Unbiased look at plants reveals how they achieve transcriptional regulation

Our world today is populated by multicellular organisms, from big trees to climate-wrecking humans. This multicellularity arose independently in plants and animals. Both animals and plants cope differently with the challenges of corralling individual cells together to form a larger organism, such as the need to communicate and coordinate between cells, to share and transport nutrients, and to form specialized structures.

One challenge posed by multicellularity is that all cells carry the same genetic code, but the cells look and behave differently: A root cell needs to elongate toward water sources and gravity, while cells in the leaves drive photosynthesis.

To achieve different outcomes from the same underlying code, cells tinker with how the code is read out, in what is called transcriptional regulation. Plants and animals also differ fundamentally in how they achieve this transcriptional regulation, as a new paper by the group of Magnus Nordborg at the GMI shows.

The results, published in Nature Genetics on September 12, open a new perspective on how plants achieve transcriptional regulation.

“Much of what we know about transcriptional regulation in plants so far is informed by research on animals and yeast,” says Yoav Voichek, postdoc in the lab of Magnus Nordborg and co-author of the study. “We wanted to look at plants in an unbiased way, thereby making it possible to uncover mechanisms and processes that are unique to plants.”

Using a parallel reporter assay in four plant species—maize, Arabidopsis, tomato and Nicotiana benthamiana—the researchers searched for sequences that influence transcription. The transcription start site (TSS) is the specific location on a gene where transcription begins. The researchers identified a region downstream of the TSS that is central for transcriptional regulation.

Looking more closely at how the sequences regulate transcription, the researchers uncovered a novelty in transcriptional regulation. “Most surprisingly, when we swap the position of this regulatory sequence, placing it upstream of the transcriptional start site, it no longer drives transcription,” Voichek says.

This finding runs counter to what would be expected from looking at transcriptional regulation in animals: In animals, regulatory sequences are position-independent, as swapping their position does not change how they regulate transcription.

Fine-tuning transcription

Within the regulatory sequence, the scientists uncovered a sequence-motif, consisting of the bases GATC, that strongly drives gene expression. “The sequence motif has a more potent influence on transcription than any DNA motif identified upstream of the transcriptional start site,” Voichek explains. The motif is evolutionarily conserved and found in all vascular plants, i.e., all land plants except for mosses, hornworts and liverworts.

The way in which the GATC-motif influences transcription illustrates how regulatory sequences can fine tune transcription in different cell types. “The higher the number of these motifs downstream of the TSS, the more strongly the gene is expressed,” Voichek says. “The motif acts like a rheostat, finely tuning genes that need to be expressed in all cell types, but at different levels.”

In the future, Voichek plans to investigate how the GATC-motif exerts control over transcription. “Our study not only shifts the understanding of transcription regulation in plants but also underscores that we need to study transcription in a diverse set of organisms to broaden our understanding of biology.”