The project will also focus on the molecular mechanisms by which SVP and its interaction partners control their targets. MADS-domain factors have been studied deeply from a genetic point of view and are recognised as key controllers of development in plants. However, little is known about the molecular aspects (DNA binding mechanisms, recruitment of complex members etc.). We have recently characterized the function of the complex composed of SVP and BASIC PENTACYSTEINE factors (BPCs) (Simonini et al., 2012). BPCs are transcription factors with affinity to GA-repeated sequences. We showed that BPC binding sites are important for BPC recruitment to the DNA but also for binding of SVP to nearby MADS-domain binding sites (CArG boxes). Within the frame of this project we will analyse the importance of the interaction between these transcription factors in more detail and provide deep mechanistic insights about complex formation and recruitment of the complex to the DNA in a context of a changing histone-landscape.