Genome-wide analysis of cis-regulatory element structure and discovery of motif-driven gene co-expression networks in grapevine

Abstract

Coordinated transcriptional and metabolic reprogramming ensures a plant’s continued growth and survival under adverse environmental conditions. Transcription factors (TFs) act to modulate gene expression through complex cis-regulatory element (CRE) interactions. Genome-wide analysis of known plant CREs was performed for all currently predicted protein-coding gene promoters in grapevine (Vitis vinifera L.). Many CREs such as abscisic acid (ABA)-responsive, drought-responsive, auxin-responsive, and evening elements, exhibit bona fide CRE properties such as strong position bias towards the transcription start site (TSS) and over-representation when compared with random promoters. Genes containing these CREs are enriched in a large repertoire of plant biological pathways. Large-scale transcriptome analyses also show that these CREs are highly implicated in grapevine development and stress response. Numerous CRE-driven modules in condition-specific gene co-expression networks (GCNs) were identified and many of these modules were highly enriched for plant biological functions. Several modules corroborate known roles of CREs in drought response, pathogen defense, cell wall metabolism, and fruit ripening, whereas others reveal novel functions in plants. Comparisons with Arabidopsis suggest a general conservation in promoter architecture, gene expression dynamics, and GCN structure across species. Systems analyses of CREs provide insights into the grapevine cis-regulatory code and establish a foundation for future genomic studies in grapevine.

Genome-Wide Characterization and Expression Profiling of Squamosa Promoter Binding Protein-Like (SBP) Transcription Factors in Wheat (Triticum aestivum L.)

“…Because motif composition is also an important indicator to classify different genes, we then analyzed and compared the motif composition of the SBP protein sequences [49,78,79]. Corresponding to the results of conserved domain analysis, the distribution of Motifs 1 and 2 were highly conserved in all sequences, and the annotation showed that they were all zinc-binding sites (Figure 13).…”

The ethylene response factor VaERF092 from Amur grape regulates the transcription factor VaWRKY33, improving cold tolerance

“…We next tested whether the AP2/ERF cis ‐regulatory elements (CREs) (GCC‐box and DRE/CRT) exhibited canonical CRE properties (Wong et al ., ). Indeed, the GCC‐box was highly enriched ( P < 1.00E‐05) in the promoters of Vv‐m (70 genes, P < 1.17E‐09) and Vv‐r (64 genes, P < 2.97E‐07) GCN genes (Figure d; Table S9).…”

“…The default output of atted‐ii (top 300 co‐expressed genes ranked by MR value) from the At‐m and At‐r GCN was further shortlisted and analyzed. Shortlisted co‐expressed genes in grapevine and A. thaliana GCNs were tested for over‐representation using MapMan BIN functional categories (Lohse et al ., ) and Fisher's exact test, and an FDR correction was applied using the appropriate species background, as previously described (Wong et al ., ). Significantly enriched BIN categories were defined as categories having an FDR of <0.05.…”

“…The position of each CRE identified and total number of occurrences were recorded and subsequently tested for position bias (i.e. clustering toward the TSS) and enrichment (based on hypergeometric distribution) in r , as previously described (Wong et al ., ).…”

VlbZIP30 of grapevine functions in drought tolerance via the abscisic acid core signaling pathway

“…These results suggest that VlbZIP30 is likely to enhance A. thaliana drought tolerance by regulating downstream genes containing a perfect G-box (CACGTG). Large-scale transcriptome analyses also show that the G-box (CACGTG) was highly enriched in stress-responsive genes in grapevines (Wong et al. , 2017).…”