Regulation of plant architecture by a new histone acetyltransferase targeting gene bodies

Yang, Xueyong; Yan, Jianbin; Zhang, Zhen; Lin, Tao; Xin, Tongxu; Wang, Bowen; Wang, Shenhao; Zhao, Ji‐Cheng; Zhang, Zhonghua; Lucas, William J.; Li, Guohong; Huang, Sanwen

doi:10.1038/s41477-020-0715-2

Cited by 40 publications

(32 citation statements)

References 61 publications

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“…Moreover, ethylene has been found to induce spontaneous tendril coiling, and TEN was shown to be recruited to exons of both ACC OXIDASE 1 ( ACO1 ) and ETHYLENE RESPONSE FACTOR 1 ( ERF1 ) to regulate their transcription. The tendril coiling capacity is substantially altered in aco-1 and aco-2 mutant plants 68 . Similarly, CLT, the ortholog of TEN in melon, was also identified as a key regulator determining tendril identity 69 .…”

Section: Cucumber Is a Climbing Plant Due To Tendrilsmentioning

confidence: 97%

“…Then, the touch-sensitive region near the tendril tip senses a thigmotropic signal and begins to climb the perceived structure within seconds or minutes via twining. Finally, tendrils coil by forming two opposing helices with approximately 10 turns on each side of a perversion point to host the plant shoot toward the attachment point 65 , 67 , 68 . Studies have shown that lignified gelatinous fiber ribbons are found on only the ventral side of tendrils, resulting in the ventral side shrinking longitudinally relative to the dorsal side through asymmetric contraction and tendril coiling in cucumber 67 .…”

Section: Cucumber Is a Climbing Plant Due To Tendrilsmentioning

confidence: 99%

“…The causal gene underlying the ten mutant is TENDRIL-LESS ( TEN ), which encodes a TCP transcription factor expressed specifically in tendrils 67 . Further study showed that the C-terminus and N-terminus of TEN perform different functions to regulate tendril identity and coiling 68 . TEN binds to intragenic enhancers (CDCCRCC motifs) of target genes through the C-terminal domain, whereas its N-terminus functions as a noncanonical histone acetyltransferase to preferentially modify the H3 globular domain; thus, the C- and N-terminus coordinately participate in chromatin loosening and host gene activation 68 .…”

Section: Cucumber Is a Climbing Plant Due To Tendrilsmentioning

confidence: 99%

“…Further study showed that the C-terminus and N-terminus of TEN perform different functions to regulate tendril identity and coiling 68 . TEN binds to intragenic enhancers (CDCCRCC motifs) of target genes through the C-terminal domain, whereas its N-terminus functions as a noncanonical histone acetyltransferase to preferentially modify the H3 globular domain; thus, the C- and N-terminus coordinately participate in chromatin loosening and host gene activation 68 . Moreover, ethylene has been found to induce spontaneous tendril coiling, and TEN was shown to be recruited to exons of both ACC OXIDASE 1 ( ACO1 ) and ETHYLENE RESPONSE FACTOR 1 ( ERF1 ) to regulate their transcription.…”

Section: Cucumber Is a Climbing Plant Due To Tendrilsmentioning

confidence: 99%

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Genetic regulation of shoot architecture in cucumber

2021

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Cucumber (Cucumis sativus L.) is an important vegetable crop species with great economic value. Shoot architecture determines the visual appearance of plants and has a strong impact on crop management and yield. Unlike most model plant species, cucumber undergoes vegetative growth and reproductive growth simultaneously, in which leaves are produced from the shoot apical meristem and flowers are generated from leaf axils, during the majority of its life, a feature representative of the Cucurbitaceae family. Despite substantial advances achieved in understanding the regulation of plant form in Arabidopsis thaliana, rice, and maize, our understanding of the mechanisms controlling shoot architecture in Cucurbitaceae crop species is still limited. In this review, we focus on recent progress on elucidating the genetic regulatory pathways underlying the determinant/indeterminant growth habit, leaf shape, branch outgrowth, tendril identity, and vine length determination in cucumber. We also discuss the potential of applying biotechnology tools and resources for the generation of ideal plant types with desired architectural features to improve cucumber productivity and cultivation efficiency.

