GOLEM: distribution of Gene regulatOry eLEMents within the plant promoters

Motivation: The regulation of gene expression during tissue development is extremely complex. One of the key regulatory mechanisms of gene expression involves the recognition of regulatory motifs by various proteins in the promoter regions of many genes. Localisation of these motifs in proximity to the transcription start site (TSS) or translation start site (ATG) is critical for regulating the initiation and rate of transcription. The levels of transcription of individual genes, regulated by these motifs, can vary signifi cantly in diff erent tissues and developmental stages, especially during tightly regulated processes such as sexual reproduction. However, the precise localisation and visualisation of the regulatory motifs within gene promoters with respect to gene transcription in specifi c tissues, can be challenging. Results: Here, we introduce a program called GOLEM (Gene regulatOry eLEMents) which enables users to precisely locate any motif of interest with respect to TSS or ATG within the relevant plant genomes across the plant Tree of Life (Marchantia, Physcomitrium, Amborella, Oryza, Zea, Solanum and Arabidopsis). The visualisation of the motifs is performed with respect to the transcript levels of particular genes in leaves and male reproductive tissues, and can be compared with genome-wide distribution regardless of the transcription level. Availability and implementation: GOLEM is freely available at https://golem.ncbr.muni.cz and its source codes are provided under the MIT licence at GitHub at https://github.com/sb-ncbr/golem.