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Peer-reviewedCC BY 4.0Frontiers in Plant Science

Developmental dynamics of transcription initiation highlight promoter shifts as a multifaceted regulatory mechanism in barley

  • Simon Pavlu1,2
  • Ondrej Kopecky1,2
  • Pavla Navratilova1
  • Hana Simkova1
  1. 1Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences
  2. 2Department of Cell Biology and Genetics, Faculty of Science, Palacky University
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Abstract

Alternative promoter usage is a widespread regulatory mechanism whereby a single gene utilizes two or more transcription start sites (TSSs), enabling the production of functionally distinct transcript and protein isoforms in a tissue-, developmental stage-, or condition-specific manner. While this phenomenon has been extensively studied in metazoans, genome-wide characterization of alternative promoter usage in crop species is still lacking. Here, we use Cap Analysis of Gene Expression (CAGE) to characterize genome-wide TSS dynamics across three stages of barley embryo development and the developing inflorescence. We identify 2,129 developmental promoter shifts relating to 1,353 genes, corresponding to ~5% of genes expressed in at least one of the four developmental stages. One-third of these shifts coincided with significant differential gene expression, and the affected genes were enriched for developmental and regulatory functions, particularly those related to cell wall biosynthesis and hormone signaling. Furthermore, for 521 genes, we predict potential effects of alternative TSS usage on translational efficiency or protein structure, suggesting regulatory consequences that extend beyond changes in transcript abundance. Together, our findings suggest that alternative promoter selection is an important regulatory mechanism during barley development and provide new insights into the developmental regulation of gene expression in cereals. Moreover, we provide a gene-level catalog of developmental promoter shifts in barley, offering a valuable resource for promoter editing and engineering to fine-tune gene expression for desirable agronomic traits.

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Cite

BibTeXRIS
BibTeX
@article{pavlu2026developmental,
  title = {{Developmental dynamics of transcription initiation highlight promoter shifts as a multifaceted regulatory mechanism in barley}},
  author = {Simon Pavlu and Ondrej Kopecky and Pavla Navratilova and Hana Simkova},
  journal = {Frontiers in Plant Science},
  year = {2026},
  month = oct,
  doi = {10.3389/fpls.2026.1975716},
  url = {https://www.frontiersin.org/articles/10.3389/fpls.2026.1975716/full},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Developmental dynamics of transcription initiation highlight promoter shifts as a multifaceted regulatory mechanism in barley
AU  - Simon Pavlu
AU  - Ondrej Kopecky
AU  - Pavla Navratilova
AU  - Hana Simkova
PY  - 2026
DA  - 2026/10/29
JO  - Frontiers in Plant Science
DO  - 10.3389/fpls.2026.1975716
UR  - https://www.frontiersin.org/articles/10.3389/fpls.2026.1975716/full
AB  - Alternative promoter usage is a widespread regulatory mechanism whereby a single gene utilizes two or more transcription start sites (TSSs), enabling the production of functionally distinct transcript and protein isoforms in a tissue-, developmental stage-, or condition-specific manner. While this phenomenon has been extensively studied in metazoans, genome-wide characterization of alternative promoter usage in crop species is still lacking. Here, we use Cap Analysis of Gene Expression (CAGE) to characterize genome-wide TSS dynamics across three stages of barley embryo development and the developing inflorescence. We identify 2,129 developmental promoter shifts relating to 1,353 genes, corresponding to ~5% of genes expressed in at least one of the four developmental stages. One-third of these shifts coincided with significant differential gene expression, and the affected genes were enriched for developmental and regulatory functions, particularly those related to cell wall biosynthesis and hormone signaling. Furthermore, for 521 genes, we predict potential effects of alternative TSS usage on translational efficiency or protein structure, suggesting regulatory consequences that extend beyond changes in transcript abundance. Together, our findings suggest that alternative promoter selection is an important regulatory mechanism during barley development and provide new insights into the developmental regulation of gene expression in cereals. Moreover, we provide a gene-level catalog of developmental promoter shifts in barley, offering a valuable resource for promoter editing and engineering to fine-tune gene expression for desirable agronomic traits.
SN  - 1664-462X
ER  -