Profiling single-cell chromatin accessibility in plants

Marand, Alexandre P.; Zhang, Xuan; Nelson, Julie G.; Reis, Pedro A. B.; Schmitz, Robert J.

doi:10.1016/j.xpro.2021.100737

Cited by 7 publications

(3 citation statements)

References 16 publications

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“…Such developmental trajectories have also been compared between species. Using an optimized protocol (88), a comparison of maize and Arabidopsis TF motif activity across phloem companion cell development revealed highly conserved and innovative TF dynamics (86).…”

Section: Scatac-seqmentioning

confidence: 99%

cis-Regulatory Elements in Plant Development, Adaptation, and Evolution

Marand

Eveland

Kaufmann

et al. 2023

Annu. Rev. Plant Biol.

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cis-Regulatory elements encode the genomic blueprints that ensure the proper spatiotemporal patterning of gene expression necessary for appropriate development and responses to the environment. Accumulating evidence implicates changes to gene expression as a major source of phenotypic novelty in eukaryotes, including acute phenotypes such as disease and cancer in mammals. Moreover, genetic and epigenetic variation affecting cis-regulatory sequences over longer evolutionary timescales has become a recurring theme in studies of morphological divergence and local adaption. Here, we discuss the functions of and methods used to identify various classes of cis-regulatory elements, as well as their role in plant development and response to the environment. We highlight opportunities to exploit cis-regulatory variants underlying plant development and environmental responses for crop improvement efforts. Although a comprehensive understanding of cis-regulatory mechanisms in plants has lagged in animals, we showcase several breakthrough findings that have profoundly influenced plant biology and shaped the overall understanding of transcriptional regulation in eukaryotes. Expected final online publication date for the Annual Review of Plant Biology, Volume 74 is May 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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Section: Scatac-seqmentioning

confidence: 99%

cis-Regulatory Elements in Plant Development, Adaptation, and Evolution

Marand

Eveland

Kaufmann

et al. 2023

Annu. Rev. Plant Biol.

Self Cite

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“…Nuclei purification using flow cytometry: We use a Moflo Astrios EQ running preservative- free flow cytometry solution. The following gating strategy and parameters were modified from Marand et al (2021).…”

Section: Methodsmentioning

confidence: 99%

“…We attempted nuclei isolation with several published nuclei isolation protocols (Marand et al 2021; Thibivilliers, Anderson, and Libault 2020; Sikorskaite et al 2013) yet did not recover robust nuclei with our target species. During troubleshooting, we observed that the tissue disruption method, the concentration of detergent, as well as centrifugation and resuspension steps significantly influenced the integrity of isolated nuclei.…”

Section: Introductionmentioning

confidence: 99%

Nuclei isolation protocol from diverse angiosperm species

Wood

Deans

et al. 2022

Preprint

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The ability to generate intact nuclei is crucial to the success of a variety of genomics experiments, such as Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq), Cleavage Under Targets and Tagmentation (CUT&Tag), and nuclei-based single cell sequencing (e.g., single nuclei ATAC-seq and single nuclei RNA-seq). For plants, the presence of the cell wall presents significant challenges in the isolation of nuclei from tissues. Here, we report an optimized nuclei isolation protocol that can be adapted for diverse angiosperm species, including maize, soybean, tomato, potato, and wheat, starting from fresh or frozen tissues. Nuclei release is achieved through chopping tissue on ice, where a key parameter affecting nuclei integrity is the concentration of detergent TritonX-100 in the nuclei isolation buffer. The method is simple, quick, and largely centrifugation-free, in which debris is removed by serial filtration. Initial nuclei release and filtration can be performed within 20 min. Fluorescence activated nuclei sorting is then used for final nuclei purification to remove other organelles such as plastids. The protocol uses 500 mg or less plant tissue as input and typically yields at least 100,000 - 200,000 purified nuclei per sample, a common input amount for downstream experiments. Throughout the protocol, we provide guidelines for optimization if performing nuclei isolation from a given species and tissue for the first time. Keywords: plant nuclei isolation, single cell genomics

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Fundamental and practical approaches for single-cell ATAC-seq analysis

et al. 2022

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Assays for transposase-accessible chromatin through high-throughput sequencing (ATAC-seq) are effective tools in the study of genome-wide chromatin accessibility landscapes. With the rapid development of single-cell technology, open chromatin regions that play essential roles in epigenetic regulation have been measured at the single-cell level using single-cell ATAC-seq approaches. The application of scATAC-seq has become as popular as that of scRNA-seq. However, owing to the nature of scATAC-seq data, which are sparse and noisy, processing the data requires different methodologies and empirical experience. This review presents a practical guide for processing scATAC-seq data, from quality evaluation to downstream analysis, for various applications. In addition to the epigenomic profiling from scATAC-seq, we also discuss recent studies in which the function of non-coding variants has been investigated based on cell type-specific cis-regulatory elements and how to use the by-product genetic information obtained from scATAC-seq to infer single-cell copy number variants and trace cell lineage. We anticipate that this review will assist researchers in designing and implementing scATAC-seq assays to facilitate research in diverse fields.

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Profiling single-cell chromatin accessibility in plants

Cited by 7 publications

References 16 publications

cis-Regulatory Elements in Plant Development, Adaptation, and Evolution

cis-Regulatory Elements in Plant Development, Adaptation, and Evolution

Nuclei isolation protocol from diverse angiosperm species

Fundamental and practical approaches for single-cell ATAC-seq analysis

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