Cytosine Methylation Changes the Preferred Cis-Regulatory Configuration of Arabidopsis WUSCHEL-Related Homeobox 14

International Journal of Molecular Sciences, Год журнала: 2025, Номер 26(2), С. 763 - 763

Опубликована: Янв. 17, 2025

The Arabidopsis transcription factor WUSCHEL-related homeobox 14 (AtWOX14) plays versatile roles in plant growth and development. However, its biochemical specificity of DNA binding, genome-wide regulatory targets, how these are affected by methylation remain uncharacterized. To clarify the biochemistry underlying function AtWOX14, using recently developed 5mC-incorporation strategy, this study performed SELEX DAP-seq for AtWOX14 both presence absence cytosine methylation, systematically curated 65 motif models identified 51,039 genomic binding sites examined 5mC affects through bioinformatic analyses. Overall, represses monomers but facilitates dimers, effect on a cytosine’s affinity to is position-dependent. Notably, we found that most preferred homodimeric configuration has changed from ER1 ER0 upon methylation. This change potential rewire network downstream as suggested GO analyses strength changes peaks Therefore, work comprehensively illustrates targets reports previously unrecognized binding.

Язык: Английский

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A conserved ARF–DNA interface underlies auxin-triggered transcriptional response

Proceedings of the National Academy of Sciences, Год журнала: 2025, Номер 122(14)

Опубликована: Апрель 1, 2025

Auxin Response Factor (ARF) plant transcription factors are the key effectors in auxin signaling. Their DNA-Binding Domain (DBD) contains a B3 domain that allows base-specific interactions with Elements (AuxREs) DNA target sites. Land plants encode three phylogenetically distinct ARF classes: closely related A- and B-classes have overlapping binding properties, contrasting different DNA-binding properties of divergent C-class ARFs. divergence likely occurred early evolution gene family, but molecular determinants underlying it remain unclear. Here, we show residues deeply conserved ARFs, variability within these is only present tracheophytes, correlating greatly expanded families. Using liverwort Marchantia polymorpha , confirm essential role DNA-contacting for function. We further B3–AuxRE interfaces not mutation-tolerant, suggesting low evolvability has led to conservation B3–DNA interface between classes. Our data support almost complete interchangeability A/B-class by performing interspecies swaps M. even lineages diverged over half billion years ago. analysis suggests specificity during common streptophyte ancestor, followed strong selection A B-class ARFs as part competition-based response system.

Язык: Английский

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To bind or not to bind: how AUXIN RESPONSE FACTORs select their target genes

Journal of Experimental Botany, Год журнала: 2023, Номер 74(22), С. 6922 - 6932

Опубликована: Июль 11, 2023

Abstract Most plant growth and development processes are regulated in one way or another by auxin. The best-studied mechanism which auxin exerts its regulatory effects is through the nuclear pathway (NAP). In this pathway, Auxin Response Factors (ARFs) transcription factors that ultimately determine genes become binding to specific DNA sequences. ARFs have primarily been studied Arabidopsis thaliana, but recent studies other species revealed family-wide specificities for different minimal functional system of NAP system, consisting a duo competing A B classes. review, we provide an overview key aspects ARF such as response elements (TGTCNN) tandem repeat motifs, consider how structural biology vitro help us understand preferences. We also highlight some related regulation levels inside cell, may alter profile tissues. finally emphasize need study systems fundamental function, characterize algal evolved, cutting-edge techniques can increase our understanding ARFs, remaining questions only be answered biology.

Язык: Английский

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Game of thrones among AUXIN RESPONSE FACTORs—over 30 years of MONOPTEROS research

Journal of Experimental Botany, Год журнала: 2023, Номер 74(22), С. 6904 - 6921

Опубликована: Июль 11, 2023

For many years, research has been carried out with the aim of understanding mechanism auxin action, its biosynthesis, catabolism, perception, and transport. One central interest is auxin-dependent gene expression regulation involving AUXIN RESPONSE FACTOR (ARF) transcription factors their repressors, AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) proteins. Numerous studies have focused on MONOPTEROS (MP)/ARF5, an activator a crucial impact plant development. This review summarizes over 30 years MP/ARF5. We indicate available analytical tools to study MP/ARF5 point known MP/ARF5-dependent during various developmental processes, namely embryogenesis, leaf formation, vascularization, shoot root meristem formation. However, questions remain about dose-dependent by isoforms in cells, composition protein complex, and, finally, all genes under direct control. In addition, information post-translational modifications marginal, knowledge consequences function limited. Moreover, epigenetic other regulators that act upstream are poorly understood. Their identification will be challenge coming years.

