Abstract Detail

Genomics / Proteomics

Wong, Darren C. J. [1], Gambetta, Greg [2], Castellarin, Simone Diego [1].

Genome-wide analysis of known and potential cis-regulatory elements in promoter regions of the grapevine (Vitis vinifera L.) genome.

The availability of the grapevine genome sequence is an invaluable resource for the characterization of gene function and organization. Genome-wide expression studies are plentiful but grape promoter regions remain poorly characterized. To date, genome analysis of plant promoters have been conducted in Arabidopsis, poplar, rice and soybean. Therefore, understanding the grapevine promoter constituents on a genome scale will shed light on the critical promoter positions, the type and frequency of cis-regulatory elements in the promoters, and the common cis-regulatory elements in transcriptional regulatory networks. A comprehensive analysis of the grapevine promoter architecture was conducted focusing on the patterns (frequency and distribution) of known and putative (hexamer and octamers) cis-regulatory elements (CRE) within promoter regions. Considering 1kb upstream of the start codon we identified core CREs (i.e TATA-related and Y-patch elements) and many putative functional regulatory element groups. Many of the aforementioned CREs have a position bias towards the transcription start site (TSS), occasionally lying between -30 to -300 bases from the TSS. The latter observation is widely adopted as supporting evidence for bona fide motifs. Similarly to other plant species, known CREs – among the others, the abscisic acid-response elements (ABREs), light-responsive elements (LREs; G-Box, SORLIP) and signaling (CGCG box) – showed position bias toward TSS. We have also identified approximately 400 putative CREs by analyzing the motive hit frequency in the promoter region. Additionally, we determined the enrichment of CREs in groups of differentially expressed (DE) genes and in clusters of co-expressed genes through a meta-analysis of previous studies investigating transcriptome changes in the grape berry during berry development or under abiotic stress conditions. We show that promoters of DE genes in young and ripe berries contain significantly enriched CREs related to LREs and ABRE, respectively; while promoters of drought inducible genes are enriched with hormone related CREs, especially ABA and ethylene. We present valuable insights on the genomic structures that underlie the transcriptional regulation in grapevine through (1) the deeper understanding of promoter structure, (2) the identification of known CREs associated with given biological process and (3) the discovery of novel overrepresented x-mers that may represent putative CREs.

1 - The University of British Columbia, Wine Research Centre, 2205 East Mall, Wine Research Centre, Vancouver, BRITISH COLUMBIA, V6T 1Z4, Canada
2 - Institut des sciences de la vigne et du vin (ISVV), 210 chemin de Leysotte, CS 50008, Villenave D’Ornon, 33882, France

Keywords:
Gene regulation
Fruit
transcriptomics
Ripening
water deficit.

Presentation Type: Poster:Posters for Topics
Session: P
Location: Hall D/The Shaw Conference Centre
Date: Monday, July 27th, 2015
Time: 5:30 PM
Number: PGP009
Abstract ID:992
Candidate for Awards:None