Position and Strand Identity of G-Quadruplex Motifs Are Associated with Distinct Functional Signatures in Plants
- 1Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
Abstract
Putative G-quadruplex (G4) sequences have been linked to transcriptional regulation in individual plant species, but a systematic, comparative view across the plant kingdom has been lacking. In this study, we analyzed putative G4-forming sequences (PQS) near transcription start sites (TSSs) in 70 plant species spanning over 1.2 billion years of evolutionary divergence, from algae to angiosperms. Using the G4Hunter algorithm, putative G4 motifs were mapped and scored separately on the coding and template DNA strands. This strand-resolved analysis identified four position/strand categories, among which template-strand motifs downstream of the TSS were the most abundant and resistant to an increase in the G4Hunter threshold. The majority of PQS-positive genes (62.4%) carry a motif in only one category, although combinatorial patterns involving two or more categories also occur. Gene Ontology enrichment analysis of Arabidopsis thaliana homologs tested in each species revealed two main recurrent patterns of modest effect size: downstream template-strand motifs were associated with chloroplast and mRNA-binding terms, and upstream template-strand motifs were associated with transcription factor activity and regulation of transcription, whereas downstream coding-strand motifs showed a weaker signal. At the level of individual genes, position-specific G4s recurred among homologs more often than expected at random, mostly downstream, where this may partly reflect the conservation of the coding sequence. These associations, based on computational prediction, provide a starting point for prioritizing candidate G4 elements for experimental validation of their role in transcriptional control in plants.
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BibTeX
@article{kaluzhny2026position,
title = {{Position and Strand Identity of G-Quadruplex Motifs Are Associated with Distinct Functional Signatures in Plants}},
author = {Dmitry N. Kaluzhny and Daiana A. Krupskaya and Olesya D. Moskalenko and Elena N. Pushkova and Nataliya V. Melnikova and Alexey A. Dmitriev},
journal = {International Journal of Molecular Sciences},
year = {2026},
month = nov,
doi = {10.3390/ijms27219823},
url = {https://www.mdpi.com/1422-0067/27/21/9823},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Position and Strand Identity of G-Quadruplex Motifs Are Associated with Distinct Functional Signatures in Plants
AU - Dmitry N. Kaluzhny
AU - Daiana A. Krupskaya
AU - Olesya D. Moskalenko
AU - Elena N. Pushkova
AU - Nataliya V. Melnikova
AU - Alexey A. Dmitriev
PY - 2026
DA - 2026/11/02
JO - International Journal of Molecular Sciences
DO - 10.3390/ijms27219823
UR - https://www.mdpi.com/1422-0067/27/21/9823
AB - Putative G-quadruplex (G4) sequences have been linked to transcriptional regulation in individual plant species, but a systematic, comparative view across the plant kingdom has been lacking. In this study, we analyzed putative G4-forming sequences (PQS) near transcription start sites (TSSs) in 70 plant species spanning over 1.2 billion years of evolutionary divergence, from algae to angiosperms. Using the G4Hunter algorithm, putative G4 motifs were mapped and scored separately on the coding and template DNA strands. This strand-resolved analysis identified four position/strand categories, among which template-strand motifs downstream of the TSS were the most abundant and resistant to an increase in the G4Hunter threshold. The majority of PQS-positive genes (62.4%) carry a motif in only one category, although combinatorial patterns involving two or more categories also occur. Gene Ontology enrichment analysis of Arabidopsis thaliana homologs tested in each species revealed two main recurrent patterns of modest effect size: downstream template-strand motifs were associated with chloroplast and mRNA-binding terms, and upstream template-strand motifs were associated with transcription factor activity and regulation of transcription, whereas downstream coding-strand motifs showed a weaker signal. At the level of individual genes, position-specific G4s recurred among homologs more often than expected at random, mostly downstream, where this may partly reflect the conservation of the coding sequence. These associations, based on computational prediction, provide a starting point for prioritizing candidate G4 elements for experimental validation of their role in transcriptional control in plants.
SN - 1422-0067
ER -