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NonFullScreenPageMode: UseOutlines Direction: L2R ViewArea: CropBox ViewClip: CropBox PrintArea: CropBox PageClip: CropBox PageLayout: SinglePage PageMode: UseOutlines Language: en-US Outlines: Item: Title: Autumn–winter progression triggers distinct transcriptional programs in Arabidopsis thaliana Children: Item: Title: Abstract Children: Item: Title: Background Item: Title: Results Item: Title: Conclusions Item: Title: Background Item: Title: Results Children: Item: Title: Seasonal decreasing temperatures lead to major changes in the Arabidopsis transcriptome Item: Title: Distinct transcriptional programs underlie autumn–winter progression Item: Title: Progressive cold sequentially triggers the COOLING and CHILLING genetic programs Item: Title: Temperature before time is the major driver of cold transcriptional reprogramming Item: Title: Transient CBF expression defines the boundary between COOLING and CHILLING program activation Item: Title: Functional circadian clock and light signaling is required for COOLING and CHILLING responses Item: Title: Daily oscillations of circadian clock and light signaling components are dampened during autumn–winter progression Item: Title: Long-term, progressive cold treatment confers robust cold acclimation Item: Title: Promoter accessibility of cold down-regulated genes is maintained during the cold season for fast reactivation in the spring Item: Title: Discussion Item: Title: Conclusions Item: Title: Methods Children: Item: Title: Plant materials Item: Title: Growth conditions and sampling in fluctuating and average decreasing temperature profiles Item: Title: Growth conditions in a weekly decreasing temperature profile Item: Title: Growth conditions in the 12 °C4 °C experiment Item: Title: Growth conditions for the thermal gradient table experiment Item: Title: RNA sequencing Item: Title: RT-qPCR Item: Title: Extraction of plant cell nuclei Item: Title: Fluorescence-Activated Nuclei Sorting and ATAC-seq sequencing library preparation Item: Title: RNA-seq processing Item: Title: Modelling the importance of time and temperature in gene expression Item: Title: Gene expression clustering analyses Item: Title: ATAC-seq processing Item: Title: ACR clustering, motif enrichment and transcription factor network analyses Item: Title: 24-h time course Item: Title: Growth rate analysis and freezing tolerance Item: Title: Statistical analyses Item: Title: Acknowledgements Item: Title: References Info: Creator: Adobe InDesign 18.5 (Windows) Producer: iLovePDF CreationDate: Thu Oct 01 05:45:40 CEST 2026 ModDate: Thu Oct 15 12:42:57 CEST 2026 ID: 0xbf24b147dc6e2341ae3c983a7d1f88c3, 0x460d86fd4f89c2b6cb97121ac91fb859 Filters: FilterPipeline: FlateDecode FilterPipeline: FlateDecode DCTDecode Images: Image: NisoImageMetadata: FormatName: image/png ImageWidth: 37 ImageHeight: 38 ColorSpace: palette color BitsPerSample: 8 BitsPerSampleUnit: integer Filter: FlateDecode Intent: RelativeColorimetric Image: NisoImageMetadata: 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