Gene regulation: diverse, complex, and utterly fascinating

The success of every organism requires each gene to be expressed in the right amount at the right place at the right time. Gene expression must be robust enough to ensure that processes like development occur reproducibly, yet flexible enough to adapt to changes in internal and external environments. Controlling gene expression is necessarily multi-faceted and combinatorial, and every step from transcription to protein degradation provides an opportunity for regulation. To put it another way, gene regulation is fundamentally an integration problem because cells must coordinate transcription, RNA processing and degradation, translation, and protein destruction in the face of these dynamic and often-changing challenges.

The ribosome is a central player integrating gene expression. It is the machine that decodes genetic instructions into proteins so that information becomes function. And it is a regulatory platform that connects protein birth, mRNA stability, protein fate, and developmental control. However, many molecular connections remain out of focus, and this gap fuels our curiosity.  

Using the powerful combination of classical molecular biology techniques and high-throughput ones, our goal is to understand how translation machinery integrates with these broader regulatory networks. We focus on four major areas:

1. Elongation Dynamics and mRNA Stability

While mRNA stability has classically been thought to be modulated via specific motifs in 3'UTRs, recent work in prokaryotes and eukaryotes has uncovered an ancient regulatory pathway where the speed of translation elongation impacts mRNA stability. We have extended these results to human cells. Synonymous codons, which encode the same amino acid, are not functionally equivalent for gene expression. "Optimal" codons support fast ribosome movement, while "non-optimal" codons slow ribosomes down. These differences in elongation speed trigger mRNA degradation, reduce translation initiation, and alter protein abundance far beyond what changes in transcript levels alone would predict.

How is slow elongation sensed in human cells? How does slow elongation trigger mRNA decay? Why do non-optimal codons specifically reduce translation initiation? How does elongation speed change in different cellular contexts, and how does the cellular environment sculpt post-transcriptional regulation?

2. The Impact of Co-translational Events on Protein Fate

The N-terminus of a protein—its first few amino acids—plays a critical role in determining protein stability, localization, and function. These N-terminal "proteoforms" arise through alternative translation initiation, RNA processing, and post-translational modifications. Many generate N-degrons: signals at the protein's extreme N-terminus that trigger its degradation. This area represents a frontier where RNA biology meets protein quality control. Regulatory decisions that begin during translation, such as which start codon is used or how the nascent chain is processed, shape the protein's entire lifecycle.

How do alternative translation initiation sites create distinct N-terminal proteoforms with different fates? What are the rules governing N-degron recognition and protein turnover? How does RNA-level regulation interface with protein-level degradation pathways?

3. 2A Peptides: Ribosome-Mediated Peptide Bond Skipping

2A peptides are fascinating 18-22 amino acid sequences that cause the ribosome to skip forming a peptide bond, releasing one protein while continuing to translate another from the same mRNA. First discovered in viruses, these sequences allow multiple proteins to be made from a single open reading frame. But their broader evolutionary distribution and mechanistic basis remains a mystery.

Recently, we systematically identified and characterized 2A peptides across eukaryotes and viruses. We predicted ~2,200 2A peptides, expanding the known class (class A) and identifying a previously unrecognized class (class B) with distinct sequence features. We identified key residues required for skipping activity, including a conserved N-terminal tryptophan in class B peptides. 2A peptides are widespread in RNA viruses and present throughout eukaryotic evolution.

How exactly does a peptide sequence make the ribosome skip a bond? What determines the efficiency of skipping? Can we engineer new 2A peptides for biotechnology applications?

4. Regulation and Evolution of Gene Expression Machinery

The molecular machines that control gene expression—ribosomes, cleavage and polyadenylation complexes, degradation machinery—don't operate constitutively. They're regulated, and they evolve. We study both dimensions.

Developmental regulation of degradation machinery: Removal of unnecessary maternal gene products and their replacement with zygotic gene products is a highly synchronized, essential process in the early animal embryo. This process is called the "maternal-to-zygotic transition" (or MZT). Although our interest stemmed from removal of maternal mRNAs, we and others have shown that removal of maternal proteins also plays an important role in the MZT.

Using Drosophila as a model system, we focus on how the embryo removes maternal proteins. We've discovered that the CTLH E3 ubiquitin ligase degrades specific RNA-binding proteins (ME31B, Cup, TRAL) only during early embryogenesis. Muskelin acts as the substrate adaptor for this complex and is itself tightly regulated during development, providing target specificity for the E3 ligase . How do embryos target maternal proteins for degradation? How is protein degradation controlled during development? What are the developmental consequences when this process goes awry?

Evolution of fundamental mechanisms: Yeast and mammalian cells are classic model systems for studying translation and mRNA decay. But there is much more evolutionary diversity in eukaryotes that demands exploration. Giardia lamblia is a deeply branching eukaryote and human pathogen. A protist, Giardia also has dramatically simplified translation and mRNA decay machinery. For instance, the "essential" translation initiation factor eIF4G is absent in Giardia.

We use Giardia and other protists to understand how core gene expression mechanisms evolved and diversified. We discovered that Giardia uses an AGURAA poly(A) signal rather than the canonical AAUAAA. Auxiliary polyadenylation elements have been gained and lost across eukaryotic evolution. We determined the Giardia ribosome structure, which revealed altered quality control pathways and differences in the peptide exit tunnel.

How does Giardia control translation initiation without eIF4G? How does it degrade mRNA? And how has evolution shaped post-transcriptional gene regulation?