ATACing Somatic Embryogenesis

How does auxin induce somatic embryogenesis? In this issue of Developmental Cell, Wang et al. uncover a regulatory role for auxin in the dynamics of chromatin accessibility and gene expression, which is critical for the establishment of developmental time-specific transcriptional regulatory networks orchestrating somatic-to-embryonic cell reprogramming and somatic embryo development. How does auxin induce somatic embryogenesis? In this issue of Developmental Cell, Wang et al. uncover a regulatory role for auxin in the dynamics of chromatin accessibility and gene expression, which is critical for the establishment of developmental time-specific transcriptional regulatory networks orchestrating somatic-to-embryonic cell reprogramming and somatic embryo development. Access to chromatin is essential for master transcription factors that play an instrumental role in complex biological processes, such as cell reprogramming and embryo development, to exert their regulatory functions (Ladstätter and Tachibana, 2019Ladstätter S. Tachibana K. Genomic insights into chromatin reprogramming to totipotency in embryos.J. Cell Biol. 2019; 218: 70-82https://doi.org/10.1083/jcb.201807044Crossref PubMed Scopus (13) Google Scholar). In the model plant Arabidopsis thaliana, genetic studies have previously identified individual master transcription factors that are necessary to elicit changes in cell state, both in somatic-to-embryonic (totipotent) cell reprogramming and in somatic embryo development (Wójcik et al., 2020Wójcik A.M. Wójcikowska B. Gaj M.D. Current perspectives on the auxin-mediated genetic network that controls the induction of somatic embryogenesis in plants.Int. J. Mol. Sci. 2020; 21: 1333https://doi.org/10.3390/ijms21041333Crossref Scopus (21) Google Scholar). However, there remains a gap in determining how the regulatory functions of these master transcription factors are dynamically and hierarchically coordinated, through changes to chromatin accessibility over space and time, to form the central core of a definable somatic embryogenesis pathway. In this issue of Developmental Cell, Wang et al., 2020Wang F.X. Shang G.D. Wu L.Y. Xu Z.G. Zhao X.Y. Wang J.W. Chromatin accessibility dynamics and a hierarchical transcriptional regulatory network structure for plant somatic embryogenesis.Dev. Cell. 2020; 54: 742-757https://doi.org/10.1016/j.devcel.2020.07.003Abstract Full Text Full Text PDF PubMed Scopus (12) Google Scholar use a multi-omics approach, including assays for transposase-accessible chromatin sequencing (ATAC-seq) and RNA sequencing (RNA-seq), to track and assess the temporal dynamics of genome-wide chromatin accessibility and gene expression during auxin-induced somatic embryogenesis. This approach, combined with reverse genetics, reveals an important role for auxin in the global control of chromatin accessibility and gene expression. The authors also reconstruct a developmental time-specific transcriptional regulatory network for the initiation and progression of somatic embryogenesis, which is composed of well-known (i.e., LEC1 and LEC2) and newly identified (i.e., WOX2 and WOX3) master transcription factors. ATAC-seq enables the mapping of genome-wide chromatin accessibility to identify basal accessible chromatin regions, as well as to determine regions differentially accessible between tissues (or cells) at different stages of embryo development or cultured in the presence or absence of a chemical stimulus (i.e., auxin). The utility of ATAC-seq can be further extended when combined with other omics-based approaches (Yan et al., 2020Yan F. Powell D.R. Curtis D.J. Wong N.C. From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis.Genome Biol. 2020; 21: 22https://doi.org/10.1186/s13059-020-1929-3Crossref PubMed Scopus (29) Google Scholar). Integration of ATAC-seq and RNA-seq analyses allows the association of changes in chromatin accessibility with changes in gene expression. Further, the integration of chromatin immunoprecipitation sequencing (ChIP-seq) data into ATAC-seq analysis can show how transcription factors and histone-modifying enzymes modulate chromatin accessibility and thereby gene expression. Together, these techniques enable de novo reconstruction of tissue-, cell-, and developmental-time-specific transcriptional regulatory networks and also allow the characterization of identified candidate master transcription factors in more detail. Several pioneering studies have established a link between auxin and chromatin accessibility (Mateo-Bonmatí et al., 2019Mateo-Bonmatí E. Casanova-Sáez R. Ljung K. Epigenetic regulation of auxin homeostasis.Biomolecules. 