CRISPR/Cas9-mediated base-editing system efficiently generates gain-of-function mutations in Arabidopsis

Chen, Yiyu; Wang, Zhiping; Ni, Hanwen; Xu, Yiru; Chen, Qijun; Jiang, Linjian

doi:10.1007/s11427-017-9021-5

Cited by 135 publications

(72 citation statements)

References 4 publications

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“…In addition to the ten-2 null-mutant, we also identified two other TEN-edited plants, ten-3 with a homozygous in-frame deletion of two amino acids (Gln 54 and Asp 55 ), and ten-4 with a homozygous in-frame deletion of 12 amino acids (Fig. 1b).…”

Section: Resultsmentioning

confidence: 94%

A non-canonical histone acetyltransferase targets intragenic enhancers and regulates plant architecture

Yang

Yan

Zhang

et al. 2020

Preprint

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31Axillary meristem development determines both plant architecture and crop yield; this 32 critical process is regulated by the TCP transcription factor (TF) family, including the 33 maize TB1 and Arabidopsis BRC1. Studies have shown that both TB1 and AtBRC1 can 34 target the gene body regions of some target genes and activate their expression; 35 however, the regulatory mechanisms remain largely unknown. Here, we show that a 36 cucumber CYC/TB1 homologue, TEN, controls the identity and mobility of tendrils. 37Through its C-terminus, TEN binds at intragenic enhancers of target genes; its N-38 terminal domain functions as a novel, non-canonical histone acetyltransferase (HAT) 39 to preferentially act on lysine 56 and 122, of the histone H3 globular domain. This HAT 40 activity is responsible for chromatin loosening and host gene activation. The N-termini 41 of all tested CYC/TB1-like proteins contain an intrinsically disordered region (IDR), 42 and despite their sequence divergence, they have conserved HAT activity. This study 43 discovered a non-canonical class of HATs, and as well, provides a mechanism by which 44 modification at the H3 globular domain is integrated with the transcription process. 45 4 TEOSINTE BRANCHED 1 (TB1), CYCLOIDEA (CYC), and PROLIFERATING 46 CELL FACTORS (TCP) transcription factors (TFs) constitute a plant-specific gene 47 family involved in a broad range of developmental processes 1 . Among them, the 48 CYC/TB1 clade of the TCP proteins plays central roles in controlling development of 49 axillary buds that give rise to either flowers or lateral shoots 1,2 . In maize (Zea mays L.), 50 the major domestication gene, TB1, suppresses branch outgrowth, a crucial 51 architectural modification that transformed teosinte into a viable crop 3 . Subsequent 52 studies on its homologues in rice 4 and Arabidopsis thaliana 5 identified their similar 53 essential roles in repressing axillary bud growth. 54Recently, a genome-wide binding profile uncovered a genetic pathway putatively 55 regulated by TB1 6 . The study reported that TB1 binds mainly to promoters, with only 56 a few peaks located within gene body regions. Nevertheless, other studies have also 57 shown that TB1, and its homologue BRANCHED1 in Arabidopsis, can bind to the gene 58 bodies of the target genes Tassels Replace Upper Ears1 (Tru1) 7 and HOMEOBOX 59 PROTEIN53 8 , respectively, to activate their expression. However, the mechanism 60 underlying how the intragenic binding of CYC/TB1-like TFs regulates gene expression 61 is still unclear. Understanding the conserved regulatory mechanism, associated with the 62 function of these CYC/TB1-like proteins, would provide insight into their core role in 63 signal integration of axillary bud repression. Such knowledge could broadly benefit 64 crop breeding programs for tailored plant architecture. 65In eukaryotes, enhancers are cis-acting DNA sequences which, when bound by 66 specific TFs, increase the transcription in a manner that is independent of their 67 orientation and distance relative to...

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Section: Resultsmentioning

confidence: 94%

A non-canonical histone acetyltransferase targets intragenic enhancers and regulates plant architecture

Yang

Yan

Zhang

et al. 2020

Preprint

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“…This technique has been successfully used for genome editing of several plant species, such as rice (Chen et al, 2017; Li et al, 2017; Ren et al, 2017), maize (Svitashev et al, 2016; Shi et al, 2017; Zong et al, 2017) and even in the hexaploid wheat (Gil-Humanes et al, 2017). Multiplex genome editing has also been demonstrated successfully from two genes belonging to the same family in Arabidopsis (Li J. F. et al, 2013) to simultaneous targeting 14 distinct genome loci with no detectable off-target events (Peterson et al, 2016).…”

Section: A New Perspective For Sugarcane Improvement: Genome Editingmentioning

confidence: 99%

Sugarcane Water Stress Tolerance Mechanisms and Its Implications on Developing Biotechnology Solutions

et al. 2017

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Sugarcane is a unique crop with the ability to accumulate high levels of sugar and is a commercially viable source of biomass for bioelectricity and second-generation bioethanol. Water deficit is the single largest abiotic stress affecting sugarcane productivity and the development of water use efficient and drought tolerant cultivars is an imperative for all major sugarcane producing countries. This review summarizes the physiological and molecular studies on water deficit stress in sugarcane, with the aim to help formulate more effective research strategies for advancing our knowledge on genes and mechanisms underpinning plant response to water stress. We also overview transgenic studies in sugarcane, with an emphasis on the potential strategies to develop superior sugarcane varieties that improve crop productivity in drought-prone environments.

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“…Nonetheless, indel rates are still lower than using traditional HDR-based CRISPR-Cas9 gene editing (Li et al, 2013; Mao et al, 2013). Base editing tools have also been successfully used in wheat, maize (Zong et al, 2017), and Arabidopsis (Chen et al, 2017). Delivery of base editing systems to plants has been performed using either transformed agrobacterium (Hooykaas and Schilperoort, 1992; Voytas, 2013) or biolistic particle bombardment (Sanford, 1988).…”

Section: Section 2: Applications Of Base Editingmentioning

confidence: 99%

Methods and Applications of CRISPR-Mediated Base Editing in Eukaryotic Genomes

et al. 2017

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The past several years have seen an explosion in development of applications for the CRISPR-Cas9 system, from efficient genome editing, to high-throughput screening, to recruitment of a range of DNA and chromatin-modifying enzymes. While homology-directed repair (HDR) coupled with Cas9 nuclease cleavage has been used with great success to repair and re-write genomes, recently developed base editing systems present a useful orthogonal strategy to engineer nucleotide substitutions. Base editing relies on recruitment of cytidine deaminases to introduce changes (rather than double stranded breaks and donor templates), and offers potential improvements in efficiency while limiting damage and simplifying the delivery of editing machinery. At the same time, these systems enable novel mutagenesis strategies to introduce sequence diversity for engineering and discovery. Here, we review the different base editing platforms, including their deaminase recruitment strategies and editing outcomes, and compare them to other CRISPR genome editing technologies. Additionally, we discuss how these systems have been applied in therapeutic, engineering, and research settings. Lastly, we explore future directions of this emerging technology.

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CRISPR/Cas9-mediated base-editing system efficiently generates gain-of-function mutations in Arabidopsis

Cited by 135 publications

References 4 publications

A non-canonical histone acetyltransferase targets intragenic enhancers and regulates plant architecture

A non-canonical histone acetyltransferase targets intragenic enhancers and regulates plant architecture

Sugarcane Water Stress Tolerance Mechanisms and Its Implications on Developing Biotechnology Solutions

Methods and Applications of CRISPR-Mediated Base Editing in Eukaryotic Genomes

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