Investigating the Distribution of Plant Gene Regulatory Motifs
from Gametophyte to Sporophyte

a 2025

Investigating the Distribution of Plant Gene Regulatory Motifs from Gametophyte to Sporophyte

NEVOSÁD, Lukáš; Božena KLODOVÁ; Jiří RUDOLF; Tomáš RAČEK; Tereza PŘEROVSKÁ et al.

Základní údaje

Originální název

Investigating the Distribution of Plant Gene Regulatory Motifs from Gametophyte to Sporophyte

Autoři

Vydání

TANGENC Conference 2025, Brno, 2025

Další údaje

Jazyk

angličtina

Typ výsledku

Konferenční abstrakt

Obor

10611 Plant sciences, botany

Stát vydavatele

Česká republika

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14740/25:00143975

Organizační jednotka

Středoevropský technologický institut

Klíčová slova anglicky

Plant genomics; Cis-regulatory elements (CREs); Gene promoters; Transcriptomics; Regulatory motif analysis

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 16. 3. 2026 09:13, Mgr. Eva Dubská

Anotace

V originále

GOLEM (Gene regulatOry eLEMents; https://golem.ncbr.muni.cz) is a user-friendly web-based tool for exploring plant genomes across including crop plants. GOLEM enables the analysis of diverse plant tissues, encompassing sporophytic organs (e.g., leaves) as well as male gametophytic developmental stages (e.g., antheridia, pollen stages, and sperm cells). The platform allows detailed investigation of the localization and distribution of cis-regulatory elements (CREs) within gene promoters, particularly in regions proximal to the transcription start site (TSS) and translation start codon (ATG). Gene sets can be defined based on tissue-specific expression levels derived from transcriptomic datasets. In addition, genome-wide analyses independent of transcriptional activity facilitate comparative studies of regulatory motif distribution and support investigations into the evolutionary dynamics of CREs across the plant Tree of Life. We demonstrate the utility of GOLEM through analyses of motifs associated with male gametophyte development (e.g., LAT52, MEF2, and DOF_core), hormone-responsive elements (e.g., GCC-box and ARR10_core), and conserved regulatory motifs (e.g., TATA-box, ABRE, TC-element, I-box, and DRE/CRT element). Furthermore, we present a novel update implemented in a private version of GOLEM that enables users to securely analyze their own unpublished datasets.

Návaznosti

EH22_008/0004581, projekt VaV

Název: Nové poznatky pro plodiny nové generace

Přiložené soubory

Abstrakt_P_P_Schrumpfova_TANGENC.docx

11_TALK__24112025_Prochazkova-Schrumpfova_WP3_tlkfjzus.pptx

Citovat

NEVOSÁD, Lukáš; Božena KLODOVÁ; Jiří RUDOLF; Tomáš RAČEK; Tereza PŘEROVSKÁ; Alžbeta MIKUŠOVÁ; Věra ŠPANIHELOVÁ; Anna HÝSKOVÁ; Radka SVOBODOVÁ; David HONYS a Petra PROCHÁZKOVÁ SCHRUMPFOVÁ. Investigating the Distribution of Plant Gene Regulatory Motifs from Gametophyte to Sporophyte. In TANGENC Conference 2025, Brno. 2025.

@proceedings{2560884,
   author = {Nevosád, Lukáš and Klodová, Božena and Rudolf, Jiří and Raček, Tomáš and Přerovská, Tereza and Mikušová, Alžbeta and Španihelová, Věra and Hýsková, Anna and Svobodová, Radka and Honys, David and Procházková Schrumpfová, Petra},
   booktitle = {TANGENC Conference 2025, Brno},
   keywords = {Plant genomics; Cis-regulatory elements (CREs); Gene promoters; Transcriptomics; Regulatory motif analysis},
   language = {eng},
   title = {Investigating the Distribution of Plant Gene Regulatory Motifs from Gametophyte to Sporophyte},
   url = {https://www.ceitec.eu/tangenc-conference-2025/a5272?_fid=0x3s},
   year = {2025}
}

TY  - CONF
ID  - 2560884
AU  - Nevosád, Lukáš - Klodová, Božena - Rudolf, Jiří - Raček, Tomáš - Přerovská, Tereza - Mikušová, Alžbeta - Španihelová, Věra - Hýsková, Anna - Svobodová, Radka - Honys, David - Procházková Schrumpfová, Petra
PY  - 2025
TI  - Investigating the Distribution of Plant Gene Regulatory Motifs from Gametophyte to Sporophyte
KW  - Plant genomics
KW  - Cis-regulatory elements (CREs)
KW  - Gene promoters
KW  - Transcriptomics
KW  - Regulatory motif analysis
UR  - https://www.ceitec.eu/tangenc-conference-2025/a5272?_fid=0x3s
N2  - GOLEM (Gene regulatOry eLEMents; https://golem.ncbr.muni.cz) is a user-friendly web-based tool for exploring plant genomes across including crop plants. GOLEM enables the analysis of diverse plant tissues, encompassing sporophytic organs (e.g., leaves) as well as male gametophytic developmental stages (e.g., antheridia, pollen stages, and sperm cells). The platform allows detailed investigation of the localization and distribution of cis-regulatory elements (CREs) within gene promoters, particularly in regions proximal to the transcription start site (TSS) and translation start codon (ATG). Gene sets can be defined based on tissue-specific expression levels derived from transcriptomic datasets. In addition, genome-wide analyses independent of transcriptional activity facilitate comparative studies of regulatory motif distribution and support investigations into the evolutionary dynamics of CREs across the plant Tree of Life. We demonstrate the utility of GOLEM through analyses of motifs associated with male gametophyte development (e.g., LAT52, MEF2, and DOF_core), hormone-responsive elements (e.g., GCC-box and ARR10_core), and conserved regulatory motifs (e.g., TATA-box, ABRE, TC-element, I-box, and DRE/CRT element). Furthermore, we present a novel update implemented in a private version of GOLEM that enables users to securely analyze their own unpublished datasets.
ER  -

Přehled o publikaci