Deciphering the molecular basis of tissue-specific gene expression in plants: Can synthetic biology help?

Yaschenko, Anna; Fenech, Mario; Mazzoni-Putman, Serina; Alonso, José M.; Stepanova, Anna N.

doi:10.1016/j.pbi.2022.102241

Cited by 18 publications

(4 citation statements)

References 102 publications

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“…Between the three tissues, 91.59% of all quantified histone PTMs were significantly different based on their M -values. This finding supports the notion that histone PTMs uphold patterns of gene expression determined during cellular differentiation and tissue formation. ,− Overall, the kidney and testes were the two most dissimilar tissues, as they differed in 72.43% of their histone PTMs. The two most similar tissues were the gills and kidney, where 64.49% of histone PTMs was significantly different.…”

Section: Discussionsupporting

confidence: 79%

A Strategy to Characterize the Global Landscape of Histone Post-Translational Modifications Within Tissues of Nonmodel Organisms

Mojica,

Kültz

2023

J. Proteome Res.

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Histone post-translational modifications (PTMs) are epigenetic marks that play a critical role in the expression and maintenance of DNA, but they remain largely uninvestigated in nonmodel organisms due to technical challenges. To begin alleviating this issue, we developed a workflow for histone PTM analysis in Mozambique tilapia (Oreochromis mossambicus), being a widespread and environmentally hardy fish, using mass spectrometry methods. By incorporating multiple protein digestion methods into the preparation of each sample, we reliably quantified 214 biologically relevant histone PTMs. All of these histone PTMs, collectively referred to as the global histone PTM landscape, were characterized in the gills, kidney, and testes of this fish. By comparing the global histone PTM landscape between the three tissues, we found that 91.59% of histone PTMs were tissue-dependent. The workflow and tools for histone PTM analysis described in this study are now publicly available and enable comprehensive investigation into the influence of environmental stress on histone PTMs in nonmodel organisms. Given the functionality and flexibility of histone PTMs, we anticipate that the study of histone PTMs in ecologically relevant contexts will provide ground-breaking insights into comparative physiology and evolution.

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Section: Discussionsupporting

confidence: 79%

A Strategy to Characterize the Global Landscape of Histone Post-Translational Modifications Within Tissues of Nonmodel Organisms

Mojica,

Kültz

2023

J. Proteome Res.

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“…Tissue-specific expression differences are one of the most critical indicators of functional differentiation among genes and facilitate the regulation of various physiological processes by eliminating their redundancy [ 79 ]. The expression profiles suggest that most TaZFPs are involved in multiple plant growth and development processes and have tissue-specific or preferential expression patterns.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of the Zinc Finger Protein Gene Subfamilies under Drought Stress in Triticum aestivum

Shen

Wang

et al. 2022

Plants

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The zinc finger protein (ZFP) family is one of plants’ most diverse family of transcription factors. These proteins with finger-like structural domains have been shown to play a critical role in plant responses to abiotic stresses such as drought. This study aimed to systematically characterize Triticum aestivum ZFPs (TaZFPs) and understand their roles under drought stress. A total of 9 TaC2H2, 38 TaC3HC4, 79 TaCCCH, and 143 TaPHD were identified, which were divided into 4, 7, 12, and 14 distinct subgroups based on their phylogenetic relationships, respectively. Segmental duplication dominated the evolution of four subfamilies and made important contributions to the large-scale amplification of gene families. Syntenic relationships, gene duplications, and Ka/Ks result consistently indicate a potential strong purifying selection on TaZFPs. Additionally, TaZFPs have various abiotic stress-associated cis-acting regulatory elements and have tissue-specific expression patterns showing different responses to drought and heat stress. Therefore, these genes may play multiple functions in plant growth and stress resistance responses. This is the first comprehensive genome-wide analysis of ZFP gene families in T. aestivum to elucidate the basis of their function and resistance mechanisms, providing a reference for precise manipulation of genetic engineering for drought resistance in T. aestivum.

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“…In molecular biology, single-cell RNA-sequencing (scRNA-seq) is a high-resolution method is growing in popularity for studying plant functional genomes and transcriptional activity at the single-cell level. This method enabled researchers to examine heterogeneity in plants within different cell types ( Yaschenko et al., 2022 ). The polyploidization events in plants were poorly understood by traditional transcriptome studies.…”

Section: Multi-omics Techniques Accelerate the Genetic Dissection Of ...mentioning

confidence: 99%

Multi-omics revolution to promote plant breeding efficiency

Mahmood

Li²,

Fan³

et al. 2022

Front. Plant Sci.

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Crop production is the primary goal of agricultural activities, which is always taken into consideration. However, global agricultural systems are coming under increasing pressure from the rising food demand of the rapidly growing world population and changing climate. To address these issues, improving high-yield and climate-resilient related-traits in crop breeding is an effective strategy. In recent years, advances in omics techniques, including genomics, transcriptomics, proteomics, and metabolomics, paved the way for accelerating plant/crop breeding to cope with the changing climate and enhance food production. Optimized omics and phenotypic plasticity platform integration, exploited by evolving machine learning algorithms will aid in the development of biological interpretations for complex crop traits. The precise and progressive assembly of desire alleles using precise genome editing approaches and enhanced breeding strategies would enable future crops to excel in combating the changing climates. Furthermore, plant breeding and genetic engineering ensures an exclusive approach to developing nutrient sufficient and climate-resilient crops, the productivity of which can sustainably and adequately meet the world’s food, nutrition, and energy needs. This review provides an overview of how the integration of omics approaches could be exploited to select crop varieties with desired traits.

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Deciphering the molecular basis of tissue-specific gene expression in plants: Can synthetic biology help?

Cited by 18 publications

References 102 publications

A Strategy to Characterize the Global Landscape of Histone Post-Translational Modifications Within Tissues of Nonmodel Organisms

A Strategy to Characterize the Global Landscape of Histone Post-Translational Modifications Within Tissues of Nonmodel Organisms

Genome-Wide Identification and Expression Analysis of the Zinc Finger Protein Gene Subfamilies under Drought Stress in Triticum aestivum

Multi-omics revolution to promote plant breeding efficiency

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