Язык: Английский

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Transcriptome-wide m6A modification and poly(A) tail length changes in moso bamboo induced by gibberellin revealed by nanopore direct RNA sequencing

Industrial Crops and Products, Год журнала: 2025, Номер 225, С. 120549 - 120549

Опубликована: Янв. 22, 2025

Язык: Английский

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Specificity landscapes of 40 R2R3‐MYBs reveal how paralogs target different cis‐elements by homodimeric binding

iMeta, Год журнала: 2025, Номер 4(2)

Опубликована: Март 5, 2025

Paralogous transcription factors (TFs) frequently recognize highly similar DNA motifs. Homodimerization can help distinguish them according to their different dimeric configurations. Here, by studying R2R3-MYB TFs, we show that homodimerization also directly change the recognized motifs between TFs. By high-throughput SELEX, profiled specificity landscape for 40 R2R3-MYBs of subfamily VIII and curated 833 motif models. The models homodimeric binding has evoked changes AtMYBs. Focusing on AtMYB2 as an example, modified its allowed it additional cis-regulatory sequences are from closely related CCWAA-box AtMYBs unique among all Genomic sites described specificities conserved in evolution involved AtMYB2-specific transcriptional activation. Collectively, this study provides rich data sequence preferences suggests alternative mechanism guides TFs respective sites.

Язык: Английский

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Synthetic deconvolution of an auxin-dependent transcriptional code

Cell, Год журнала: 2025, Номер unknown

Опубликована: Апрель 1, 2025

Язык: Английский

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Clade-D auxin response factors regulate auxin signaling and development in the moss Physcomitrium patens

PLoS Biology, Год журнала: 2023, Номер 21(6), С. e3002163 - e3002163

Опубликована: Июнь 14, 2023

Auxin response factors (ARFs) are a family of transcription that responsible for regulating gene expression in to changes auxin level. The analysis ARF sequence and activity indicates there 2 major groups: activators repressors. One clade ARFs, clade-D, is sister clade-A activating but unique they lack DNA-binding domain. Clade-D ARFs present lycophytes bryophytes absent other plant lineages. transcriptional clade-D as well how regulate expression, not understood. Here, we report the model bryophyte Physcomitrium patens have role development this species. Δarfd dub protonemata exhibit delay filament branching, chloronema caulonema transition. Additionally, leafy gametophore lines lags behind wild type. We evidence ARFd1 interacts with via their PB1 domains, repressing ARFs. Based on these results, propose which enhance by interacting DNA bound Further, show must form oligomers full activity.

Язык: Английский

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Plant Synthetic Promoters

Опубликована: Апрель 17, 2024

The article features the structure and functions of plant synthetic promoters frequently exercised to precisely regulate complex regulatory routes. composition native together with interacting proteins is presented provide a better understanding tasks associated promoter development. production conferred on relatively small libraries produced generally by basic molecular or genetic engineering methods such as cis-element shuffling domain swapping. Moreover, preparation large-scale supported DNA fragments, directed evolution, machine deep learning methodologies presented. A particularly interesting group are bidirectional forms that enable putative expression up 6–8 genes one element. introduction controlled several after transgenic event strongly decreases frequency problems segregation patterns random integration multiple transgenes. These complications commonly observed during crop development through traditional, multistep transformation constructs containing single gene. Another path solving low complexity homology already tested fragments orthogonal systems composed trans-factors do not occur in nature arise from different species. Their structure, functions, applications rendered article.

Язык: Английский

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Plant Synthetic Promoters

Applied Sciences, Год журнала: 2024, Номер 14(11), С. 4877 - 4877

Опубликована: Июнь 4, 2024

This article examines the structure and functions of plant synthetic promoters frequently used to precisely regulate complex regulatory routes. It details composition native their interacting proteins provide a better understanding tasks associated with promoter development. The production is performed by relatively small libraries produced generally basic molecular or genetic engineering methods such as cis-element shuffling domain swapping. also describes preparation large-scale supported DNA fragments, directed evolution, machine deep-learning methodologies. broader application novel, reduces prevalence homology-based gene silencing improves stability transgenes. A particularly interesting group are bidirectional forms, which can enable expression up eight genes one element. introduction controlled several after transgenic event strongly decreases frequency problems segregation patterns random integration multiple These complications commonly observed during crop development enabled traditional, multistep transformation using constructs containing single gene. As previously tested fragments demonstrate low complexity homology, abundance be increased orthogonal systems composed trans-factors that do not occur in nature arise from different species. Their structure, functions, applications rendered article. Among them presented based on transcription activator-like effectors (dTALEs), dTALE activated (STAPs) dCas9-dependent artificial (ATFs). Synthetic valuable tools for providing precise spatiotemporal regulation introducing logic gates into traits important research studies Precisely regulated metabolic routes less prone undesirable feedback energy waste, thus improving efficiency crops.

Язык: Английский

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