Integration of Single-cell Omics with Gene Regulatory Network Reconstruction maximizes dissection of molecular processes

In multicellular organisms, the functionality of cells requires the acquisition of specific identities and molecular fingerprints. The analysis of organisms at the cellular level using single-cell omics techniques and Gene Regulatory Network inference will facilitate the understanding of the specific mechanisms governing biological processes.


Over the last decades, research on postembryonic root development has been facilitated by "omics" technologies. Among these technologies, microarrays first, and RNA sequencing (RNA-seq) later, have provided transcriptional information on the underlying molecular processes establishing the basis of System Biology studies in roots. Cell fate specification and development have been widely studied in the primary root, which involved the identification of many cell type transcriptomes and the reconstruction of gene regulatory networks (GRN). The study of lateral root (LR) development has not been an exception. However, the molecular mechanisms regulating cell fate specification during LR formation remain largely unexplored. Recently, single-cell RNA-seq (scRNA-seq) studies have addressed the specification of tissues from stem cells in the primary root. scRNA-seq studies are anticipated to be a useful approach to decipher cell fate specification and patterning during LR formation. In this review, we address the different scRNA-seq strategies used both in plants and animals and how we could take advantage of scRNA-seq to unravel new regulatory mechanisms and reconstruct GRN. In addition, we discuss how to integrate scRNA-seq results with previous RNA-seq datasets and GRN. We also address relevant findings obtained through single-cell based studies and how LR developmental studies could be facilitated by scRNA-seq approaches and subsequent GRN inference. The use of single-cell approaches to investigate LR formation could help to decipher fundamental biological mechanisms such as cell memory, synchronization, polarization, or pluripotency.


Original Paper:

Serrano-Ron, L., Cabrera, J., Perez-Garcia, P., Moreno-Risueno, M.A. 2021. Unraveling Root Development Through Single-Cell Omics and Reconstruction of Gene Regulatory Networks. Frontiers in Plant Science 12, 671. DOI: 10.3389/fpls.2021.661361