Abstract
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; https://golem.ncbr.muni.cz), 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).
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Claims 2
Claim · model-written summary
GOLEM enables users to locate any motif of interest with respect to TSS or ATG within plant genomes across the plant Tree of Life.
- Taxon
- Chara, Marchantia, Physcomitrium, Azolla, Ceratopteris, Amborella, Oryza, Zea, Solanum and Arabidopsis
Marchantia
Arabidopsis
Solanum
Oryza
Zea_fragment.jpg?width=60)
Amborella
Chara
Ceratopteris
Physcomitrium
Azollae2 - Outcome
- locate any motif of interest with respect to TSS or ATGe1
- Comparator
- TSS or ATGe1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“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”
e2“Chara, Marchantia, Physcomitrium, Azolla, Ceratopteris, Amborella, Oryza, Zea, Solanum and Arabidopsis”
Claim · model-written summary
Motif visualization is performed relative to transcript levels of particular genes in leaves and male reproductive tissues and can be compared with genome-wide distribution.
- Taxon
- Chara, Marchantia, Physcomitrium, Azolla, Ceratopteris, Amborella, Oryza, Zea, Solanum and ArabidopsisMarchantiaArabidopsisSolanumOryzaZeaAmborellaCharaCeratopterisPhyscomitriumAzollae2
- Organ / stage
- leaves and male reproductive tissuese3
- Outcome
- visualization of the motifse3
- Comparator
- genome-wide distributione3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e3“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”
e2“Chara, Marchantia, Physcomitrium, Azolla, Ceratopteris, Amborella, Oryza, Zea, Solanum and Arabidopsis”