Transcriptional profiling of Arabidopsis root hairs and pollen defines an apical cell growth signature Jörg D. Becker, Seiji Takeda, Filipe Borges, Liam Dolan, José A. Feijó To cite this version: Jörg D. Becker, Seiji Takeda, Filipe Borges, Liam Dolan, José A. Feijó. Transcriptional profiling of Arabidopsis root hairs and pollen defines an apical cell growth signature. BMC Plant Biology, BioMed Central, 2014, 14, pp.1-14. 10.1186/s12870-014-0197-3. hal-02639633 HAL Id: hal-02639633 https://hal.inrae.fr/hal-02639633 Submitted on 28 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License Becker et al. BMC Plant Biology 2014, 14:197 http://www.biomedcentral.com/1471-2229/14/197 RESEARCH ARTICLE Open Access Transcriptional profiling of Arabidopsis root hairs and pollen defines an apical cell growth signature Jörg D Becker1*, Seiji Takeda2,5, Filipe Borges1,6, Liam Dolan2,3 and José A Feijó1,4 Abstract Background: Current views on the control of cell development are anchored on the notion that phenotypes are defined by networks of transcriptional activity. The large amounts of information brought about by transcriptomics should allow the definition of these networks through the analysis of cell-specific transcriptional signatures. Here we test this principle by applying an analogue to comparative anatomy at the cellular level, searching for conserved transcriptional signatures, or conserved small gene-regulatory networks (GRNs) on root hairs (RH) and pollen tubes (PT), two filamentous apical growing cells that are a striking example of conservation of structure and function in plants. Results: We developed a new method for isolation of growing and mature root hair cells, analysed their transcriptome by microarray analysis, and further compared it with pollen and other single cell transcriptomics data. Principal component analysis shows a statistical relation between the datasets of RHs and PTs which is suggestive of a common transcriptional profile pattern for the apical growing cells in a plant, with overlapping profiles and clear similarities at the level of small GTPases, vesicle-mediated transport and various specific metabolic responses. Furthermore, cis-regulatory element analysis of co-regulated genes between RHs and PTs revealed conserved binding sequences that are likely required for the expression of genes comprising the apical signature. This included a significant occurrence of motifs associated to a defined transcriptional response upon anaerobiosis. Conclusions: Our results suggest that maintaining apical growth mechanisms synchronized with energy yielding might require a combinatorial network of transcriptional regulation. We propose that this study should constitute the foundation for further genetic and physiological dissection of the mechanisms underlying apical growth of plant cells. Keywords: Pollen, Pollen tube, Root hair, Transcriptome, Apical growth, Tip growth, Apical signature, Arabidopsis Background in different databases allow formal analysis of the tran- Current views on the control of cell and organ develop- scriptional profiles of specific cell types or organs, hold- ment are anchored on the notion that phenotypes are ing the promise that subsequently these can be distilled defined by precise networks of transcriptional activity, into specific transcriptional signatures. At the moment acting in a concerted way through a specific combi- this holy grail of transcriptional regulation is still nation of transcription factors to specify cell fate [1]. A unattainable, although the majority of these large scale direct test of this general principle is facilitated by pre- biology approaches end up being extremely useful to the cise transcriptome analysis using microarrays or RNAseq development of smaller scale approaches, focused on a [2]. This approach in combination with Fluorescence gene or small group of genes [2]. There are likely to be Activated Cell Sorting (FACS), has allowed the charac- multiple reasons for this limitation, including (1) the terisation of transcriptomic profiles of isolated cells from limited understanding of additional levels of post- simple organs, such as pollen [3-5], or more complex transcriptional/epigenetic regulation that define the final ones like roots [6,7]. The large amounts of information phenotype, (2) the absence of a proper understanding at a formal/mathematical level of network organization and * Correspondence: [email protected] functioning, or (3) these transcriptional profiles do not 1Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal Full list of author information is available at the end of the article translate into any sort of accessible mechanistic profile, © 2014 Becker et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Becker et al. BMC Plant Biology 2014, 14:197 Page 2 of 14 http://www.biomedcentral.com/1471-2229/14/197 but are an emergent property of the complexity of other hairs must be seen in the context of the root, a very com- underlying levels of organization based on fundamental plex organ where various hierarchical levels of transcrip- chemical and physical properties of DNA and proteins. tional integration are expected [7]. While much is known There is no easy way to circumvent these limitations at about root transcriptomics in general, the profile of isolated our present understanding of biology, but usable clues root hairs is still lacking, limiting the possibility of compara- could arise from applying an analogue to comparative tive analysis with pollen tubes, and search for conserved anatomy at the cellular level, such as searching for con- transcriptional network motifs. The advent of more power- served transcriptional signatures that could be used for ful and revealing ways of imaging signal integration in roots further genetic or physiological dissection [8,9]. Such an (see for example [29,30]) makes it even more obvious the approach can be conceptually rooted into evolutionary need of specific transcriptomics of root hairs, one of the developmental biology (evo-devo), in which specific and physiologically more important cell types in roots. defined small gene-regulatory networks (GRNs) may act Here we compare the transcriptional profile of isolated as defined modules that may have been co-opted during root hairs and pollen with other cell and organ types to evolution to perform related functions [10]. Modular test the hypothesis that there are conserved transcrip- GRNs are intrinsically robust and quasi-independent tomic signatures that define functions in similarly grow- complexes of genes, allowing the possibility of disentan- ing cells. Root hair transcriptomics was previously gling evolutionary pathways through comparison with approached by a number of studies using FACS of la- similar modules from unrelated species or organs. This belled root cell types and nuclei, respectively [6,7,31-33], architectural feature of the modules, coupled to their by dataset subtraction from root hair development mu- power to generate diversity, makes inter-GRN connec- tants [34,35], or by a combination of mutants and FACS tion elements major targets of adaptive evolution [11]. [36]. Here we developed a new way of isolating mRNA Plant-microbe interactions have been recently pro- directly from mechanically purified frozen wild type root posed to constitute an attractive system to test some of hairs. We conclude that root hairs and pollen have highly these concepts, as the communication module seems overlapping transcriptional profiles, with clear similarities to have been both phylogenetically re-deployed and at the level of small GTPases, vesicle-mediated transport functionally adapted along co-evolution of both plants and various specific metabolic responses, likely defining and microbes [12]. the unique regulatory processes that occur in these cell Apical growth in filamentous cells is a striking example types. We propose that this study should constitute the of conservation of structure and function in plants. As foundation for further genetic and physiological dissection opposed to most plant cells, which grow diffusively over of the mechanisms underlying apical growth of plant cells. large volumes, these are defined by growing over a rela- tively small volume at the tip, by exocytosis of specific Results cell wall precursors [13,14]. This form of growth is Isolation of Arabidopsis root hairs common among fungi and in some animal cells (neurite The purity of total RNA isolated from root hairs was outgrowth during the development