2019; 9: 623https://doi.org/10.3390/biom9100623Crossref Scopus (11) Google Scholar). However, a genome-wide measurement of chromatin accessibility to auxin and a time course ATAC-seq analysis in plants was not reported until Wang et al., 2020Wang F.X. Shang G.D. Wu L.Y. Xu Z.G. Zhao X.Y. Wang J.W. Chromatin accessibility dynamics and a hierarchical transcriptional regulatory network structure for plant somatic embryogenesis.Dev. Cell. 2020; 54: 742-757https://doi.org/10.1016/j.devcel.2020.07.003Abstract Full Text Full Text PDF PubMed Scopus (12) Google Scholar. Based on these findings, the authors conclude that during the course of auxin-induced somatic embryogenesis (0–72 h), the genome-wide landscape of chromatin accessibility undergoes extensive changes at different time points. These changes are taking place concurrently with altered expression of distinct clusters of genes, including well-known and newly identified master transcription factors for somatic embryogenesis. The integrated analysis of multi-omics data further suggests that auxin modulates chromatin accessibility and gene expression through complex, hierarchically organized actions of master transcription factors in a developmental-stage-dependent manner. It is noteworthy, though, that while the implications of this seminal study are important in determining how auxin controls the initiation and progression of somatic embryo development at the chromatin level, it does come with some notable caveats. A major one is that the readouts from their multi-omics experiments rely on bulk instead of single-cell measurements, and thus the relative importance of cell-specific chromatin accessibility in establishing differential gene expression in various cell types cannot be adequately addressed. Measuring changes in chromatin accessibility and gene expression at the single-cell level, as pointed out by the authors, is therefore a necessary future step to determine the molecular identity of the progenitor cell that gives rise to a somatic embryo. This may be addressed using emerging single-cell multi-omics technologies that enable simultaneous measurement of multiple types of molecules in the same individual cell (Chappell et al., 2018Chappell L. Russell A.J.C. Voet T. Single-cell (multi)omics technologies.Annu. Rev. Genomics Hum. Genet. 2018; 19: 15-41https://doi.org/10.1146/annurev-genom-091416-035324Crossref PubMed Scopus (65) Google Scholar). Only when we decode the so-called “embryonic” nature of individual somatic cells, as well as their specific pattern of transcriptional regulatory network connectivity, will we gain access to a molecular link that explains the functional relationship between the reprogramming capacity of a somatic cell to auxin-induced epigenetic totipotency and the multi-level regulatory plasticity of master transcription factors. In view of the above, the following questions remain to be answered in future research: How are auxin signals transduced epigenetically to coordinates a diverse array of tissue- (and cell-) and developmental-time-specific somatic embryogenesis programs via transcriptional regulation? What are the master transcription factors in these programs? Can we identify a small set of master transcription factors to reprogram any somatic cell type into a totipotent state? In most eukaryotes, including plants, a subset of master transcription factors called “pioneer transcription factors” or “pioneer factors” are known to have an intrinsic ability to scan and target nucleosomal DNA sites in closed chromatin and initial the local opening of chromatin, thereby creating a permissive chromatin structure for gene activation and network rewiring (Zaret and Mango, 2016Zaret K.S. Mango S.E. Pioneer transcription factors, chromatin dynamics, and cell fate control.Curr. Opin. Genet. Dev. 2016; 37: 76-81https://doi.org/10.1016/j.gde.2015.12.003Crossref PubMed Scopus (186) Google Scholar). Interestingly, LEC1, one of the master transcription factors required for both zygotic and somatic embryogenesis in Arabidopsis, acts as a pioneer transcription factor (Tao et al., 2017Tao Z. Shen L. Gu X. Wang Y. Yu H. He Y. Embryonic epigenetic reprogramming by a pioneer transcription factor in plants.Nature. 2017; 551: 124-128https://doi.org/10.1038/nature24300Crossref PubMed Scopus (74) Google Scholar; Jo et al., 2020Jo L. Pelletier J.M. Hsu S.-W. Baden R. Goldberg R.B. Harada J.J. Combinatorial interactions of the LEC1 transcription factor specify diverse developmental programs during soybean seed development.Proc. Natl. Acad. Sci. U.S.A. 2020; 117: 1223-1232https://doi.org/10.1073/pnas.1918441117Crossref PubMed Scopus (18) Google Scholar). The mechanistic basis for chromatin regulation by LEC1 appears to be conserved between animals and plants (Sartorelli and Puri, 2018Sartorelli V. Puri P.L. Shaping gene expression by landscaping chromatin architecture: lessons from a master.Mol. Cell. 2018; 71: 375-388https://doi.org/10.1016/j.molcel.2018.04.025Abstract Full Text Full Text PDF PubMed Scopus (26) Google Scholar). Thus, future research is needed to determine whether master/pioneer transcription factors have evolutionarily conserved roles in the epigenetic control of embryo development. Understanding whether and how chromatin accessibility and gene expression are dynamically regulated by concerted action of auxin and master/pioneer transcription factors over space and time (Figure 1) will enhance our ability to precisely control the initiation and progression of somatic embryo development at will for plant cloning and regeneration purposes. Chromatin Accessibility Dynamics and a Hierarchical Transcriptional Regulatory Network Structure for Plant Somatic EmbryogenesisWang et al.Developmental CellAugust 4, 2020In BriefSomatic embryogenesis provides a powerful system to produce genetically modified crops and to obtain artificial seeds. In combination with reverse genetics, ATAC-seq, ChIP-seq, and RNA-seq, Wang et al. reveal a hierarchical transcriptional regulatory network for somatic embryogenesis. Full-Text PDF Open Archive