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Section: Cucumber Is a Climbing Plant Due To Tendrilsmentioning

confidence: 97%

Section: Cucumber Is a Climbing Plant Due To Tendrilsmentioning

confidence: 99%

Section: Cucumber Is a Climbing Plant Due To Tendrilsmentioning

confidence: 99%

Section: Cucumber Is a Climbing Plant Due To Tendrilsmentioning

confidence: 99%

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Genetic regulation of shoot architecture in cucumber

2021

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“…In cucumber, branches and tendrils are homologous lateral organs (Yang et al, 2020). In early spring, WI1983Hde showed a very severe determinate growth habit and grew only to within 10 nodes.…”

Section: Absent Expression Of Cstfl1 and Cstfl1d Has Major Impacts On Cucumber Architecturementioning

confidence: 99%

TERMINAL FLOWER 1 and TERMINAL FLOWER 1d respond to temperature and photoperiod signals to inhibit determinate growth in cucumber

Wen

Pan

Chen

et al. 2021

Plant Cell & Environment

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Plants monitor environmental cues to balance their vegetative and productive growth by optimizing their inflorescence architecture. TERMINAL FLOWER 1 (TFL1) and its orthologs regulate the inflorescence structure in cucumber, yet the mechanisms underlying their responses to environmental factors and the formation of terminal flowers remain elusive. Here, we performed map-based cloning to identify the gene that controls a season-dependent determinate growth phenotype and found that it was caused by the complete deletion of CsTFL1 in the genome of cucumber line WI1983Hde. In the CsTFL1 deletion plants (CsTFL1 del ), determinate growth could be partially rescued by high-temperature and long-day conditions. The expressions of CsTFL1 and its ortholog CsTFL1d could be upregulated by long-day and hightemperature signals. Knockdown of CsTFL1d resulted in determinate growth and the formation of terminal flowers in WT. These results indicate that the induction of CsTFL1d expression by long-day and high-temperature might partially rescue determinate growth of CsTFL1 del . Furthermore, biochemical analyses showed that CsTFL1d interacts directly with CsNOT2a, which indicated that CsTFL1d and CsTFL1 function via similar regulatory mechanism. Our data suggest that CsTFL1 and CsTFL1d co-contribute to inhibit determinate growth by responding to temperature and photoperiod signals. It provides mechanistic insights into how environmental cues sculpt the inflorescence architecture of cucumber.

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Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks

et al. 2022

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Accessible chromatin regions are critical components of gene regulation but modeling them directly from sequence remains challenging, especially within plants, whose mechanisms of chromatin remodeling are less understood than in animals. We trained an existing deep learning architecture, DanQ, on leaf ATAC-seq data from 12 angiosperm species to predict the chromatin accessibility of sequence windows within and across species. We also trained DanQ on DNA methylation data from 10 angiosperms, because unmethylated regions have been shown to overlap significantly with accessible chromatin regions in some plants. The across-species models have comparable or even superior performance to a model trained within species, suggesting strong conservation of chromatin mechanisms across angiosperms. Testing a maize held out model on a multi-tissue scATAC panel revealed our models are best at predicting constitutively-accessible chromatin regions, with diminishing performance as cell-type specificity increases. Using a combination of interpretation methods, we ranked JASPAR motifs by their importance to each model and saw that the TCP and AP2/ ERF transcription factor families consistently ranked highly. We embedded the top three JASPAR motifs for each model at all possible positions on both strands in our sequence window and observed position-and strand-specific patterns in their importance to the model. With our cross-species "a2z" model it is now feasible to predict the chromatin accessibility and methylation landscape of any angiosperm genome.

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Regulation of plant architecture by a new histone acetyltransferase targeting gene bodies

Cited by 40 publications

References 61 publications

Genetic regulation of shoot architecture in cucumber

Genetic regulation of shoot architecture in cucumber

TERMINAL FLOWER 1 and TERMINAL FLOWER 1d respond to temperature and photoperiod signals to inhibit determinate growth in cucumber

Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks

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