ZHAO LAB - Research

Students, I want to share with you a story of myself. During my postdoctoral training in Scott Poethig’s lab at Penn, my research was built on a landmark Poethig lab Cell paper (figure above) that proposed how tiny regulators, called microRNAs, might control the timing of plant development in a sequential manner. This model had guided people's view of plant development for more than a decade and exhibited in textbooks many times. When my own findings were published after years of work, Scott handed me a copy of that Cell paper. In the upper right corner, he had written: ‘For Jianfei – who changed the paradigm.’

That note captured the essence of my years of work. My research challenged the old model and showed that plant development is not guided by one simple sequence, but by two small regulators (microRNAs) that work independently to control key stages of growth. This discovery answered a century-old question, offered a new way of thinking about plant development ("changed the paradigm"), and opened novel directions for research and biotechnology.

Having Scott connected my work to—and even beyond—that seminal paper was both humbling and inspiring. It felt like carrying the torch of discovery forward.

Today, I’m honored to share my own research journey to encourage you to stay curious of surroundings, think critically and independently even for the textbook contents. I hope to carry that torch with you, the students of DePaul, as we explore new frontiers together.

Research is to see what everybody else has seen, and to think what nobody else has thought. — Albert Szent-Györgyi, Nobel Laureate

In our lab, we are uncovering the mysteries of developmental timing—a centuries-old scientific pursuit—armed with new clues and technologies that bring us closer to understanding its secrets.

I hope to use this main research webpage to share a story with you... If you are a student, you have only one guiding rule on this journey, and one rule only: think independently (with AI-facilitated decision making).

To delve deeper into the idea of plant “age” and its changes, we need rewind more than two centuries ago to the times of Johann Wolfgang von Goethe. Famous for his poetry and literary achievements, Goethe was also a pioneering naturalist who looked at plants and saw metamorphosis everywhere.

In his book, The Metamorphosis of Plants, he recognized a sequence of expansions and contractions in plants – a rhythm of growth that unfolds in stages.

Plant Shoot Maturations Events are Dynamic

How did people start to unravel the mechanisms that regulate plant developmental timing?

It usually starts with the studies of mutants. The earliest indication of the genetic components regulating Vegetative Phase Change comes from observations with specific, naturally occuring maize mutants:

The first insights came from a group of dominant mutants, Teopod1 (Tp1), Teopod2 (Tp2), Congrass (Cg1) and dwarf1 (d1) mutants that showed prolonged juvenile phase, where traits normally restricted to the early stages of growth were expressed for a longer period.
Mutants, glossy15 (gl15) and Early phase change (epc), that are with the opposite characteristics—a shortened juvenile phase are also studied.

Studies into the Tp1, Tp2 and Cg1 mutants revealed that their prolonged juvenile phenotypes was linked to the microRNA156 (miR156), In these mutants, ultra high miR156 suppress its target genes, members within the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) family. The SPL proteins are transcription factors that are necessary to activate genes responsible for adult traits. Therefore, by keeping the SPL genes suppressed, the persistent miR156 effectively traps the plant in a prolonged juvenile state. Later studies established a clear, functional link between the miR156-SPL pathway with the regulation of developmental timing (in specific, vegetative phase change).

On the other hand, the maize gl15 mutant, which is probably the most well-known mutant with a truncated juvenile stage (accelerated vegetative phase change), suggested that its phenotype is regulated by a different microRNA, miR172, which promotes the transition to the adult phase by downregulating GL15 gene.

What are MicroRNAs?

You may have heard of quite a few kinds of RNAs, like mRNA (messenger RNA), tRNA (transfer RNA), and rRNA (ribosomal RNA). Like all these RNAs, microRNAs are also transcribed from genomic DNA. However, unlike messenger RNAs that encode proteins, microRNAs (miRNAs) are short—usually about 20–24 nucleotides long—and they are sequence-specific but do not code for proteins. Instead, their main role is to regulate gene expression. In plants, miRNAs are crucial for controlling developmental timing, organ formation, and responses to environmental stresses.

They work by binding to specific messenger RNAs with complementary sequences, leading to the cleavage or repression of those target mRNAs. In this way, plant miRNAs act like fine-tuners, ensuring that the right genes are expressed at the right time and place, and they play a significant regulatory role in controlling plant developmental timing.

microRNA with Their Targets are Central in Regulating Plant Developmental Timing, especially Vegetative Phase Change and the Acquisition of Reproductive Competence.

Biogenesis, Processings and Functions of Plant MicroRNAs

microRNA156/157, miR172, and their targets

Evolution of miR156 and miR172 Gene Family

It is the Spatio-temporal Changes of microRNA with Their Targets (When, where, and the fold they are expressed) Regulating Plant Developmental Timing

So, what controls the Spatio-Temporal Changes of the miRNAs and their targets? (This is the exact questions that have been pursued for over Two decades, but still no conclusive answers)

In Acacia, juvenile leaves (left) and adult leaves (right) exhibit distinct shapes, separated by transitional forms that bridge the two stages. In the case as shown above, the transtion starts by Leaf 7. This transitioning point could be accelerated or delayed by environmental cues (light, temperature, nutrient, etc)

Current Working Model for Vegetative Phase Change

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