Publication details
GOLEM: A Tool for Visualizing the Distribution of Gene Regulatory Elements in Plant Promoters
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| Year of publication | 2025 |
| Type | Conference abstract |
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| Description | The regulation of gene expression during tissue development is highly complex. A fundamental mechanism in this process involves the recognition of regulatory motifs, also known as cis-regulatory elements (CREs), by various proteins within gene promoter regions. The precise positioning of these motifs near the transcription start site (TSS) or translation start site (ATG) plays a critical role in initiating transcription and determining its rate. The expression levels of individual genes, governed by these motifs, can vary significantly across tissues and developmental stages, particularly in processes such as sexual reproduction. However, accurately identifying and visualizing these motifs in relation to gene expression within specific tissues remains a challenge. To address this, we present GOLEM (Gene regulatOry eLEMents; https://golem.ncbr.muni.cz), a freely accessible tool designed to precisely map motifs of interest relative to the TSS or ATG across a broad range of plant genomes spanning the plant Tree of Life, including Chara, Marchantia, Physcomitrium, Azolla, Ceratopteris, Amborella, Oryza, Zea, Solanum, and Arabidopsis. GOLEM enables motif visualization in relation to gene transcript levels in leaves and male reproductive tissues while also allowing comparison with genome-wide distributions independent of transcription levels. Furthermore, users can export lists of genes containing specific CREs at defined positions with high expression in selected tissues for further analysis. |