Barcaccia, G.

Gabelli, G.

Josè Tomàs, M. P.

Lucchin, M.

Luis, O. R.

Magon, G.

Pirrello, C.

Vannozzi, A.

English

Josè Tomàs, M. P.

Archivio istituzionale della ricerca - Fondazione Edmund Mach

Proceedings of the LXVI SIGA Annual CongressBari, 5/8 September, 2023ISBN: 978-88-944843-4-2Poster Communication Abstract – 6.27 THE DAP-SEQ AS A TOOL TO EXPLORE GRAPEVINE FLORAL CISTROMEMAGON G.*, PIRRELLO C.**, GABELLI G.*, LUIS O. R.***, JOSÈ TOMÀS M. P.***, BARCACCIA G.*, LUCCHIN M.*, VANNOZZI A.**) Dipartimento di Agronomia, Animali, Alimenti, Risorse naturali eAmbiente (DAFNAE), Università degli Studi di Padova, Viale dell’Università16, 35020 Legnaro (PD), Italy**) Fondazione Edmund Mach, Via Edmund Mach 1, 38098 San Michele all'Adige(TN), Italy***) Institute for Integrative Systems Biology (I2SYSBIO) – CSIC,Universitat de Valencia, Carrer del Catedràtic Agustín Escardino Benlloch,46980 Paterna, Valencia, SpainMYB108A, DAP-seq, NGS, flower, antherIn the post-genomics Era, the enormous amount of data generated by omicstechnologies being stored in public databases considerably exceeds theanalytical capacities of humans, making it imperative to use increasinglypowerful computational resources to process, analyse and store thisinformation. Nowadays, several studies aim at specifically addressing thisissue in grapevine (Vitis vinifera L.), a plant which is quicklyestablishing itself as an appealing ‘model’ species for studying non-climacteric fleshy fruits. In addition to genomics and transcriptomics, therecent development of regulatory genomics, also known as “regulomics”, hasgarnered growing interest in crop species as transcriptional regulation ofgenes plays a critical role in any biological process, including phenotypicplasticity and fruit development. DNA-Affinity Purification Sequencing (DAP-Seq) is a high-throughput experimental procedure that allows to discovertranscription factors binding sites (TFBS) interrogating genomic DNA within vitro-expressed TFs. DAP-Seq is the ultimate approach for TFBS discoveryand provides a scalable alternative for non-conventional model specieswhere genetic transformation is difficult, to rapidly and inexpensivelyinvestigate large number of TFs. The idea behind this assay is to combinenext-generation sequencing (NGS) of a genomic DNA library with in vitroexpression of affinity-purified TFs to generate cistrome maps for a widerange of species. In this study, we took advantage of DAP-Seq toinvestigate the cistrome landscape of a representative subset of grapevineTFs. These TFs have been previously identified by means of an RNA-Seqapproach performed on ten different grapevine floral whorls): calyx,calyptra, anther, filament, stigma, ovary and embryo, in both pre- and post-anthesis, and their expression was proven to be highly specific for a givenwhorl. Taking advantage of some systems biology in silico analysis, foreach TF it was isolated a subset of target genes featured by a similarexpression pattern and by a high specificity degree for the related floralorgan. These genes were designed as “high confidence targets” (HCTs) andwere used to generate tissue-specific regulatory networks to infer thefunction of a given TF based on the identification of its target genes.Subsequently, the putative role of the TFs was empowered by a cisregulatory elements enrichment analysis, finding in this way the mostprobable binding site of a TF basing on its own cistrome. Among all theTFs, the attention was finally focused on VvMYB108A, a transcriptionalregulator which was observed to be highly specific for anther development.The analysis of the related HCTs regulative network and the de novo motifdiscovery strongly support the putative role of this VvMYB108A in malefertility specific molecular mechanisms.

The DAP-Seq as a tool to explore grapevine floral cistrome

https://openpub.fmach.it/bitstream/10449/81797/2/2023%20LXVI%20SIGA%20Pirrello%206.27.pdf

The DAP-Seq as a tool to explore grapevine floral cistrome

Abstract

Similar works

Full text

Available Versions

Archivio istituzionale della ricerca - Fondazione Edmund Mach