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Series GSE192407 Query DataSets for GSE192407
Status Public on May 07, 2023
Title HSFA2 and HSFA3 binding after heat acclimation [DAP-seq]
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Transcriptional regulation is a key aspect of environmental stress responses. Heat stress (HS) induces transcriptional memory that allows plants to respond more efficiently to a recurrent HS. In light of more frequent temperature extremes due to climate change, improving heat tolerance in crops is an important breeding goal. However, not all HS-inducible genes show sustained induction/transcriptional memory and it is unclear what distinguishes memory and non-memory genes. To address this issue and understand the (epi-) genome architecture in transcriptional memory after HS, we investigated genome-wide target genes of the two key memory heat shock transcription factors, HSFA2 and HSFA3. We determined the binding kinetics of these factors to their target genes and asked whether genes that show sustained induction of transcription carry specific features that allow prediction and potentially engineering of memory gene behaviour. HSFA2 and HSFA3 show near identical binding patterns. In vitro binding strength as determined by DAP-seq analysis correlates strongly with in vivo binding strength, confirming the importance of sequence features. However, no single distinctive sequence motif appears to be required for memory behaviour. Instead, HS memory genes are characterized by a combination of features: low expression levels in the absence of HS, chromatin environment and an enrichment of H3K4 methylation after HS. Our findings are confirmed by an orthogonal transcriptomic data set using both de novo clustering and an established definition of memory genes. In summary, our findings provide an integrated view of HSF-dependent transcriptional memory and shed light on its sequence and chromatin determinants. They will contribute to the prediction and engineering of genes with transcriptional memory.
Overall design Identification of binding sites for HSFA1b, HSFA2 and HSFA3 in Arabidopsis thaliana using DAP-seq.
Contributor(s) Jiang L, Kappel C, Lenhard M, Bäurle I
Citation(s) 37254211
Submission date Dec 21, 2021
Last update date Aug 06, 2023
Contact name Isabel Bäurle
Phone +49 331 9772647
Organization name Universität Potsdam
Department Institut für Biochemie und Biologie
Street address Karl-Liebknecht-Str. 24-25
City Potsdam
ZIP/Postal code 14476
Country Germany
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (13)
GSM5746462 A1b-A2-A3
GSM5746463 A1b-A2
GSM5746464 A1b-A3
This SubSeries is part of SuperSeries:
GSE192431 HSFA2 and HSFA3 binding after heat acclimation
BioProject PRJNA791363
SRA SRP351965

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Supplementary file Size Download File type/resource
GSE192407_RAW.tar 546.6 Mb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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