Single-nuclei RNA-sequencing of plant tissues

Sunaga-Franze, Daniele Yumi; Muiño, Jose M.; Braeuning, Caroline; Xu, Xiaocai; Zong, Minglei; Smaczniak, Cezary; Yan, Wenhao; Fischer, Cornelius; Vidal, Ramón; Kliem, Magdalena; Kaufmann, Kerstin; Sauer, Sascha

doi:10.1101/2020.11.14.382812

Cited by 9 publications

(9 citation statements)

References 45 publications

(73 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As a proof-of-concept demonstration in plant, our results showed that protoplasting-free large-scale single-nucleus sequencing is sufficient for cell type classification and marker gene identification in Arabidopsis roots. As we are preparing this manuscript, several groups have also recently adopted the nuclei-based protoplasting-free strategy independently to investigate various plant tissues[35-39]. Eliminating protoplasting as a prerequisite would enable large-scale single-cell profiling on a wide range of tissues and plant species.…”

Section: Discussionmentioning

confidence: 99%

Single-nucleus full-length RNA profiling in plants incorporates isoform information to facilitate cell type identification

Long

Jia

et al. 2020

Preprint

View full text Add to dashboard Cite

The broad application of large-scale single-cell RNA profiling in plants has been restricted by the prerequisite of protoplasting. We recently found that the Arabidopsis nucleus contains abundant polyadenylated mRNAs, many of which are incompletely spliced. To capture the isoform information, we combined 10x Genomics and Nanopore long-read sequencing to develop a protoplasting-free full-length single-nucleus RNA profiling method in plants. Our results demonstrated using Arabidopsis root that nuclear mRNAs faithfully retain cell identity information, and single-molecule full-length RNA sequencing could further improve cell type identification by revealing splicing status and alternative polyadenylation at single-cell level.

show abstract

Section: Discussionmentioning

confidence: 99%

Single-nucleus full-length RNA profiling in plants incorporates isoform information to facilitate cell type identification

Long

Jia

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…After liquid nitrogen evaporated totally, 5 ml of Honda buffer (2.5% Ficoll 400, 5% Dextran T40, 0.4 M sucrose, 10 mM MgCl 2 , 1 μM DTT, 0.5% Triton X- 100, 1 tablet/50 ml cOmplete Protease Inhibitor Cocktail, 0.4 U/μl RiboLock, 25 mM Tris-HCl, pH 7.4) was added to the tube. Nuclei were released at 4 °C by homogenizing the tissue on a gentleMACS Dissociator with a running program as described previously (Sunaga-Franze et al 2021). The resulting homogenate was filtered through a 70 μm strainer, and another 5ml Honda buffer was applied onto the filter to collect the remaining nuclei.…”

Section: Methodsmentioning

confidence: 99%

“…Denyer et al 2019) or nuclei isolation (e.g. Sunaga-Franze et al 2021) combined with high-throughput transcriptome sequencing (scRNA-seq/snRNA-seq) allow to characterize the transcriptomes of hundreds of thousands cells at single-cell resolution. However, the physical location of these cells is lost during the experimental process.…”

Section: Introductionmentioning

confidence: 99%

A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data

Neumann

Smaczniak

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

Identity and functions of plant cells are influenced by their precise cellular location within the plant body. Cellular heterogeneity in growth and differentiation trajectories results in organ patterning. Therefore, assessing this heterogeneity at molecular scale is a major question in developmental biology. Single-cell transcriptomics (scRNA-seq) allows to characterize and quantify gene expression heterogeneity in developing organs at unprecedented resolution. However, the original physical location of the cell is lost during the scRNA-seq procedure. To recover the original location of cells is essential to link gene activity with cellular function and morphology. Here, we reconstruct genome-wide gene expression patterns of individual cells in a floral meristem by combining single-nuclei RNA-seq with 3D spatial reconstruction. By this, gene expression differences among meristematic domains giving rise to different tissue and organ types can be determined. As a proof of principle, the data are used to trace the initiation of vascular identity within the floral meristem. Our work demonstrates the power of spatially reconstructed single cell transcriptome atlases to understand plant morphogenesis. The floral meristem 3D gene expression atlas can be accessed at http://threed-flower-meristem.herokuapp.com

show abstract

“…1) 20 . Apart from plant roots, there is growing interest in using scRNAseq technologies to profile the development of other important plant tissues, including leaf 21,22 , flower 23 , pollen and sperm 24 , and seed endosperm 25 . Single-cell RNA-seq has also moved beyond Arabidopsis, with studies emerging for tomato 26 , rice 27 , maize [28][29][30][31] , and moss 32 .…”

Section: The Technologiesmentioning

confidence: 99%

Plant single-cell solutions for energy and the environment

et al. 2021

View full text Add to dashboard Cite

Progress in sequencing, microfluidics, and analysis strategies has revolutionized the granularity at which multicellular organisms can be studied. In particular, single-cell transcriptomics has led to fundamental new insights into animal biology, such as the discovery of new cell types and cell type-specific disease processes. However, the application of single-cell approaches to plants, fungi, algae, or bacteria (environmental organisms) has been far more limited, largely due to the challenges posed by polysaccharide walls surrounding these species’ cells. In this perspective, we discuss opportunities afforded by single-cell technologies for energy and environmental science and grand challenges that must be tackled to apply these approaches to plants, fungi and algae. We highlight the need to develop better and more comprehensive single-cell technologies, analysis and visualization tools, and tissue preparation methods. We advocate for the creation of a centralized, open-access database to house plant single-cell data. Finally, we consider how such efforts should balance the need for deep characterization of select model species while still capturing the diversity in the plant kingdom. Investments into the development of methods, their application to relevant species, and the creation of resources to support data dissemination will enable groundbreaking insights to propel energy and environmental science forward.

show abstract

Single-nuclei RNA-sequencing of plant tissues

Cited by 9 publications

References 45 publications

Single-nucleus full-length RNA profiling in plants incorporates isoform information to facilitate cell type identification

Single-nucleus full-length RNA profiling in plants incorporates isoform information to facilitate cell type identification

A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data

Plant single-cell solutions for energy and the environment

Contact Info

Product

Resources

About