Project leader: GIULIO PAVESI (giulio.pavesi@unimi.it)

Project leader: GIULIO PAVESI (giulio.pavesi@unimi.it)

Location: Department of Biosciences, University of Milan, Italy

RESEARCH PROJECT SUMMARY

The modern “high-throughput” or “next-generation” sequencing techniques have opened new avenues in every aspect of genetics and genomics research. In particular, when applied downstream of experiments like chromatin or riboprotein immunoprecipitation (ChIP-Seq, RIP-Seq, respectively), they allow researchers to study at a unprecedented level of detail the mechanisms of regulation of transcription (epigenetic mechanisms or interactions between transcription factors and DNA) and translation (RNA binding proteins – RNA interactions). These experiments have become quite affordable in the last few years, and this fact has yielded an explosion in the data produced, where bioinformatics analysis plays a key role in order to obtain significant results.

Our research group has been and is currently involved in different studies in co-operation with other groups in this field, that produce data related to histone modifications, transcription factors and RNA binding proteins in different organisms (see for example [1,2]). In this framework, our task concerns the analysis of the data, either through the fine tuning and adaptation of existing methods, but in particular with the development of novel tools [3,4]. Thus, the goal of the project will be twofold: on one hand it will involve more basic research on the development and testing of novel bioinformatic methods, for which the state of the art is still far from having reached standard analysis procedures, and on the other their application to real analyses and case studies. The PhD student will thus perform both the analyses, by using tools developed by us or by others to be applied to the different case studies, but more importantly will be involved in the development and testing of novel methods for different steps of the typical analysis pipelines for ChIP-Seq data, and their implementation in suitable software tools.

1: Fleming JD, Pavesi G, Benatti P, Imbriano C, Mantovani R, Struhl K. NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors. Genome Res. 2013 Aug;23(8):1195-209.

2: Mihailovic M, Wurth L, Zambelli F, Abaza I, Militti C, Mancuso FM, Roma G, Pavesi G, Gebauer F. Widespread generation of alternative UTRs contributes to sex-specific RNA binding by UNR. RNA. 2012 Jan;18(1):53-64.

3: Zambelli F, Pesole G, Pavesi G. PscanChIP: Finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments. Nucleic Acids Res. 2013 Jul;41:W535-43.

4: Zambelli F, Prazzoli GM, Pesole G, Pavesi G. Cscan: finding common regulators of a set of genes by using a collection of genome-wide ChIP-seq datasets. Nucleic Acids Res. 2012 Jul;40W510-5.

Project leader: PAOLO PESARESI (paolo.pesaresi@unimi.it)

Location: Department of Biosciences, University of Milan, Italy

RESEARCH PROJECT SUMMARY

Reproductive success in plants is dependent on the timing of the switch from vegetative to reproductive phase coinciding with optimal environmental and developmental conditions. This is a key step that dramatically influences plant productivity, one of most important aspects in agriculture. Plants have evolved an elaborate regulatory network that integrates endogenous and environmental signal to ensure that flowering start when conditions are most favourable. During the last two decades, functional genomics studies have revealed the existence of a complex network of genetic interactions responsible of integrating the different types of signals, both internal and external that plant receives and that define when plants can enter into the reproductive phase (Liu et al., 2009). However, the molecular characterization of the floral transition process is far from being completed, therefore new studies flanked by new research methods are needed to identify and characterize the proteins and protein complexes that play key roles in the transition to the reproductive phase (Jang et al., 2009).

One of key player in floral transition is SVP (Short Vegetative Phase), a MADS-Box transcritpion factor studied for a long time at genetic level. It has been reported (Liu et al., 2007) that the ectopic expression of this transcription factor causes late flowering, whereas plants lacking SVP flowers earlier than WT. In addition, based on data obtained via yeast-2-hybrid assay (Gregis et al., 2009), it appears that SVP regulates floral transition through the association to a multi-subunit protein complex, however evidences of such a protein complex have not been provided, yet, in planta. During the last two years, in our laboratory we have developed a protocol that allows to coimmunoprecipitate nuclear protein complexes in their native state, followed by Mass-spectrometry analyses to identify the different immune-precipitated subunits. Such a strategy has been applied to SVP, and the obtained data indicate that SVP interacts with a large set of enzymes involved in acetylation, deacetylations and metylation of histones (Cohen et al., 2009; Berr et al., 2010). Based on these findings, and in agreement with recent publications in this field (Smaczniak et al., 2012), it appears that SVP controls flowering time in Arabidopsis by chromatin remodeling-dependent expression of key genes involved in floral transition.

The aim of this project is to validate the interaction of SVP with such enzymes and to dissect their direct involvement in flowering time determination through functional studies in the model species Arabidopsis thaliana.

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