Advancements in Genomic Research Reveal Alternative Transcription Initiation Sites in Thousands of Soybean Genes

Nov 20, 2024

By Lindsey Berebitsky

Rosalind Franklin, James Watson and Francis Crick discovered the structure of DNA—that molecular blueprint for life—over 70 years ago. Today, scientists are still uncovering new ways to read it.

In 2010, Jianxin Ma, a professor of agronomy, and his collaborators built the first reference genome for soybeans on the widely studied Williams 82 variety. Thousands of scientists and plant breeders have since used that genome in their own research on the genetic makeup underlying various characteristics, such as seed protein and oil content, plant architecture and productivity, and disease resistance and abiotic stress tolerance in soybeans.

Through the last decade, Ma, who is the Indiana Soybean Alliance Inc. Endowed Chair in Soybean Improvement, has been recognized internationally for his contribution to the soybean genome as well as for his continued research and innovation in the field. His most recent work, published in The Plant Cell, used advancements in genomic research to fill in gaps of the original soybean reference genome.

"The reference genome was like a dictionary when we announced it," Ma said. "Each gene was like a single word. However, there was a piece of critical information lacking: transcription initiation sites for individual genes."

Transcription initiation sites are locations in the DNA where a specialized transcription-factor protein can attach and then build an mRNA copy of the gene in front of it. That mRNA is read and translated at a cell's ribosome to create more proteins, important for the chemical and physical function of every organism.

Knowing where the mRNA begins formation on the DNA strand is a significant part of understanding how genes are expressed. These initiation sites contain regulatory elements and provide information to the cell about when and where to transcribe each gene to make protein, and how frequently to do so at any point in time.

In genetics, it has generally been accepted that each gene has one transcription initiation site, located downstream of a core promoter region and typically around a TATA box—a DNA sequence rich in thymine and adenine repeats. But Ma and his colleagues no longer think this is the case

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Video: Spring 2026 weather outlook for Wisconsin; What an early-arriving El Niño could mean

Northeast Wisconsin is a small corner of the world, but our weather is still affected by what happens across the globe.

That includes in the equatorial Pacific, where changes between El Niño and La Niña play a role in the weather here -- and boy, have there been some abrupt changes as of late.

El Niño and La Niña are the two phases of what is collectively known as the El Niño Southern Oscillation, or ENSO for short. These are the swings back and forth from unusually warm to unusually cold sea surface temperatures in the Pacific Ocean along the equator.

Since this past September, we have been in a weak La Niña, which means water temperatures near the Eastern Pacific equator have been cooler than usual. That's where we're at right now.

Even last fall, the long-term outlook suggested a return to neutral conditions by spring and potentially El Niño conditions by summer.

But there are some signs this may be happening faster than usual, which could accelerate the onset of El Niño.

Over the last few weeks, unusually strong bursts of westerly winds farther west in the Pacific -- where sea surface temperatures are warmer than average -- have been observed. There is a chance that this could accelerate the warming of those eastern Pacific waters and potentially push us into El Niño sooner than usual.

If we do enter El Nino by spring -- which we'll define as the period of March, April and May -- there are some long-term correlations with our weather here in Northeast Wisconsin.

Looking at a map of anomalously warm weather, most of the upper Great Lakes doesn't show a strong correlation, but in general, the northern tiers of the United States do tend to lean to that direction.

The stronger correlation is with precipitation. El Niño conditions in spring have historically come with a higher risk of very dry weather over that time frame, so this will definitely be a transition we'll have to watch closely as we move out of winter.