ERP122790 PRJEB39290 ena-STUDY-Glasgow Polyomics-08-07-2020-09:00:38:005-1413 Cell-type specific epigenetic de-repression of the transcription factor ZAT6 establishes a spatially delimited transcriptional network in Arabidopsis roots Gene function in multicellular organisms is intimately linked to location. Gene expression atlases of plant tissues based on single-cell transcriptomics have provided an essential resource for predicting gene function. However, regulatory networks within cell-type specific gene-sets remain to be unravelled. The cell layers surrounding the xylem vessels in mature roots occupy a strategically important position for controlling root-to-shoot transport and signalling, and their function relies on cell-type specific expression of enzymes and transporters. We generated a pHKT1-NTF Arabidopsis line to analyse transcripts and epigentic marks in this location using FACS RNA- and INTACT ChIP-sequencing. Here we show that several thousand genes are preferentially expressed in the tagged cell types. Less than a hundred display a location-specific decrease in H3K27me3, but they are statistically diagnostic for the tissue and strongly enriched for transcription factors. In addition to regulating key embryonic genes during cell differentiation, H3K27me3 might therefore determine cell-type specific transcriptomes in mature tissues by de-repressing a small core-set of transcription factors. As a proof of principle, we show that one of the cell-type specific H3K27me3-depleted transcription factors, ZAT6, regulates over a hundred downstream genes, enriched for ethylene and oxylipin-signalling pathways. The ZAT6-regulome is cell-type delimited and depends on the histone demethylase REF6, which removes H3K27me3 from ZAT6. Our findings pave the way for bottom-up deconstruction of regulatory cascades in a crucial location within the plant vasculature. Gene function in multicellular organisms is intimately linked to location. Gene expression atlases of plant tissues based on single-cell transcriptomics have provided an essential resource for predicting gene function. However, regulatory networks within cell-type specific gene-sets remain to be unravelled. The cell layers surrounding the xylem vessels in mature roots occupy a strategically important position for controlling root-to-shoot transport and signalling, and their function relies on cell-type specific expression of enzymes and transporters. We generated a pHKT1-NTF Arabidopsis line to analyse transcripts and epigentic marks in this location using FACS RNA- and INTACT ChIP-sequencing. Here we show that several thousand genes are preferentially expressed in the tagged cell types. Less than a hundred display a location-specific decrease in H3K27me3, but they are statistically diagnostic for the tissue and strongly enriched for transcription factors. In addition to regulating key embryonic genes during cell differentiation, H3K27me3 might therefore determine cell-type specific transcriptomes in mature tissues by de-repressing a small core-set of transcription factors. As a proof of principle, we show that one of the cell-type specific H3K27me3-depleted transcription factors, ZAT6, regulates over a hundred downstream genes, enriched for ethylene and oxylipin-signalling pathways. The ZAT6-regulome is cell-type delimited and depends on the histone demethylase REF6, which removes H3K27me3 from ZAT6. Our findings pave the way for bottom-up deconstruction of regulatory cascades in a crucial location within the plant vasculature. ENA-FIRST-PUBLIC 2021-01-05 ENA-LAST-UPDATE 2020-07-08