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…

Analyse et modélisation des transferts thermiques dans un sol de vignoble. Effets des techniques culturales

Natural factors such as the environment in which the vine is grown play an important role in the quality of the wine. If you want to produce a good wine, it is indeed essential to produce quality grapes. To do this, we must enhance and optimize the terroir effect which, for the moment, plays a role that is not very well known. It is therefore essential, for example, to have scientifically established and well quantifiable relationships in order to have the system of areas of controlled origin accepted. R. Morlat (1989) and G. Seguin (1970) have already carried out studies on the role of certain soil factors on grape quality. In particular, they showed the importance of soil temperature and water content.

Les micro-zones et les technologies traditionnelles de la viniculture en Géorgie

La Géorgie est un pays d’une tradition très ancienne de viticulture et de viniculture. Là, dans les micro zones spécifiques, en précisant le lieu on produit de différents types du vin d’une

Natural sparkling wine pétillant naturel: technological features and sensory profile

The article presents the results of a study on the technological features of producing sparkling wines of the Pétillant Naturel (Pet-Nat) type, made using the ancestral method from the Muscat Ottonel and Pinot Noir grape varieties.

Exploring resilience and competitiveness of wine estates in Languedoc-Roussillon in the recent past: a multi-level perspective

The Languedoc-Roussillon wineries are facing a decline in wine yields particularly PGI yields due to many factors. Climate change is just ones, but is expected to increase in the future. There is also structurally a large heterogeneity of yield profiles among terroirs, varieties and strategies. This work investigates the link between yield, competitiveness and resilience to explore how resilient winegrowers have been in the recent past. To this end two approaches have been combined; (i) an accountancy database analysis at estate scale and (ii) municipality level competitiveness analysis. A new resilience indicator that characterizes the capacity of an estate to absorb yield variation is also defined. The FADN database between 2000 and 2018 of ex-Languedoc-Roussillon (France) and other data are used to analyse the current situation and the past evolution of competitiveness and resilience by type of estate (type of farm: PGI and/or PDO & type of commercialization: bulk and/or bottles). The net margin, which defines competitiveness, is not correlated to yield for all types but depends on the type of commercialization and the level of specialisation. The resilience indicator shows that the net margin of estates specialized in PGI is particularly sensitive to yield declines. We also show that price evolutions seem to compensate the effect of yield losses for the majority of types. Municipality scale analysis shows the links between local pedoclimate, yield, commercialization strategies and price. Overlapping a PDO with a PGI does not always increase a municipality’s PGI competitiveness. It is difficult to make links between causes and effects due to the complexity of the wine production system. Production diversification may be a solution. Resorting to the two level of analysis helps resolving the data gap that is necessary to explore the links between yield and economic performance of the wine estates in the long term.

Significance of factors making Riesling an iconic grape variety

Riesling is the iconic grape variety of Germany and accounts for 23% of the German viticulture acreage, which comprises 45% of the worldwide Riesling plantings. Riesling wines offer a wide array of styles from crisp sparkling wines to highly concentrated and sweet Trockenbeerenauslese or Icewines. However, its thin berry skin makes Riesling more vulnerable to detrimental environmental threats than other white wine varieties.