Ancient Plant Gene Regulatory Elements Discovered

Next-generation sequencing research is a little bit like translating text. The books of life, written in nucleotide code, are often long and complex. Nowhere is this more apparent than in plant genomes. They are the Infinite Jest to animal genomes’ Cat in the Hat. Plant genomes are often incredibly long and complex, featuring extensive non-coding regions that have proven to be significant obstacles to understanding and manipulating plants at the genetic level.

Now, in a new study, researchers have revealed a store of hidden genetic elements that could make the task of reading plant genomes far easier and more precise.¹ Across 284 plant species, scientists found about 2.3 million conserved non-coding sequences (CNSs). These elements help plants regulate their genes, and their conservation through time suggests they have important roles in how plants develop and grow. Understanding these elements could help researchers manipulate plant genomes more easily. The team published their findings in Science and shared them in a publicly accessible database.

Putting Plants in the Conservatory

Genomics and bioengineering have given scientists a toolkit for pruning plant genomes. These efforts can yield more resilient, nutritious crops in response to changing climatic conditions. But identifying which gene sequences to tweak to alter targeted traits hasn’t been easy. Part of the issue is plant genomes’ deep and complex regulatory sequences that control the expression of protein-coding genes. “That complexity has made it very difficult to trace regulatory DNA far back in time,” said Idan Efroni, a coauthor of the study and a genomicist at the Hebrew University of Jerusalem, in a statement.

Plant genomes often have extensive duplications, causing genes to become lost or rearranged, which makes it difficult to connect coding genes to their regulatory elements. “As a result, most known plant CNSs were thought to be evolutionarily young,” said Madelaine Bartlett, a study coauthor and plant scientist at the University of Cambridge, in the statement.

To better understand the evolutionary history of these regulatory networks and how they control plant gene expression, the researchers created a new comparative genomics platform called Conservatory.

Ancient Elements, Modern-Day Relevance

Conservatory unlocked this data by using deep phylogenetic sampling to track the relationship between genes and their regulators even after the two had become separated in the thick reeds of plants’ genomes. The tool captured sequence conservation across the vast timescales of evolution and showed that some of the regulatory elements are hundreds of millions of years old.

Conservatory revealed that many ancient regulatory elements sit in hotspots near developmental genes. When the researchers disrupted these genes, they led to developmental defects in the plants, highlighting their importance. The team analyzed eight well-studied gene regulators of leaf, flower, meristem, and epidermal development. Every single regulator overlapped with ancient CNSs identified by Conservatory.

“These sequences have been hiding in plain sight,” said Efroni. “What we show here is that deeply conserved regulatory programs do exist and they are, in fact, widespread.”

The findings clashed with previously held ideas about where regulatory elements had to be located. In some cases, the CNSs were distant from the genes they regulated. The authors suggested that this might mean traditional tools for assessing gene relationships are missing important expression patterns.

Even though the CNSs identified are ancient, the authors hope their findings will change researchers’ understanding of plants today, providing better targets for efforts to manipulate plant genomes. “These sequences are not frozen relics,” said coauthor Kirk Amundson, a plant biologist at the University of Massachusetts Amherst, in the statement. “They can move, duplicate and diversify, yet still preserve the regulatory logic required for development.”