Přehled o publikaci

GOLEM (Gene regulatOry eLEMents, https://golem.ncbr.muni.cz) is a user-friendly tool for visualizing gene regulatory motifs in plant promoters, specially of the genes showing higher expression in male reproductive tissues or leaves, across the selected plant genomes within the plant evolution (streptophyte algae, mosses, ferns, basal angiosperm, monocots and dicots). We demonstrate GOLEM’s utility with motifs associated with male gametophyte development (e.g., LAT52, MEF2, and DOF_core), hormone-responsive elements (e.g., GCC-box, ARR10_core), and conserved motifs (e.g., TATA-box, ABRE, TC-element, I-box, and DRE/CRT element). Promoter analysis using GOLEM revealed that TATA-box-containing promoters are linked to genes expressed during late pollen development but not early pollen development in dicot plants. It was also shown that the LAT52 motif, motif associated with late pollen development, is preferentially located in the 5′ UTR. Moreover, GOLEM demonstrated that the ethylene-responsive element (GCC-box) exhibits a conserved pattern downstream of ATG throughout evolution, even in streptophyte algae. In contrast, the ARR10-binding motif (ARR10_core), associated with cytokinin response, does not show a conserved distribution across evolution, starting from streptophyte algae. This aligns with the fact that components of both signaling cascades are present in land plants, however, the streptophyte algae lacks some components of cytokinin signaling pathway. Additionally, a new Omics Repository focused on plants, which is being developed to support the storage, acquisition, and analysis of omics data also in crop plants, will be discussed.