Identification of Plant Enhancers and Their Constituent Elements by STARR-seq in Tobacco Leaves

Jores, Tobias; Tonnies, Jackson; Dorrity, Michael W.; Cuperus, Josh T.; Fields, Stanley; Queitsch, Christine

doi:10.1105/tpc.20.00155

Cited by 73 publications

(83 citation statements)

References 61 publications

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“…To maximize the use of natural variation, and for synthetic biology to realize its full potential, deeper knowledge of regulatory modules is paramount to facilitate crop improvement. Numerous reporter assays are now being developed and implemented for the identification and functional characterization of CRMs ( Inoue and Ahituv, 2015 ; Ricci et al, 2019 ; Sun et al, 2019 ; Jores et al, 2020 ), but there is still a need for more epigenome maps from many different cell types and growth conditions.…”

Section: Introductionmentioning

confidence: 99%

Cis-regulatory sequences in plants: Their importance, discovery, and future challenges

2021

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The identification and characterization of cis-regulatory DNA sequences and how they function to coordinate responses to developmental and environmental cues is of paramount importance to plant biology. Key to these regulatory processes are cis-regulatory modules (CRMs), which include enhancers and silencers. Despite the extraordinary advances in high-quality sequence assemblies and genome annotations, the identification and understanding of CRMs, and how they regulate gene expression, lag significantly behind. This is especially true for their distinguishing characteristics and activity states. Here, we review the current knowledge on CRMs and breakthrough technologies enabling identification, characterization, and validation of CRMs; we compare the genomic distributions of CRMs with respect to their target genes between different plant species, and discuss the role of transposable elements harboring CRMs in the evolution of gene expression. This is an exciting time to study cis-regulomes in plants; however, significant existing challenges need to be overcome to fully understand and appreciate the role of CRMs in plant biology and in crop improvement.

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Section: Introductionmentioning

confidence: 99%

Cis-regulatory sequences in plants: Their importance, discovery, and future challenges

2021

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“…In maize, both proximal and distal ACRs were found to show a general enhancement of activity, relative to randomly selected regions with similar features (Ricci et al, 2019). On the other hand, a modified version of STARR-seq using transient transfection in tobacco leaves found that four known plant enhancers gave the strongest transcriptional output when placed immediately upstream of a minimal promoter and were not active when placed in the 3'UTR of the reporter gene (Jores et al, 2020). Further studies are needed to tease out the functional determinants and optimal architecture of the various classes of regulatory elements.…”

Section: Genome-wide Identification Of Cis-regulatory Regionsmentioning

confidence: 98%

“…In plants, these operational definitions are even more vague; however, studies have begun to tease out some common trends. Plant adapted versions of massively parallel promoter and enhancer reporter assays such as self-transcribing active regulatory region sequencing (STARR-seq; Ricci et al, 2019;Jores et al, 2020), show that many ACRs are capable of enhancing gene expression (Ricci et al, 2019). Traditional STARR-seq works by inserting fragments either from randomly sheared genomic sequence, BAC libraries, or small fragments such as those from ATAC-seq and placing them downstream of a cassette containing a minimal promoter fused to GFP (Arnold et al, 2013).…”

Section: Genome-wide Identification Of Cis-regulatory Regionsmentioning

confidence: 99%

Mapping Regulatory Determinants in Plants

2020

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The domestication and improvement of many plant species have frequently involved modulation of transcriptional outputs and continue to offer much promise for targeted trait engineering. The cis-regulatory elements (CREs) controlling these trait-associated transcriptional variants however reside within non-coding regions that are currently poorly annotated in most plant species. This is particularly true in large crop genomes where regulatory regions constitute only a small fraction of the total genomic space. Furthermore, relatively little is known about how CREs function to modulate transcription in plants. Therefore understanding where regulatory regions are located within a genome, what genes they control, and how they are structured are important factors that could be used to guide both traditional and synthetic plant breeding efforts. Here, we describe classic examples of regulatory instances as well as recent advances in plant regulatory genomics. We highlight valuable molecular tools that are enabling large-scale identification of CREs and offering unprecedented insight into how genes are regulated in diverse plant species. We focus on chromatin environment, transcription factor (TF) binding, the role of transposable elements, and the association between regulatory regions and target genes.

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“…These cell types are suitable for the use of direct transformation methods such as electroporation, gene gun bombardment, and microinjection. However, generation of these cell lines is often inefficient depending on the species used, produces fragile cells, and may not behave as an intact plant would ( Jores et al, 2020 ). A recent study utilized an industrially scalable delivery of self-replicating viral vectors to transform a variety of crop species, such as tomato, potato, and spinach, with successful alterations to reproduction, stature, and drought tolerance ( Torti et al, 2021 ).…”

Section: Opportunities and Obstacles In Using Plants As A Production Platformmentioning

confidence: 99%

Utilizing Plant Synthetic Biology to Improve Human Health and Wellness

2021

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Plants offer a vast source of bioactive chemicals with the potential to improve human health through the prevention and treatment of disease. However, many potential therapeutics are produced in small amounts or in species that are difficult to cultivate. The rapidly evolving field of plant synthetic biology provides tools to capitalize on the inventive chemistry of plants by transferring metabolic pathways for therapeutics into far more tenable plants, increasing our ability to produce complex pharmaceuticals in well-studied plant systems. Plant synthetic biology also provides methods to enhance the ability to fortify crops with nutrients and nutraceuticals. In this review, we discuss (1) the potential of plant synthetic biology to improve human health by generating plants that produce pharmaceuticals, nutrients, and nutraceuticals and (2) the technological challenges hindering our ability to generate plants producing health-promoting small molecules.

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Identification of Plant Enhancers and Their Constituent Elements by STARR-seq in Tobacco Leaves

Abstract: A high-throughput assay in transiently transformed tobacco leaves identifies enhancers, characterizes their functional elements and detects condition-specific enhancer activity.

Cited by 73 publications

References 61 publications

Cis-regulatory sequences in plants: Their importance, discovery, and future challenges

Cis-regulatory sequences in plants: Their importance, discovery, and future challenges

Mapping Regulatory Determinants in Plants

Utilizing Plant Synthetic Biology to Improve Human Health and Wellness

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