terclim by ICS banner
IVES 9 IVES Conference Series 9 Preliminary steps of a protocol to isolate transcription factors bound to a specific DNA locus in grapevine using CRISPR-dCas9 system

Preliminary steps of a protocol to isolate transcription factors bound to a specific DNA locus in grapevine using CRISPR-dCas9 system

Abstract

Cis-acting regulatory elements are DNA sequences that can be bound by transcription factors to regulate the expression of genes in a condition-dependent and tissue-specific way. It is nowadays possible to search for DNA motives and sequences that a given transcription factor is binding or at least can, but it is still hard to have a glance at all the transcription factors that are contemporaneously located at the same locus. Inspired by an existing technique that uses the CRISPR-Cas system in mammal cells, we are trying to develop a protocol to study such regulation in Vitis vinifera. Using the highly sequence-specific binding capacity of a catalytically inactive Cas9 protein (dCas9), our idea is to set up a system to target a desired sequence and precipitate all the crosslinked proteins and distantly interacting chromatin at this locus and analyze them. After conducting preliminary assays on protoplast system, we got introduced to the CRISPR-FISH technique, that uses dCas9 and a fluorescent guide to label telomeres on nuclei directly isolated from a small quantity of fixed leaves with a very simple procedure. We used part of such technique to easily obtain the chromatin that was needed for our trials and eventually performed the pull-down of the targeted DNA sequences directly on these nuclei after transforming them with the dCas9 complex. Sequencing the obtained fragments allows to verify the specificity of the tool. Far from having eliminated the idea of using protoplasts as model system, we proceed developing both approaches in parallel.

DOI:

Publication date: June 13, 2024

Issue: Open GPB 2024

Type: Poster

Authors

Aurélien Devillars1*, Silvia Farinati1, Edoardo Bertini2, Chiara Fattorini2, Sara Lissandrini2, Adriana Fernanda Soria Garcia1, Bhanu Prakash Potlapalli3, Andreas Houben3, Sara Zenoni2 and Alessandro Vannozzi1

1 Department of Agriculture Food Natural Resources Animals and Environment, University of Padova, Agripolis, Legnaro, Italy
2 Department of Biotechnology, University of Verona, Verona, Italy
3 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany

Contact the author*

Keywords

Molecular Biology, Grapevine, Gene Regulation, CRISPR-Cas9, Protoplasts

Tags

IVES Conference Series | Open GPB | Open GPB 2024

Citation

Related articles…

Mitigation of retronasal smoke flavor carryover in the sensory analysis of smoke affected wines

With the steady rise in wildfire occurrence in wine regions around the world, there are quality issues beginning to face the wine industry. These fires produce clouds of smoke which have the ability to carry organic molecules across vast distances that can be absorbed by grapes. When these compounds make their way into the final wine, unpleasant smokey and burnt flavors are present, along with a lasting ashy finish. Along with the volatile compounds carried by smoke, once incorporated into the fruit these compounds become bound to sugars, forming glycosidic compounds.

Which heat test really represents the haze risk of a white Sauvignon wine ?

AIM: Different heat tests are used to predict a white wine haze risk after bottling. The most used tests are 30-60 min. at 80°C. Nevertheless, there is a lack of information about the relationship between the wine haze observed after such tests and the turbidities observed in the bottles after the storage/transport of the wines in more realistic Summer conditions (35-46°C during 3-12 days)

Arinto clones tolerant to climate change: in depth transcriptomic study of tolerant and sensitive genotypes

Drought and heat waves deriving from climate change have been affecting grapevine plants and altering wine characteristics in the past years, and effects are expected to get worst. Innovative approaches to address this problem have been undertaken in several varieties, that consist in exploring intravarietal variability to identify genotypes that are tolerant to abiotic stress. Such is the case of the variety Arinto, where an experimental population of 165 clones installed according to a resolvable row-column design with 6 replicates, was scanned for several parameters, including surface leaf temperature (SLT). Linear mixed models were fitted to the data of the traits evaluated, and the empirical best linear unbiased predictors (EBLUPs) of genotypic effects for each trait were obtained as well as the coefficient of genotypic variation (CVG) and broad sense heritability.

Utilizing ozone for the management of powdery mildew (Erysiphe necator Schwein.) in vineyards: potential and challenges

Powdery mildew, caused by fungal pathogens, poses a significant threat to grapevines in the DOCa Rioja region. In efforts to improve control strategies while reducing reliance on conventional phytosanitary products, ozone could constitute a potential alternative. However, it has short persistence, thus requiring frequent treatments. This study aimed to assess the suitability of ozone as an active substance for controlling powdery mildew within a phytosanitary strategy aimed at reducing conventional phytosanitary product usage. The strategy integrating ozone with conventional products yielded powdery mildew levels comparable to conventional treatments in both disease incidence and severity.

A population genetic study of Vitis vinifera L. subsp. sylvestris Gmelin based on 3.000 individuals from 20 countries

Until the 19th century, the wild form of cultivated grapevines (vitis vinifera l. subsp. sylvestris gmelin, v. sylvestris) was ubiquitous in many european and west asian regions. However, many factors like deforestation, the intensification of agriculture, or the introduction of several pests and pathogens decimated its presence in these growing sites, and natural populations are now mostly restricted to river-bank forests and creeks with specific soil and climate conditions. in fact, v. sylvestris is now considered an endangered subspecies that is protected by law in many european countries to prevent its loss.