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

Abstract

Transcription factors (TFs) are essential for the regulation of gene expression and cell fate determination. Characterising the transcriptional activity of TF genes in space and time is a critical step towards understanding complex biological systems. The vegetative gametophyte meristems of bryophytes share some characteristics with the shoot apical meristems of flowering plants. However, the identity and expression profiles of TFs associated with gametophyte organization are largely unknown. With only ∼450 putative TF genes, Marchantia (Marchantia polymorpha) is an outstanding model system for plant systems biology. We have generated a near-complete collection of promoter elements derived from Marchantia TF genes. We experimentally tested reporter fusions for all the TF promoters in the collection and systematically analysed expression patterns in Marchantia gemmae. This allowed us to build a map of expression domains in early vegetative development and identify a set of TF-derived promoters that are 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. In addition, we provide an online database of expression patterns for all promoters in the collection. We expect that these promoter elements will be useful for cell-type-specific expression, synthetic biology applications, and functional genomics.

Find your way: Building an atlas from transcription factor activities in the Marchantia gemma

“…C) Expression pattern of multiple fluorescent reporters of TFs in the apical region of Marchantia gemmae (color blocks correspond to panel B ). Adapted from Romani et al (2024) , Figures 1, 4, 5.…”

“…Several TF subfamilies have only a single family member and can be easily studied without facing redundancy issues. Facundo Romani and colleagues ( Romani et al 2024 ) systematically isolated a majority of the promoter elements of Marchantia TFs and mapped the expression pattern of transcriptional reporters to the gemmae. The authors extracted the 5′ untranslated regions together with adjacent upstream sequences from putative TF-encoding genes, covering about 82% of all TF genes in the Marchantia genome.…”