Cis-Regulatory Element Based Gene Finding: An Application in Arabidopsis Thaliana

Li, Yong; Zhu, Yanming; Liu, Yang; Shu, Yongjun; Meng, Fanjiang; Lu, Yanmin; Liu, Bei; Bai, Xi; Guo, Dianjing

doi:10.1142/9781848163324_0015

Cited by 2 publications

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“…To improve these ML and DL approaches, they are trained on synthetic, random DNA fragments to test a larger sequence space; models trained on such synthetic data can predict genomic activity better than those solely trained on genome DNA [46,251]. More complex relationships between synthetic promoter structure, activity and DNA methylation or histone acetylation status are efficiently addressed by multilayered DL algorithms, while the ML models could not grasp these labyrinthine qualities precisely [242,[247][248][249][250].…”

Section: Discussionmentioning

confidence: 99%

“…However, such ML approaches cannot properly predict the properties of synthetic promoter sequences in the context of other regulatory elements such as the position of enhancers, 3 ′ and 5 ′ UTRs, DNA methylation or histone acetylation status [50,245,246]. These details should be included in the more advanced form of ML, known as deep learning (DL), which uses multi-layer perceptron (MLP), convolutional neural networks (CNN) and generative adversarial networks (GAN) to analyze complex patterns and relationships in data [49,85,242,[247][248][249][250]. DL models implemented in over 20,000 mRNA datasets in seven model organisms from bacteria to humans indicated that the expression of a gene is controlled not by a single regulatory motif or region, but by the entire gene regulatory structure and specific combinations of regulatory elements [49].…”

Section: Machine Learning and Deep Learning Support To Synthetic Prom...mentioning

confidence: 99%

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Plant Synthetic Promoters

Szymczyk,

Majewska

2024

Applied Sciences

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

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Section: Discussionmentioning

confidence: 99%

Section: Machine Learning and Deep Learning Support To Synthetic Prom...mentioning

confidence: 99%

Plant Synthetic Promoters

Szymczyk,

Majewska

2024

Applied Sciences

View full text Add to dashboard Cite

show abstract

“…Such basic ML approaches cannot properly predict the properties of synthetic promoter sequences in the context of other regulatory elements such as the position of enhancers, 3' and 5UTR, DNANA methylatio or histone acetylation status [50,242,[245][246][247]. These details should be included in the more advanced form of ML, known as DL, which uses neural networks such as artificial neural networks (ANN) and convolutional neural networks (CNN), offering multiple layers to analyze complex pa erns and relationships in data [85,248,249].…”

Section: Machine Learning and Deep Learning Support To Synthetic Prom...mentioning

confidence: 99%

Plant Synthetic Promoters

Szymczyk,

Majewska

2024

Preprint

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

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Cis-Regulatory Element Based Gene Finding: An Application in Arabidopsis Thaliana

Cited by 2 publications

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Plant Synthetic Promoters

Plant Synthetic Promoters

Plant Synthetic Promoters

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