terclim by ICS banner
IVES 9 IVES Conference Series 9 From protein-centered to gene-centered approaches to investigate DNA-protein interactions in grapevine

From protein-centered to gene-centered approaches to investigate DNA-protein interactions in grapevine

Abstract

DNA-binding proteins play a pivotal role in critical cellular processes such as DNA replication, transcription, recombination, repair, and other essential activities. Consequently, investigating the interactions between DNA and proteins is of paramount importance to gain insights into these fundamental cellular mechanisms. Several methodologies have been devised to uncover DNA-protein interactions, which can be broadly categorized into two approaches. The “protein-centered” approach focuses on identifying the DNA sequences bound by a specific transcription factor or a set of TFs. Techniques falling within this category include chromatin immunoprecipitation, and protein-binding microarrays. The “gene-centered” approach entails using one or more DNA sequences as bait to explore the TFs that bind to these specific DNA elements. Methods belonging to this approach encompass yeast one-hybrid (Y1H), PICh, and Reverse ChIP. Both methodologies offer distinct advantages and face limitations, largely stemming from challenges related to complexity, efficiency, and specificity. With the emergence of next-generation sequencing (NGS) protocols and the CRISPR/Cas system, new avenues for investigating trans-cis interactions in organisms have opened. In our research focusing on grapevines, we discuss advancements in both protein- and gene-centered approaches. Firstly, we present the implementation of a DNA Affinity Purification (DAP-seq) protocol in grapevines to explore the cistrome associated with various TFs from the WRKY and MYB families. Secondly, we address the challenge of developing an innovative gene-centered approach utilizing a CRISPR/Cas system for in-situ purification of regulatory elements. This approach aims not only to identify proteins associated with specific genomic regions but also to elucidate long-range DNA interactions.

DOI:

Publication date: June 13, 2024

Issue: Open GPB 2024

Type: Article

Authors

Aurélien Devillars1, Gabriele Magon1, Silvia Farinati1, Valerio Licursi2, Gabriele Magris3, Sara Zenoni3, Bhanu Prakash Potlapalli4, Andreas Houben4, Alessandro Vannozzi1*

1 Department of Agriculture Food Natural Resources Animals and Environment, University of Padova, Agripolis, Legnaro, Italy
2 Institute of Molecular Biology and Pathology, CNR c/o Department of Biology and Biotechnologies, Sapienza University of Rome, Via degli Apuli, 4 – 00185 Rome
3 University of Udine, via Delle Scienze 206
4 Department of Biotechnologies, University of Verona, Strada le Grazie 1, Verona (VR), Italy
4 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany

Contact the author*

Keywords

DAP-seq, Grapevine, Gene Regulation, CRISPR-Cas9, Protoplasts

Tags

IVES Conference Series | Open GPB | Open GPB 2024

Citation

Related articles…

Vineyard nutrient budget and sampling protocols

Vineyard nutrient management is crucial for reaching production-specific quality standards, yet timely evaluation of nutrient status remains challenging. The existing sampling protocol of collecting vine tissue (leaves and/or petioles) at bloom or veraison is time-consuming. Additionally, this sampling practice is too late for in-season fertilizer applications (e.g. N is applied well before bloom). Therefore alternative early-season protocols are necessary to predict the vine nutrient demand for the upcoming season. The main goals of this project are to 1) optimize existing tissue sampling protocols; 2) determine the amount of nutrients removed at the end of the growing season.

Oospore germination dynamics and disease forecasting model for a precision management of downy mildew 

Downy mildew, caused by Plasmopara viticola, is the most economically impactful disease affecting grapevines. This polycyclic pathogen triggers both primary and secondary infection cycles, resulting in significant yield losses when effective disease control measures are lacking. Over the winter, the pathogen survives by forming resting structures, the oospores, derived from sexual reproduction, which produce the inoculum for primary infections. To optimize grapevine downy mildew control and obtain the desired levels of production while minimizing chemical inputs, it is crucial to optimize the timeframe for fungicide application. Disease forecasting models are useful to identify the infection risk.

Anthocyanins in tannat wines rapidly evolve toward unidentified red-coloured pigments

To assess the relationship between the reported low-stability of Tannat colour during wine storage and its pigment composition and evolution

Application of regenerative agriculture to viticulture: The REVINE project

Conventional viticulture improved the quality of production, but the economic costs can be unsustainable. Today, producers need to consider consumers’ demands for healthy, eco-friendly products. Institutions promote sustainable agriculture, with regenerative agriculture being the latest generation of methodologies focused on recovering losses and ensuring future sustainability. The revine project studies regenerative agricultural technology applied in mediterranean countries to provide precise indications for soil processing and effective vineyard treatments.

Arsenic in berries and its correlation with natural soil content: experience in Trentino (Italy)

l lavoro presenta l’evoluzione dei contenuti di arsenico nelle uve durante lo sviluppo e la maturazione, e la sua distribuzione nell’acino; verifica inoltre la relazione tra i contenuti di As nelle uve