We are ecstatic to announce that our ERC Starting Grant 2022 project "TRANS-3" (TRANscriptional and Splicing Topological Regulations Architecting Nuclear Structure in TRANS) was selected for funding.
Our project was awarded a budget of ~€1.77M and will be developed over a period of 5 years.
We are eager to get started and we are looking for motivated postdocs to join us - check out the job ad below and kindly help us spread the word!
We have been working towards this goal for many years now, and we could not have reached it without the support of mentors, colleagues, and friends that dedicated their time and energies to help us build our most exciting project yet.
For those not in the know, ERC Starting Grants are awarded to scientists with 2-7 years of research experience since their PhD. In the 2022 call only ~13,9% of nearly 3,000 applications could be supported: less than 30 of these are for projects that will be developed in Italy, and only 7 of these are in the life sciences arena. Our proposal lies in the so-called Life Sciences 1 (LS1) panel: "Molecules of Life: Biological Mechanisms, Structures and Functions", which encompasses the disciplines of molecular biology, biochemistry, structural biology, molecular biophysics, synthetic and chemical biology, drug design, innovative methods and modelling. This has been a historically underrepresented panel for scientists in Italy, which previously secured less than 2.5% of all LS1 proposals. We are thus especially proud to represent this important arena, which is essential for innovation in our country and the whole of Europe.
Below are the title and abstract of our project, followed by a narrative description of our motivations and goals.
Beyond the chromosome: unravelling the interplay between inter-chromosomal genome architecture and mRNA biogenesis
In TRANS-3 we will develop the theoretical and experimental framework to understand inter-chromosomal genome structure and activity. Despite advances in sequencing chromosomes and mapping their three-dimensional (3D) organization, a full picture of 3D genome structure that details how the borders of various chromosome territories functionally interface one another is still missing. As an analogy, our world map does not indicate most natural corridors or manmade infrastructure that connect countries to one another. Worse, we barely understand how such connections function. My recent work has identified one of the few functional inter-chromosomal (trans) DNA interactions known to date: a splicing factory involving over ten chromosomes and orchestrated by the muscle-specific protein RBM20 around its key target, the TTN pre-mRNA. I hypothesize that this exemplifies how mRNA biogenesis instructs the formation of trans-interacting chromatin domains (TIDs) around mRNA factories, nuclear compartments that facilitate gene regulation.
We will test this general hypothesis by dissecting the mechanisms and function of a specific, disease-relevant model: the RBM20 mRNA splicing factory. We will then explore the global impact of these regulations. First (WP1) we will mechanistically assess how mRNA factories form and act through live imaging of the nuclear positioning and alternative splicing dynamics of an RBM20-regulated locus. Secondly (WP2) we will examine the physiological role of mRNA factories by studying the effects of disease-associated mutations in RBM20 and the TTN regulator GATA4, and of genetic variability in TTN regulatory regions. Finally (WP3) we will develop and deploy a novel pipeline to identify, validate, and study new TIDs and mRNA factories through the combination of molecular biology, bioinformatics, biochemistry, and single cell biology.
In all, TRANS-3 will venture beyond the chromosome frontier towards a deeper understanding of nuclear structure-function.
The Heart of the Matter: How the Structure of DNA Influences Heart Disease
The human body is composed of over two hundred types of cells, each as different from one another as the heart, blood, and brain. And yet, each of the one hundred trillion human cells shares the same genetic code. How can we reconcile this apparent paradox? In a word: structure.
The 46 DNA molecules that make up the human genetic code - the so-called chromosomes - are about two meters long in total. And yet, they are jealously preserved in a structure, the cellular nucleus, no larger than a hundredth of a millimeter - another paradox? In reality, this is possible because the DNA filament is extremely thin - about two millionths of a millimeter - and can therefore be folded upon itself. Anyone who has had the unpleasant experience of winding a ball of yarn knows how difficult it can be. Now imagine having to do it for 46 balls of yarn that have to intertwine with each other in a limited space. To complicate matters, DNA cannot simply be all compacted upon itself: this would make it useless! Some portions of the chromosomes, the so-called genes, which are necessary for cellular function, must be left free. To top it off, there are over 200 types of patterns to follow in folding human DNA, as many as the types of cells that make up our body. This is where the answer to our opening question lies: each cell only leaves unfolded a portion of its genetic code, namely the portion that contains the genes that characterize the function of that cell, such as the contractile proteins of muscle, the hemoglobin of blood, or the neurotransmitters of the brain.
In the last twenty years, we have made tremendous strides in understanding human DNA. In addition to determining its sequence, we have mapped how the various chromosomes are folded in many different cell types. However, we are missing a fundamental detail: how are the various chromosomes packaged together? To make an analogy, it's like having detailed maps of Italy and other European countries - complete with cities and other points of interest, and the infrastructure that connects them such as roads, railways, and navigable rivers - but having no idea how to cross national borders. It would be quite difficult to get from Turin to Paris if we didn't know about the existence of the Sandro Pertini airport, the Frejus tunnels or Mont Blanc, or the various mountain passes and valleys: we would risk getting lost for weeks in the Alps and end up retreating!
The purpose of our "TRANS-3" project, funded by the European Research Council (ERC), is to launch an exploratory expedition beyond the borders of individual chromosomes, to map their connections and understand their function. This information will allow for a better understanding of how the nucleus structure is altered by various diseases, and could lead to new drugs capable of curing them.
Our expedition starts from the discovery of the first example of how chromosomes are not simply packed into the nucleus like socks in a messy teenager's drawer, but can develop specific and important connections. We have identified a type of DNA folding that involves ten chromosomes and occurs only in muscle cells such as those in the heart. This structure brings together a series of genes essential for cardiac function and all regulated by a protein exclusively expressed in muscle and called RBM20. Like in an assembly line, we believe that gathering the necessary machinery and components for the expression of these genes increases their efficiency. Furthermore, we know that mutations in both the RBM20 protein and its main regulatory target, the gene encoding the titin contractile protein, lead to severe cardiac diseases characterized by rhythm disorders and insufficient blood supply to the body. Therefore, we aim to examine in detail the functioning of the RBM20 "factories" both under normal conditions and following mutations that alter their function. These studies will use genetic engineering, super-resolution microscopy, genomic sequencing, and bioengineering methodologies applied to stem cells differentiated into cardiac muscle.
Starting from the outpost of RBM20, we plan to explore the rest of the boundaries between the various chromosomes in heart cells. Similar to space exploration, this ambitious mission will require us to develop new technologies. In our case, we will optimize methods for mapping interactions between DNA molecules, analyzing data from a statistical point of view, identifying the proteins and genes involved, and finally validating the function of these linking structures. It will be a difficult journey, but we have five years ahead of us, a good budget, a close-knit team, and important international collaborations. Most importantly, we are armed with the motivation that even small successes in this frontier field could have important and partly unpredictable implications for understanding and treating not only cardiac diseases but also others.
Thank you for reading through the end; stay tuned for regular updates on our project!