Photoperiod-responsive changes in chromatin accessibility in phloem companion and epidermis cells of Arabidopsis leaves

Abstract

Photoperiod plays a key role in controlling the phase transition from vegetative to reproductive growth in flowering plants. Leaves are the major organs perceiving day-length signals, but how specific leaf cell-types respond to photoperiod remains unknown. We integrated photoperiod-responsive chromatin accessibility and transcriptome data in leaf epidermis and vascular companion cells of Arabidopsis thaliana by combining INTACT (Isolation of Nuclei Tagged in specific Cell/Tissue types) with ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) and RNA-sequencing. Despite a large overlap, vasculature and epidermis cells responded differently. Long-day predominantly induced accessible chromatin regions (ACRs); in the vasculature, more ACRs were induced and these were located at more distal gene regions, compared with the epidermis. Vascular ACRs induced by long day were highly enriched in binding sites for flowering-related transcription factors. Among the highly ranked genes (based on chromatin and expression signatures in the vasculature), we identified TREHALOSE-6-PHOSPHATASE SYNTHASE 9 (TPS9) as a flowering activator, as shown by the late flowering phenotypes of T-DNA insertion mutants and transgenic lines with phloem-specific knockdown of TPS9. Our cell-type-specific analysis sheds light on how the long-day photoperiod stimulus impacts chromatin accessibility in a tissue-specific manner to regulate plant development.

Leaf and shoot apical meristem transcriptomes of quinoa (Chenopodium quinoaWilld.) in response to photoperiod and plant development

“…As a result, we selected 222 genes differentially responding to photoperiod, which putatively control flowering time in leaves (Table 2, Figure 3). Among the resulting DEGs and based on a literature survey, we found several genes with a known function in photoperiodic regulation of flowering time in other species like TREHALOSE-PHOSPHATASE/SYNTHASE 9 ( CqTPS9 ), PHYTOCHROMEB ( CqPHYB ), ZEITLUPE ( CqZTL ) and BLUE-LIGHT INHIBITOR OF CRYPTOCHROMES ( CqBIC1 ) (Figure 3 and Supplementary Table 4) (Blázquez & Weigel, 1999; Más et al ., 2003; Wang et al ., 2016; Tian et al ., 2021).…”

An ethylene‐responsive transcription factor and a B‐box protein coordinate vegetative growth and photoperiodic flowering in chrysanthemum

“…Photoperiodic control has been revealed to be one of the several mechanisms used by land plants to initiate reproductive growth from vegetative growth (Tian et al, 2021). Photoperiod-dependent flowering is well known to occur in the LD model plant, Arabidopsis, and the CO-FT module plays a central role in floral induction (Blumel et al, 2015).…”

“…Arabidopsis has six genetically defined pathways for accomplishing the transition from vegetative growth to reproductive growth, including photoperiod, autonomous, vernalization, GA, growth temperature, and age (Blumel et al, 2015; Srikanth & Schmid, 2011). Photoperiodic control has been revealed to be one of the several mechanisms used by land plants to initiate reproductive growth from vegetative growth (Tian et al, 2021). Photoperiod‐dependent flowering is well known to occur in the LD model plant, Arabidopsis , and the CO‐FT module plays a central role in floral induction (Blumel et al, 2015).…”

MINI‐AC: inference of plant gene regulatory networks using bulk or single‐cell accessible chromatin profiles

“…The Arabidopsis phloem and epidermis cell-type specific bulk datasets were downloaded from the supplementary dataset 2 of Tian et al (2021) and the induced ACRs for phloem and epidermis were selected. For Arabidopsis, bulk differentially AC regions between mesophyll and stem cells were obtained from Kulkarni et al (2019) (original study;Sijacic et al, 2018).…”