GOLEM: A Tool for Visualizing the Distribution of Gene Regulatory Elements in Plant Promoters

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F25%3A00143986" target="_blank" >RIV/00216224:14740/25:00143986 - isvavai.cz</a>

Result on the web

<a href="https://olomouc.ueb.cas.cz/en/cpnw" target="_blank" >https://olomouc.ueb.cas.cz/en/cpnw</a>

DOI - Digital Object Identifier

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Result language

angličtina

Original language name

GOLEM: A Tool for Visualizing the Distribution of Gene Regulatory Elements in Plant Promoters

Original language 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.

Czech name

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Czech description

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Type

O - Miscellaneous

CEP classification

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OECD FORD branch

10611 - Plant sciences, botany

Project

<a href="/en/project/EH22_008%2F0004581" target="_blank" >EH22_008/0004581: TowArds Next GENeration Crops (TANGENC)</a><br>

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2025

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů