Targeted DNA demethylation of the
            <i>Arabidopsis</i>
            genome using the human TET1 catalytic domain

Gallego-Bartolomé, Javier; Gardiner, Jason; Liu, Wanlu; Papikian, Ashot; Ghoshal, Basudev; Kuo, Hsuan Yu; Zhao, Jiannan; Segal, David J.; Jacobsen, Steven E.

doi:10.1073/pnas.1716945115

Cited by 212 publications

(164 citation statements)

References 49 publications

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“…In addition, CRISPR/ Cas-mediated cis-engineering has also been achieved to edit the epigenome. However, only a handful of cases have been described in Arabidopsis that show epigenome editing by altering DNA methylation 65,66 and histone acetylation 67 . Because of the few examples in epigenome editing, the following sections will only describe the applications of cis-engineering of DNA.…”

Section: Recent Progress In Crispr/cas-mediated Cisengineering In Plantsmentioning

confidence: 99%

Perspectives of CRISPR/Cas-mediated cis-engineering in horticulture: unlocking the neglected potential for crop improvement

Sapkota

Knaap

2020

Hortic Res

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Directed breeding of horticultural crops is essential for increasing yield, nutritional content, and consumer-valued characteristics such as shape and color of the produce. However, limited genetic diversity restricts the amount of crop improvement that can be achieved through conventional breeding approaches. Natural genetic changes in cisregulatory regions of genes play important roles in shaping phenotypic diversity by altering their expression. Utilization of CRISPR/Cas editing in crop species can accelerate crop improvement through the introduction of genetic variation in a targeted manner. The advent of CRISPR/Cas-mediated cis-regulatory region engineering (cis-engineering) provides a more refined method for modulating gene expression and creating phenotypic diversity to benefit crop improvement. Here, we focus on the current applications of CRISPR/Cas-mediated cis-engineering in horticultural crops. We describe strategies and limitations for its use in crop improvement, including de novo cis-regulatory element (CRE) discovery, precise genome editing, and transgene-free genome editing. In addition, we discuss the challenges and prospects regarding current technologies and achievements. CRISPR/Cas-mediated cis-engineering is a critical tool for generating horticultural crops that are better able to adapt to climate change and providing food for an increasing world population.

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Section: Recent Progress In Crispr/cas-mediated Cisengineering In Plantsmentioning

confidence: 99%

Perspectives of CRISPR/Cas-mediated cis-engineering in horticulture: unlocking the neglected potential for crop improvement

Sapkota

Knaap

2020

Hortic Res

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“…Vice versa , targeted epigenetic repression in mammalian cells can be achieved by demethylation of H3K4/K9 through the histone demethylase LSD1 (Kearns et al ). The potential of developing new epialleles for generating traits of interest has been successfully demonstrated in Arabidopsis by targeted demethylation of a specific cytosine residue in the promoter of the FWA gene, resulting in a heritable late‐flowering phenotype (Gallego‐Bartolomé et al ).…”

Section: Modifications and Extensions Of Cas Endonucleasesmentioning

confidence: 99%

The CRISPR/Cas revolution continues: From efficient gene editing for crop breeding to plant synthetic biology

Kumlehn

Pietralla

Hensel

et al. 2018

JIPB

101

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Since the discovery that nucleases of the bacterial CRISPR (clustered regularly interspaced palindromic repeat)‐associated (Cas) system can be used as easily programmable tools for genome engineering, their application massively transformed different areas of plant biology. In this review, we assess the current state of their use for crop breeding to incorporate attractive new agronomical traits into specific cultivars of various crop plants. This can be achieved by the use of Cas9/12 nucleases for double‐strand break induction, resulting in mutations by non‐homologous recombination. Strategies for performing such experiments − from the design of guide RNA to the use of different transformation technologies − are evaluated. Furthermore, we sum up recent developments regarding the use of nuclease‐deficient Cas9/12 proteins, as DNA‐binding moieties for targeting different kinds of enzyme activities to specific sites within the genome. Progress in base deamination, transcriptional induction and transcriptional repression, as well as in imaging in plants, is also discussed. As different Cas9/12 enzymes are at hand, the simultaneous application of various enzyme activities, to multiple genomic sites, is now in reach to redirect plant metabolism in a multifunctional manner and pave the way for a new level of plant synthetic biology.

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“…2) These findings hint towards a possibility where genes involved in nitrogen and carbohydrate metabolism were repeatedly deployed or targeted for gene body methylation during evolution, to help balance their expression for optimal function. In future it will be interesting to identify specific genes in these processes and generate epi-alleles by targeted epigenome editing using CRISPR-technology (Gallego-Bartolome et al, 2018) to generate Pigeonpea and soybean varieties with higher protein content, without altering the DNA sequence.…”

Section: Discussionmentioning

confidence: 99%

Patterns of gene-body-methylation conservation and its divergent association with gene expression in Pigeonpea and Soybean

Junaid¹,

Singh²,

Gaikwad³

2020

Preprint

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Pigeonpea and Soybean are closely related agronomically important legumes that diverged ∼23 million years ago followed by a whole genome duplication event in Soybean. However, the impact of divergence on their epigenomes is not known. Comparative epigenomics is a powerful tool to understand shaping of epigenomes and its functional consequences during evolution. In this study, we investigated the conservation and divergence of Gene body methylation (GbM) and gene-expression patterns between the two species. We compared their genome-wide DNA methylation landscape at single-base resolution and studied the influence of GbM on duplicate gene retention. Our results indicate that during the divergence of Pigeonpea and Soybean, the effects of methylation on gene expression evolved in a heterogeneous manner. GbM features-slow evolution rate and increased length remained conserved in Pigeonpea and Soybean. We also found that contrary to high CG-methylation conservation, non-CG methylated genes remained diverged during evolution due to transposons insertion in adjacent sequences. The methylation differences in paralogs were associated with expression divergence. Notably, we found that variably methylated marks are less likely to target evolutionary conserved sequences. Finally, our findings identify conservation of nitrogen-related genes during evolution, which are promising candidates for epi-alleles for crop improvement.

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Targeted DNA demethylation of the Arabidopsis genome using the human TET1 catalytic domain

Cited by 212 publications

References 49 publications

Perspectives of CRISPR/Cas-mediated cis-engineering in horticulture: unlocking the neglected potential for crop improvement

Perspectives of CRISPR/Cas-mediated cis-engineering in horticulture: unlocking the neglected potential for crop improvement

The CRISPR/Cas revolution continues: From efficient gene editing for crop breeding to plant synthetic biology

Patterns of gene-body-methylation conservation and its divergent association with gene expression in Pigeonpea and Soybean

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