“SINGLE CELL STEREO-SEQUENCING”

   Plants are sessile in nature consequently during environmental adaptation their transcriptional activities must be frequently altered, suggesting that the transcriptome responses of specific cell types to different signals are heterogeneous1. Transcriptomics aids in profiling these complex heterogeneous signals which are expressed as RNA molecules through microarray analysis or RNA sequencing (RNA-seq). Because of low throughput screening in these methods, recent advancements like single cell sequencing has made its way. Further to study the spatiotemporal expression of the transcript, spatial-transcriptomics methods like single cell stereo-sequencing were developed.

SpaTial Enhanced Resolution Omics-sequencing (Stereo-seq) is one of the tools to study spatially resolved transcriptomics of complex biological processes. It combines the DNA nanoball (DNB) - patterned arrays and in situ RNA capture to create Stereo-seq. DNB templates containing random barcodes are deposited on the patterned array, to obtain the matrix containing the coordinate identity (CID). Followed by, unique molecular identifiers (UMI) and polyT sequence-containing oligonucleotides are ligated CID sequence2. Despite of large field view and sensitivity of the stereo-seq, it can’t identify cell subtypes. Hence, combining spatial transcriptomics platforms with scRNA-seq to improve tissue cell resolutionsingle cell stereo-seq has been developed. It combines stereo-seq with single-cell RNA-seq to improve resolution and identify cell subtypes.

There are studies which used single-cell stere-seq to track the spatial expression of genes in some of the crop plants. In one of these studies,soybean for nodule formation was tracked to get 12 cell subtype clusters along with a cell subtype-specific gene GLYMA_02G004800 which is responsible for nodule maturation. They could also figure out the developmental trajectories of the nodule cells3. In another study, stereo-seq revealed region-specific four cell subtypes along with their different photosynthesis-related gene expression levels and developed transcriptome profile in Arabidopsis leaves4.

Ultimately, single-cellstereo-seq is expected to enable impactful discoveries in plant science in several ways, such as the study of plant responses to environmental changes, including salinity, extreme temperatures, drought, nutrient deficiencies, pathogenic infection, and mutualistic interactions. Stereo-seq data can also be integrated with epigenomic data for a better understanding of spatial epigenetic regulation in tissue sections. Single cell stereo-seq still has scope for improvement in terms of sectioning for screening, raising sub-cellular resolution, and developing data analysis tools.

References 

1. BAWA, G., LIU, Z., YU, X., TRAN, L.S.P. AND SUN, X., 2023, Introducing single cell stereo-sequencing technology to transform the plant transcriptome landscape. Trends Plant Sci.135: 1206-1215.

 2. CHEN, A., LIAO, S., CHENG, M., MA, K., WU, L., LAI, Y., QIU, X., YANG, J., XU, J., HAO, S. AND WANG, X., 2022, Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays. Cell, 185(10):1777-1792. 

3. LIU, Z., KONG, X., LONG, Y., LIU, S., ZHANG, H., JIA, J., CUI, W., ZHANG, Z., SONG, X., QIU, L. AND ZHAI, J., 2023, Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation. Nat. Plants,1-10. 

4. XIA, K., SUN, H.X., LI, J., LI, J., ZHAO, Y., CHEN, L., QIN, C., CHEN, R., CHEN, Z., LIU, G. AND YIN, R., 2022, The single-cell stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves. Dev.Cell, 57(10):1299-1310.