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An Arabidopsis root phloem pole cell atlas reveals PINEAPPLE genes as transitioners to autotrophy [10x scRNA-seq]

ABSTRACT: Single cell sequencing has recently allowed the generation of exhaustive root cell atlases. However, some cell types are elusive and remain underrepresented. Here, we use a second-generation single cell approach, where we zoom in on the root transcriptome by sorting cells with specific markers, to profile the phloem poles at an unprecedented resolution. Our data highlight the similarities among the developmental trajectories and gene regulatory networks communal to protophloem sieve element (PSE) adjacent lineages in relation to PSE enucleation, a key event in phloem biology. As a signature for early PSE-adjacent lineages, we have identified a set of DNA-binding with one finger (DOF) transcription factors, the PINEAPPLEs (PAPL), that act downstream of PHLOEM EARLY DOF (PEAR) genes, and are important to guarantee a proper root nutrition in the transition to autotrophy. Our data provide a holistic view of the phloem poles that act as a functional unit in root development.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE181999 | GEO | 2022/04/29

REPOSITORIES: GEO

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An Arabidopsis root phloem pole cell atlas reveals PINEAPPLE genes as transitioners to autotrophy [bulk RNA-seq]

Project description:Single cell sequencing has recently allowed the generation of exhaustive root cell atlases. However, some cell types are elusive and remain underrepresented. Here, we use a second-generation single cell approach, where we zoom in on the root transcriptome by sorting cells with specific markers, to profile the phloem poles at an unprecedented resolution. Our data highlight the similarities among the developmental trajectories and gene regulatory networks communal to protophloem sieve element (PSE) adjacent lineages in relation to PSE enucleation, a key event in phloem biology. As a signature for early PSE-adjacent lineages, we have identified a set of DNA-binding with one finger (DOF) transcription factors, the PINEAPPLEs (PAPL), that act downstream of PHLOEM EARLY DOF (PEAR) genes, and are important to guarantee a proper root nutrition in the transition to autotrophy. Our data provide a holistic view of the phloem poles that act as a functional unit in root development.

2022-04-29 | GSE182672 | GEO

An Arabidopsis root phloem pole cell atlas reveals PINEAPPLE genes as transitioners to autotrophy

Project description:An Arabidopsis root phloem pole cell atlas reveals PINEAPPLE genes as transitioners to autotrophy

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Transcriptomics of lateral root initiation in Maize

2013-07-16 | GSE45691 | GEO

Transcriptomics of lateral root initiation in Maize

Project description:We developed a method to synchronize the induction of lateral roots in primary and adventitious roots of Zea mays, and used it to perform a genome-wide transcriptome analysis of the pericycle cells in front of the phloem poles during lateral root initiation. Lateral roots were induced in primary and adventitious roots of Maize. For the primary root, plants were germinated and grown 64 hours in NPA 50 ÂµM, and then transfered to NAA 50 ÂµM. For the adventitious roots, plants were germinated and grown in water for 6 days, then tranfered 4 days in NPA 25 ÂµM, and finally transfered to NAA 25 ÂµM. For all these roots, pericycle cells located in front of the phloem poles in segments of roots located between 5 and 10 mm distance from the root tip were isolated using laser capture microdissection after cryosection. Material was sampled at 0 hours (NPA) and after 2, 3 and 4 hours of NAA treatment, for both the primary and adventitious roots and also after 6 hours and 9 hours of NAA treatment for the adventitious roots.

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Mobile PEAR transcription factors integrate hormone and miRNA cues to prime cambial growth

Project description:In addition to apical growth, plants undergo radial growth to increase girth, a particularly prominent feature in trees. During both apical and radial growth the phytohormones auxin and cytokinins form symmetries that govern further growth patterns. But whereas the gene regulatory networks interpreting the hormonal fields during apical growth are well established, such networks are not known for the radial growth. We show here that the initiation of radial growth occurs around early protophloem sieve element (PSE) cell files of the root procambial tissue in Arabidopsis. In this domain cytokinin signalling promotes expression of a pair of novel mobile transcription factors, PHLOEM EARLY DOF (PEAR1, PEAR2) and their four homologs (OBP2, DOF6, TMO6 and HCA2), collectively called PEAR proteins. The PEAR proteins form a short-range concentration gradient peaking at PSE and activating gene expression that promotes radial growth. The expression and function of PEAR proteins are antagonized by well-established polarity transcription factors, HD-ZIP III, whose expression is concentrated in the more internal domain of radially non-dividing procambial cells by the function of auxin and mobile miR165/166. The PEAR proteins locally promote transcription of their inhibitory HD-ZIP III genes, thereby establishing a negative feedback loop that forms a sharp boundary demarking the zone of cell divisions. Taken together, we have established a network, in which the PEAR - HD-ZIP III module integrates the spatial information of the hormonal domains and miRNA gradients during root procambial development, to provide a pre-pattern with actively dividing and more quiescent zones, thus priming radial growth.

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An Arabidopsis root phloem pole cell atlas reveals PINEAPPLE genes as transitioners to autotrophy [10x scRNA-seq]

Project description:An Arabidopsis root phloem pole cell atlas reveals PINEAPPLE genes as transitioners to autotrophy [10x scRNA-seq]

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An Arabidopsis root phloem pole cell atlas reveals PINEAPPLE genes as transitioners to autotrophy [bulk RNA-seq]

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