Naturally occurring variation in gene-associated transposable elements impacts gene expression and phenotypic diversity in woodland strawberry DOI
Ileana Tossolini,

Rocio Tolley,

Julia Llinares-Gómez

et al.

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: April 22, 2025

Abstract Transposable elements (TEs) constitute a major portion of plant genomes and play key roles in shaping genome architecture, regulating gene expression, driving evolution. In this study, we generated comprehensive curated TE library for the woodland strawberry (Fragaria vesca) by integrating two bioinformatic pipelines (EDTA DeepTE). Our annotation revealed that TEs account approximately 37% F. vesca genome. Analysis TE-derived inverted repeats (IRs) miniature inverted-repeat transposable (MITEs) demonstrated their association with 24-nt small interfering RNA (siRNA) production differential DNA methylation patterns across tissues, suggesting role epigenetic regulation particularly during fruit ripening. This MITE-mediated regulatory mechanism was confirmed evaluating expression chromatin organization at FvH4_7g18570, which encodes alcohol acyl transferase (FvAAT1). Three MITEs located upstream or downstream FvAAT1 coding sequence were shown to influence epigenetically expression. Furthermore, analyzed 210 re-sequenced accessions from European germplasm collection identify annotate insertion deletion polymorphisms. A principal component analysis (PCA) based on these polymorphisms subpopulation structures reflect geographic origins. genome-wide study (GWAS) uncovered significant associations between specific economically important traits, including aroma-related volatile compounds size. Among them, hAT MITE near FvH4_2g00610 correlated increased levels γ-decalactone, desirable aroma compound strawberries. These findings underscore functional significance as contributors phenotypic diversity through novel functions. By into population-genomic studies, work provides valuable insights development quality traits. It also highlights potential harnessing TE-mediated variation breeding initiatives editing strategies improve quality.

Language: Английский

Cryo-EM structures of the plant plastid-encoded RNA polymerase DOI Creative Commons
Xiaoxian Wu,

Wenhui Mu,

Li Fan

et al.

Cell, Journal Year: 2024, Volume and Issue: 187(5), P. 1127 - 1144.e21

Published: Feb. 1, 2024

Language: Английский

Citations

17
Epigenetic gene regulation in plants and its potential applications in crop improvement DOI
Heng Zhang,

Jian-Kang Zhu

Nature Reviews Molecular Cell Biology, Journal Year: 2024, Volume and Issue: 26(1), P. 51 - 67

Published: Aug. 27, 2024

Language: Английский

Citations

8
Redox regulation of gene expression: proteomics reveals multiple previously undescribed redox-sensitive cysteines in transcription complexes and chromatin modifiers DOI
Avilien Dard, Frank Van Breusegem, Amna Mhamdi

et al.

Journal of Experimental Botany, Journal Year: 2024, Volume and Issue: 75(15), P. 4476 - 4493

Published: April 20, 2024

Redox signalling is crucial for regulating plant development and adaptation to environmental changes. Proteins with redox-sensitive cysteines can sense oxidative stress modulate their functions. Recent proteomics efforts have comprehensively mapped the proteins targeted by modifications. The nucleus, epicentre of transcriptional reprogramming, contains a large number that control gene expression. Specific transcription factors long been recognized as key players in decoding redox signals nucleus thus responses. Consequently, regulation nuclear machinery its cofactors has received less attention. In this review, we screened proteomic datasets on core complexes chromatin modifiers Arabidopsis thaliana. Our analysis indicates affects every step transcription, from initiation elongation termination. We report previously undescribed subunits discuss emerging challenges unravelling landscape redox-regulated processes involved transcription.

Language: Английский

Citations

6
Harnessing promoter elements to enhance gene editing in plants: perspectives and advances DOI Creative Commons
Nikita Gondalia, Luis Felipe Quiroz, Linyi Lai

et al.

Plant Biotechnology Journal, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 27, 2025

Summary Genome‐edited plants, endowed with climate‐smart traits, have been promoted as tools for strengthening resilience against climate change. Successful plant gene editing (GE) requires precise regulation of the GE machinery, a process controlled by promoters, which drives its transcription through interactions factors (TFs) and RNA polymerase. While constitutive promoters are extensively used in constructs, their limitations highlight need alternative approaches. This review emphasizes promise tissue/organ specific well inducible enable targeted spatiotemporal manner no effects on other tissues. Advances synthetic biology paved way creation offering refined control over expression augmenting potential GE. The integration these novel systems presents significant opportunities conditional genome editing. Moreover, advent bioinformatic artificial intelligence is revolutionizing characterization regulatory elements, enhancing our understanding roles plants. Thus, this provides insights into strategic use promoter to enhance precision, efficiency specificity GE, setting stage innovative crop improvement strategies.

Language: Английский

Citations

0
Naturally occurring variation in gene-associated transposable elements impacts gene expression and phenotypic diversity in woodland strawberry DOI
Ileana Tossolini,

Rocio Tolley,

Julia Llinares-Gómez

et al.

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: April 22, 2025

Abstract Transposable elements (TEs) constitute a major portion of plant genomes and play key roles in shaping genome architecture, regulating gene expression, driving evolution. In this study, we generated comprehensive curated TE library for the woodland strawberry (Fragaria vesca) by integrating two bioinformatic pipelines (EDTA DeepTE). Our annotation revealed that TEs account approximately 37% F. vesca genome. Analysis TE-derived inverted repeats (IRs) miniature inverted-repeat transposable (MITEs) demonstrated their association with 24-nt small interfering RNA (siRNA) production differential DNA methylation patterns across tissues, suggesting role epigenetic regulation particularly during fruit ripening. This MITE-mediated regulatory mechanism was confirmed evaluating expression chromatin organization at FvH4_7g18570, which encodes alcohol acyl transferase (FvAAT1). Three MITEs located upstream or downstream FvAAT1 coding sequence were shown to influence epigenetically expression. Furthermore, analyzed 210 re-sequenced accessions from European germplasm collection identify annotate insertion deletion polymorphisms. A principal component analysis (PCA) based on these polymorphisms subpopulation structures reflect geographic origins. genome-wide study (GWAS) uncovered significant associations between specific economically important traits, including aroma-related volatile compounds size. Among them, hAT MITE near FvH4_2g00610 correlated increased levels γ-decalactone, desirable aroma compound strawberries. These findings underscore functional significance as contributors phenotypic diversity through novel functions. By into population-genomic studies, work provides valuable insights development quality traits. It also highlights potential harnessing TE-mediated variation breeding initiatives editing strategies improve quality.

Language: Английский

Citations

0