Insulators in Plants: Progress and Open Questions

Kurbidaeva, Amina; Purugganan, Michael D.

doi:10.3390/genes12091422

Cited by 10 publications

(8 citation statements)

References 78 publications

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“…Alternatively, position effects based on chromatin structure and/or nearby transcriptional regulatory sequences may lead to increased expression and/or extend expression of A. lyrata YKT61 farther into meiosis, resulting in carryover into non- ClvR bearing gametes carrying a LOF mutation in YKT61. Incorporation of chromatin insulators 71 and/or targeting of other essential genes can minimize such effects.…”

Section: Resultsmentioning

confidence: 99%

Cleave and Rescue gamete killers create conditions for gene drive in plants

Oberhofer,

Johnson,

Ivy

et al. 2023

Preprint

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Gene drive elements promote the spread of linked traits, even when their presence confers a fitness cost to carriers, and can be used to change the composition or fate of wild populations. Cleave and Rescue (ClvR) drive elements sit at a fixed chromosomal position and include a DNA sequence-modifying enzyme such as Cas9/gRNAs (the Cleaver/Toxin) that disrupts endogenous versions of an essential gene, and a recoded version of the essential gene resistant to cleavage (the Rescue/Antidote).ClvRspreads by creating conditions in which those lackingClvRdie because they lack functional versions of the essential gene. We demonstrate the essential features ofClvRgene drive in the plantArabidopsis thalianathrough killing of gametes that fail to inherit aClvRthat targets the essential gene YKT61, whose expression is required in male and female gametes for their survival. Resistant (uncleavable but functional) alleles, which can slow or prevent drive, were not observed. Modeling shows plantClvRs can be used to rapidly drive population modification or suppression. Possible applications in weed control, plant breeding and conservation are discussed.

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Section: Resultsmentioning

confidence: 99%

Cleave and Rescue gamete killers create conditions for gene drive in plants

Oberhofer,

Johnson,

Ivy

et al. 2023

Preprint

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“…Due to the difference in insertion sites and copy number, the expression level of transgenes is highly variable due to positional effects and gene silencing. Inclusion of specific DNA sequences such as matrix attachment regions (MARs) and genetic insulators have been shown to reduce positional effects, suppress chromatin silencing and increase transgene expression [ 70 ] ( Figure 2 ). MARs are AT-rich DNA sequences that are believed to bind nuclear matrix and promote organization of chromosomal DNA in transcriptionally active states [ 71 , 72 , 73 ].…”

Section: Elements Of Genetic Constructs For Transcriptional Enhanceme...mentioning

confidence: 99%

“…MARs are AT-rich DNA sequences that are believed to bind nuclear matrix and promote organization of chromosomal DNA in transcriptionally active states [ 71 , 72 , 73 ]. Genetic insulators are DNA cis-acting elements that can inactivate the effect of distal or nearby enhancers, blockers and promoters on the expression of a gene when placed between the genes and the regulatory sequences of transcription [ 70 ]. NI29 is a genetic insulator from Arabidopsis with a 16-bp palindromic sequence.…”

Section: Elements Of Genetic Constructs For Transcriptional Enhanceme...mentioning

confidence: 99%

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Maximizing the Production of Recombinant Proteins in Plants: From Transcription to Protein Stability

Feng

Fan

et al. 2022

IJMS

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The production of therapeutic and industrial recombinant proteins in plants has advantages over established bacterial and mammalian systems in terms of cost, scalability, growth conditions, and product safety. In order to compete with these conventional expression systems, however, plant expression platforms must have additional economic advantages by demonstrating a high protein production yield with consistent quality. Over the past decades, important progress has been made in developing strategies to increase the yield of recombinant proteins in plants by enhancing their expression and reducing their degradation. Unlike bacterial and animal systems, plant expression systems can utilize not only cell cultures but also whole plants for the production of recombinant proteins. The development of viral vectors and chloroplast transformation has opened new strategies to drastically increase the yield of recombinant proteins from plants. The identification of promoters for strong, constitutive, and inducible promoters or the tissue-specific expression of transgenes allows for the production of recombinant proteins at high levels and for special purposes. Advances in the understanding of RNAi have led to effective strategies for reducing gene silencing and increasing recombinant protein production. An increased understanding of protein translation, quality control, trafficking, and degradation has also helped with the development of approaches to enhance the synthesis and stability of recombinant proteins in plants. In this review, we discuss the progress in understanding the processes that control the synthesis and degradation of gene transcripts and proteins, which underlie a variety of developed strategies aimed at maximizing recombinant protein production in plants.

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“…In the broader context, gene expression is regulated by various coding and noncoding regions encompassing far-localized elements; these include enhancers, silencers, insulators, gene-embedded promoters, introns, 3 ′ and 5 ′ untranslated regions (UTRs), and terminators. These affect not only the chromatin state or assembly of the RNA polymerase II preinitiation complex, but also the 3 ′ -end processing, stability, translation efficiency, and nuclear-to-cytoplasmic export of mRNAs [49][50][51][52][53][54].…”

Section: Introductionmentioning

confidence: 99%

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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Insulators in Plants: Progress and Open Questions

Cited by 10 publications

References 78 publications

Cleave and Rescue gamete killers create conditions for gene drive in plants

Cleave and Rescue gamete killers create conditions for gene drive in plants

Maximizing the Production of Recombinant Proteins in Plants: From Transcription to Protein Stability

Plant Synthetic Promoters

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