GOLEM: A tool for visualizing the distribution of Gene regulatOry eLEMents within the plant promoters with a focus on male gametophyte

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61389030%3A_____%2F25%3A00618495" target="_blank" >RIV/61389030:_____/25:00618495 - isvavai.cz</a>

Alternative codes found

RIV/00216224:14310/25:00140332

Result on the web

<a href="https://doi.org/10.1111/tpj.70037" target="_blank" >https://doi.org/10.1111/tpj.70037</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1111/tpj.70037" target="_blank" >10.1111/tpj.70037</a>

Result language

angličtina

Original language name

GOLEM: A tool for visualizing the distribution of Gene regulatOry eLEMents within the plant promoters with a focus on male gametophyte

Original language description

Gene expression regulation during tissue development is extremely complex. A key mechanism of gene regulation is the recognition of regulatory motifs, also known as cis-regulatory elements (CREs), by various proteins in gene promoter regions. Localization of these motifs near the transcription start site (TSS) or translation start site (ATG) is crucial for transcription initiation and rate. Transcription levels of individual genes, regulated by these motifs, can vary significantly across tissues and developmental stages, especially in processes like sexual reproduction. However, the precise localization and visualization of these motifs in relation to gene expression in specific tissues can be challenging. Here, we introduce a freely available tool 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 (Chara, Marchantia, Physcomitrium, Azolla, Ceratopteris, Amborella, Oryza, Zea, Solanum and Arabidopsis). The visualization 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. Additionally, genes with specific CREs at defined positions and high expression in selected tissues can be exported for further analysis. GOLEM's functionality is illustrated by its application to conserved motifs (e.g. TATA-box, ABRE, I-box, and TC-element), hormone-responsive elements (GCC-box, ARR10_binding motif), as well as to male gametophyte-related motifs (e.g., LAT52, MEF2, and DOF_core).

Czech name

—

Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10611 - Plant sciences, botany

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2025

Confidentiality

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

Name of the periodical

Plant Journal

ISSN

0960-7412

e-ISSN

1365-313X

Volume of the periodical

121

Issue of the periodical within the volume

5

Country of publishing house

US - UNITED STATES

Number of pages

17

Pages from-to

e70037

UT code for WoS article

001435582300001

EID of the result in the Scopus database

2-s2.0-86000094595