Structure and function of lncRNA-protein complexes involved in transcription regulation
Figure 1: A variety of complementary approaches will be used to derive structure-functional relationships for lncRNAs and nuclear protein complexes involved in transcription regulation.
The Marcia group will use structural biology and biophysical approaches to study the molecular interactions between long non-coding RNAs (lncRNAs) and nuclear proteins and how their complexes regulate gene expression processes.
Previous and current research
My research interests focus on the structural and functional characterization of various classes of macromolecules, ranging from membrane proteins to large RNA enzymes, which are involved in fundamental metabolic pathways, including electron transport, signalling and splicing. My primary expertise is in the field of X-ray crystallography, which I complement with other methods, such as electron microscopy, analytical ultracentrifugation, biochemical techniques, spectroscopy, mass-spectrometry, bioinformatics and functional assays.
I previously determined crystal structures of membrane flavoprotein sulfide:quinone oxidoreductase (SQR) and revealed various steps of the complex SQR catalytic cycle, including substrate binding, flavin-mediated catalysis, sulfide polymerization, and product release. My results had significant impact on the understanding of human SQR, which regulates the homeostasis of gasotransmitter hydrogen sulfide in liver and brain and prevents serious neurodegenerative diseases and lethal encephalopathies.
Successively, I solved various structures of a self-splicing group II intron, revealing the molecular mechanism of hydrolytic splicing and the role played by monovalent ions within an unprecedented catalytic metal ion cluster. My results also shed new light on a related, yet much more complex, splicing machinery, the human spliceosome.
Currently, I am working on ribonucleoproteins (RNPs) formed by histone modification complexes and lncRNAs, which represents one of the most urgent matters of research in cellular and structural biology. Such RNPs are involved in primary physiological processes, such as epigenetics, hormone-signaling, development, stem cell biology, and brain function. Consequently, these RNPs are implicated in severe pathological states, including neurodegenerative and vascular diseases, developmental disorders, and cancer. Structural information on these RNPs is limited to certain protein subunits or their subdomains. Little is known on how these enzymes are regulated by lncRNAs and no 3-D structure of lncRNAs is available. By means of state-of-the-art biophysical techniques, my research aims to answer the following questions: How can many thousands different lncRNAs form tight complexes with a relatively limited set of nuclear protein complexes? Which level of selectivity characterizes the formation of such complexes? How is selectivity achieved? What structural motifs are involved in recognition? How complex is the structural architecture of the intervening lncRNAs and how is it maintained? How are chromatin-binding ability and enzymatic activity of the intervening proteins regulated by lncRNAs at a molecular level? While initially focusing on lncRNAs that are better known and characterized, I will also develop high-throughput methods and perform computational analyses to discover novel lncRNA classes and motifs suitable for structure determination.
In summary, my research aims to reveal the mechanism of lncRNA recognition within nuclear RNPs and the molecular bases for their cellular functions, which are currently unknown. Such studies will have direct medical implications and lead to the development of new therapeutic approaches to cure some of the most invasive diseases of our modern societies.
Future projects and goals
- Identify the recognition motifs that guide formation of tight complexes between lncRNAs and nuclear proteins.
- Determine structures of such ribonucleoproteins.
- Building on structural insights, understand the molecular mechanism by which lncRNAs exert their cellular functions.