The landscape of transcription factor promoter activity during vegetative development in Marchantia

The landscape of transcription factor promoter activity during vegetative development in Marchantia

2024 | Facundo Romani, Susanna Sauret-Güeto, Marius Rebmann, Davide Annese, Ignacy Bonter, Marta Tomaselli, Tom Dierschke, Mihails Delmans, Eftyhios Frangedakis, Linda Silvestri, Jenna Rever, John L. Bowman, Ignacio Romani, Jim Haseloff
Transcription factors (TFs) are essential for regulating gene expression and cell fate determination. Characterizing the transcriptional activity of TF genes in space and time is critical for understanding complex biological systems. The vegetative gametophyte meristems of bryophytes share some characteristics with the shoot apical meristems of flowering plants, but the identity and expression profiles of TFs associated with gametophyte organization are largely unknown. Marchantia (Marchantia polymorpha) is an outstanding model system for plant systems biology with only ~450 putative TF genes. Researchers generated a near-complete collection of promoter elements from Marchantia TF genes and experimentally tested reporter fusions for all the TF promoters in the collection. This allowed them to build a map of expression domains in early vegetative development and identify a set of TF-derived promoters active in the stem-cell zone. The cell markers provide additional tools and insight into the dynamic regulation of the gametophytic meristem and its evolution. An online database of expression patterns for all promoters in the collection was also provided. These promoter elements are expected to be useful for cell-type-specific expression, synthetic biology applications, and functional genomics. The study aimed to systematically explore the behavior of promoter elements from TF genes in Marchantia and to map the resulting expression patterns. The researchers characterized a near-complete collection of promoter elements derived from TFs encoded in the genome of Marchantia. These transcriptional reporters were used to survey the regulatory landscape in the vegetative gametophytes of Marchantia. The approach offers an unbiased and comprehensive way to explore TF expression patterns. Comparative analysis of the reporters allowed the researchers to recognize expression domains and cell types in Marchantia gemmae and provide important insights into the genetic programs underpinning the organization of Marchantia stem cells. They also identified cell-type specific promoters across different stages of gemma development. Surprisingly, the set of TF reporters found in the stem-cell zone (SCZ) is largely evolutionary unrelated to TFs known from the sporophyte meristem of vascular plants. The imaging data for all tested promoters is available via a web-based database to accelerate functional genomics studies and cell-type specific engineering. The researchers identified expression domains in Marchantia gemmae and characterized the expression patterns of TFs in specific cell types. They found that the variability between individuals is relatively low and the dimensions of the tissue follow a normal distribution. Excluding promoters with dim or no expression levels, for each representative reporter, they oriented the image to align the two apical notches to the horizontal axis, subtracted the background, and made a profile of the fluorescence intensity along the notch axis. The length of the profile was normalized by the distance between notches and then smoothed to reduce the noise of the signal. To avoid small variations between left and right notch, they averaged them. Finally, they normalized the signal to the maximumTranscription factors (TFs) are essential for regulating gene expression and cell fate determination. Characterizing the transcriptional activity of TF genes in space and time is critical for understanding complex biological systems. The vegetative gametophyte meristems of bryophytes share some characteristics with the shoot apical meristems of flowering plants, but the identity and expression profiles of TFs associated with gametophyte organization are largely unknown. Marchantia (Marchantia polymorpha) is an outstanding model system for plant systems biology with only ~450 putative TF genes. Researchers generated a near-complete collection of promoter elements from Marchantia TF genes and experimentally tested reporter fusions for all the TF promoters in the collection. This allowed them to build a map of expression domains in early vegetative development and identify a set of TF-derived promoters active in the stem-cell zone. The cell markers provide additional tools and insight into the dynamic regulation of the gametophytic meristem and its evolution. An online database of expression patterns for all promoters in the collection was also provided. These promoter elements are expected to be useful for cell-type-specific expression, synthetic biology applications, and functional genomics. The study aimed to systematically explore the behavior of promoter elements from TF genes in Marchantia and to map the resulting expression patterns. The researchers characterized a near-complete collection of promoter elements derived from TFs encoded in the genome of Marchantia. These transcriptional reporters were used to survey the regulatory landscape in the vegetative gametophytes of Marchantia. The approach offers an unbiased and comprehensive way to explore TF expression patterns. Comparative analysis of the reporters allowed the researchers to recognize expression domains and cell types in Marchantia gemmae and provide important insights into the genetic programs underpinning the organization of Marchantia stem cells. They also identified cell-type specific promoters across different stages of gemma development. Surprisingly, the set of TF reporters found in the stem-cell zone (SCZ) is largely evolutionary unrelated to TFs known from the sporophyte meristem of vascular plants. The imaging data for all tested promoters is available via a web-based database to accelerate functional genomics studies and cell-type specific engineering. The researchers identified expression domains in Marchantia gemmae and characterized the expression patterns of TFs in specific cell types. They found that the variability between individuals is relatively low and the dimensions of the tissue follow a normal distribution. Excluding promoters with dim or no expression levels, for each representative reporter, they oriented the image to align the two apical notches to the horizontal axis, subtracted the background, and made a profile of the fluorescence intensity along the notch axis. The length of the profile was normalized by the distance between notches and then smoothed to reduce the noise of the signal. To avoid small variations between left and right notch, they averaged them. Finally, they normalized the signal to the maximum
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