Neurons growing in a microfluidics device

The Murn Lab

For Creative Research of RNA Biology
INSPIRATION

Few if any fields of research have pervaded our lives as profoundly as the field of RNA biology in recent years. To appreciate the scope, one only has to consider research into the RNA virus causing COVID-19 that has led to the development of highly efficient RNA-based vaccines, the Nobel prize-winning RNA research into CRISPR that has just a few years ago revolutionized essentially all areas of biomedical research, or the rapidly growing number of RNA-based therapeutics that can now treat some of the most devastating human diseases. The Murn lab draws inspiration from these and many other landmark discoveries and innovations that highlight the central role of RNA as life's indispensable molecule. We are committed to solving fundamental problems in the field of RNA biology to illuminate life at the level of molecules, cells, and organisms while keeping a keen eye on potential practical implications. 

 

We are currently pursuing three major unsolved problems in the field. First, we would like to understand how RNA-binding proteins (RBPs), which regulate essentially every event in the lifetime of an RNA molecule, convey their instructions to the core effectors of RNA processing. At present, lack of this knowledge arguably presents the the biggest gap in our understanding of RBP activities and thus gene regulation. Second, we are fascinated by the fact that extant cells, including human, have retained some of the most ancient RNA-based enzymes (or ribozymes), despite having replaced most others with much more economical and versatile protein-only complexes. What attributes might be rendering these molecular relics superior to proteins in modern-day cells? Taking deep conservation as an indicator of an important function, we are exploring the unannotated roles of two such relics, RNase P and RNase MRP, in mammalian cells. Third, motivated by our own preliminary data, we are trying to decipher how RNA modifications, the collective of which is sometimes referred to as the 'epitranscriptome', are differentially written in different tissues and how they may play particularly critical roles in development, functioning, and disease of the nervous system.

Our studies make heavy use of genome-wide and computational approaches in combination with traditional biochemistry, genetics, in vitro cell differentiation paradigms, and genetically modified mice to allow for systems-level understanding of RNA networks and their regulatory principles. To support our research activities, we develop novel RNA technologies and receive funding from federal (NIH, NSF, DOD) and state sources.

Some of our recent stories
  • The nexus between RNA-binding proteins and their effectors

Beyond their recognition of RNA and their general functions, little is still known about how RNA-binding proteins (RBPs) mechanistically regulate RNA processing. Our analysis shows that numerous RBPs converge onto fewer effectors of RNA processing, forming a distinct regulatory level that contributes to the hierarchical organization of RNA networks. We find that RBP–effector interactions are dominated by contacts between short linear motifs within intrinsically disordered regions of RBPs and structured domains of effectors, allowing for high specificity but transient nature of the interactions. The RBP–effector interface serves as a versatile platform that senses intra- or extracellular stimuli and converts them into biological responses via transient or stable adjustment of RNA processing. We further find that dysregulation of contacts between RBPs and their effectors often causes human disease and that pharmacological or genetic targeting of the RBP–effector nexus carries significant therapeutic potential for neuromuscular disorders, immune disorders, and cancer. Find our story in Nature Reviews Genetics.

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Organization of RNA networks.
  • Post-translational modulation of  RNA-binding proteins
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A model for phosphorylation-dependent regulation of cell morphogenesis by Unkempt.

Reversible regulation of RBP–effector contacts is typically achieved by PTMs, of which phosphorylation has arguably garnered the most attention, particularly in the context of signal-regulated RNA processing events. The fast turnover of phosphorylation in fact renders this PTM particularly well-suited to mediating rapid responses of several types of RNA processing to a variety of signals. We found that the activity of the RNA-binding protein Unkempt, a key regulator of cell morphogenesis, is regulated by nutrient levels and growth factors via phosphorylation by mTORC1. Find out more about this story on bioRxiv. .

  • A closer look identifies novel small regulatory RNAs

High-throughput RNA sequencing (RNA-seq) has greatly advanced small non-coding RNA discovery, but the widely used library construction protocols often give rise to biased sequencing results. We collaborated with Qi Chen's group to develop an improved library preparation method, called PANDORA-seq, that identified numerous previously unseen small regulatory RNAs primarily derived from tRNAs and rRNAs. Read the story at Nature Cell Biology.

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An expanded repertoire of tsRNAs identified in mouse embryonic stem cells. 
  • Control of cell morphogenesis by an RNA-binding protein

Cell shape is one of the most distinctive features of all somatic cells yet little is known about how it is specified. We discovered a molecular program, controlled at the RNA level, that determines the early shape of neurons. We found that a deeply conserved RNA-binding protein, called Unkempt, coordinates an entire morphology program to establish the early bipolar shape of neurons during embryonic development of an organism. A testament to the power of post-transcriptional control and the activities of RBPs! See the story in Genes & Development.

The story of Unkempt  on the cover page
  • A 'heavy-duty' mode of RNA sequence recognition

Following up on our initial story on the RNA-binding protein Unkempt (see above) we wondered how the six CCCH zinc fingers of Unkempt - the largest such array of any mammalian protein - operate to recognize a relatively short stretch of RNA sequence. We found that the six zinc fingers form two bulky RNA-binding folds, each recognizing a distinct trinucleotide RNA motif. Presence of both motifs and their relative position within coding regions of targeted genes is critical for high-affinity RNA binding, which, in turn, is required for translational repression of Unkempt-target genes. Find the story at Nature Structural and Molecular Biology..

Co-crystal structure of one of the zinc fingers clustered bound to the signature UAG motif.
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