Periodic Reporting for period 1 - TxnEvoClim (Climate adaptation in Arabidopsis thaliana through evolution of transcription regulation)
Okres sprawozdawczy: 2022-03-01 do 2024-02-29
Our project investigated how differences in gene expression help plants adapt to different climates. Just as animals adapt to their environment, so do plants, and a significant part of this adaptation involves changing the way their genes are expressed, rather than changing the genes themselves. This is especially important as climate changes, potentially affecting the survival and health of plants.
Using the model plant Arabidopsis thaliana, we studied vast amounts of data on how the plant's genes are expressed in ecotypes adapted to different environments. Our goal was to understand how these changes relate to the climates to which the plants are adapted, discover the genetic changes that drive these adaptations, and determine if we can predict which plants will thrive in new conditions as the climate continues to change.
Interestingly, while studying the natural variation in gene expression among Arabidopsis ecotypes, we made a surprising discovery. Many genetic variations that could explain changes in gene expression were found in an unexpected part of the genome. Instead of being located between genes, as expected, this enrichment occurred within the genes themselves. This serendipitous finding shifted the focus of our project to a fundamental question: Do regions within genes contain important regulatory information that affects gene expression? To answer this question, we developed a synthetic system that allowed us to screen tens of thousands of regulatory sequence combinations. The results showed that plants do use regions within transcribed gene regions to control expression. Furthermore, we found that regulatory sequences function differently depending on whether they are inside or outside these regions, in stark contrast to animal regulatory sequences, which are indifferent to their position.
These findings are likely to have implications for practices of genetic engineering in plants.
Using the model plant Arabidopsis thaliana, we studied vast amounts of data on how the plant's genes are expressed in ecotypes adapted to different environments. Our goal was to understand how these changes relate to the climates to which the plants are adapted, discover the genetic changes that drive these adaptations, and determine if we can predict which plants will thrive in new conditions as the climate continues to change.
Interestingly, while studying the natural variation in gene expression among Arabidopsis ecotypes, we made a surprising discovery. Many genetic variations that could explain changes in gene expression were found in an unexpected part of the genome. Instead of being located between genes, as expected, this enrichment occurred within the genes themselves. This serendipitous finding shifted the focus of our project to a fundamental question: Do regions within genes contain important regulatory information that affects gene expression? To answer this question, we developed a synthetic system that allowed us to screen tens of thousands of regulatory sequence combinations. The results showed that plants do use regions within transcribed gene regions to control expression. Furthermore, we found that regulatory sequences function differently depending on whether they are inside or outside these regions, in stark contrast to animal regulatory sequences, which are indifferent to their position.
These findings are likely to have implications for practices of genetic engineering in plants.
As a follow-up to our initial result, we set out to investigate the role of sequences downstream of the transcription start site (TSS) in controlling gene expression. To this end, we established a massively parallel reporter assay (MPRA). In the MPRA, we systematically measured the expression of a reporter gene in plant cells in conjunction with 10^4-10^5 different regulatory sequences. Importantly, the position of the candidate regulatory sequence with respect to the TSS of the gene was separately tested and compared. The results were intriguing and unequivocal - the same sequence gave completely different results depending on its position relative to the TSS. This is in stark contrast to the position independence of animal enhancers. Furthermore, the results were consistent across four different flowering plants tested - A. thaliana, tomato, maize, and N. benthamiana.
Downstream enhancers were highly enriched for a DNA motif with a G-A-T-C core. This motif was sufficient to drive gene expression in a dose-dependent manner. Even compared to motifs upstream of the TSS, this motif had the strongest effect. Its effect was tissue dependent, but functional almost everywhere in the plant body - it was strongest in root meristems and weakest in dry seeds. The regulatory module defined by this motif, enriched in secretory pathway genes, acts like a rheostat during development to tune ~7000 genes. Furthermore, we have shown that this motif functions in all vascular plants.
These results have been presented at numerous scientific conferences and published as a preprint titled "Widespread transcriptional regulation from within transcribed regions in plants". https://www.biorxiv.org/content/10.1101/2023.09.15.557872v1.
Downstream enhancers were highly enriched for a DNA motif with a G-A-T-C core. This motif was sufficient to drive gene expression in a dose-dependent manner. Even compared to motifs upstream of the TSS, this motif had the strongest effect. Its effect was tissue dependent, but functional almost everywhere in the plant body - it was strongest in root meristems and weakest in dry seeds. The regulatory module defined by this motif, enriched in secretory pathway genes, acts like a rheostat during development to tune ~7000 genes. Furthermore, we have shown that this motif functions in all vascular plants.
These results have been presented at numerous scientific conferences and published as a preprint titled "Widespread transcriptional regulation from within transcribed regions in plants". https://www.biorxiv.org/content/10.1101/2023.09.15.557872v1.
The results of my project highlight a fundamental difference between plant and animal regulatory sequences and underscore the importance of a thorough understanding of the principles that govern the organization of regulatory sequences around plant genes. First, these findings are likely to impact plant researchers by directing the search for regulatory sequences to regions that have been understudied in transcriptional regulation studies. Second, our results provide a valuable tool for enhancing gene expression in transgenes, potentially increasing gene transcription level and the complexity of gene expression. Finally, research on the fundamental properties of transcriptional regulation in eukaryotes has focused primarily on animals and yeast. Since these two groups belong to only one branch of the eukaryotic tree of life, we are likely to overlook significant differences in how transcription works. Our project has revealed one such difference and highlights the importance of studying the fundamental properties of transcriptional regulation in other branches of the eukaryotic tree of life.