CRISPR-Locate · Linking sequence to function of long noncoding RNAs with CRISPR.
Horizon 2020 — Marie Skłodowska-Curie Actions
- Duration
- 2021-08-01 → 2023-07-31
- EU contribution
- €184,591
- Participants
- 2
- Scheme
- MSCA-IF
Lines connect the coordinator with its partners.
Results in brief
Linking sequence to function of long noncoding RNAs with CRISPR.
After the Human Genome Project, scientists were amazed to find lots of RNA molecules that don't make proteins. In addition to the 19,000 genes that code for proteins, our genetic material contains at least 20,000 long noncoding RNA (lncRNA) genes. Some recent estimates even suggest there could be as many as 100,000 of these genes. Researchers are working hard to figure out what these lncRNA genes do, but they're discovering new ones faster than they can study them. Right now, we only know the functions of less than 1% of these lncRNAs. These findings have posed a big challenge: understanding the important roles of lncRNAs in our bodies. To do this, scientists need to answer a key question – how are the functions of lncRNAs determined by their chemical sequence? Scientists believe that, like proteins, lncRNAs are made up of different building blocks that give them specific shapes and functions. This project aimed to tackle this puzzle by creating a method that can identify different parts of lncRNA molecules and figure out what they do in the cell. For the first time, this allowed us to study many lncRNA components on a large scale, helping to unlock the secrets of how lncRNAs work.
Data: CORDIS, © European Union
Project objective
A great surprise in the wake of the Human Genome Project has been the discovery of vast numbers of RNAs that do not encode proteins. Alongside 19,000 protein-coding genes, our genome contains at least 20,000 long noncoding RNA (lncRNA) genes, but recent estimates push that number to 100,000. Extensive annotation efforts are presently discovering lncRNAs far faster than their functions can be elucidated, and thus only <1% of lncRNAs have been experimentally characterised. These discoveries have created a grand challenge of understanding lncRNAs’ biological significance. To do this, we must solve the pressing question of how lncRNAs’ functions are encoded in their primary sequence. As a proxy of lncRNAs function we can use subcellular localisation since lncRNAs function as a mature RNA molecule. One hypothesis is that, similar to proteins, lncRNAs are modular molecules composed of separable functional domains. Previous studies, including my own, have used conventional methods to identify domains in a handful of lncRNAs by laborious deletion experiments. I propose to advance this field, via a novel high-throughput technique, CRISPR-Locate, capable of detecting lncRNA domains and their function in their natural endogenous context. I will delete ⁓1000 different lncRNA domains at the same time and simultaneously insert RNA tags at their place. Subsequently, I will fractionate cells by their compartments and purify tagged lncRNAs. Afterwards, I will sequence all the tagged lncRNAs and, by comparing the change in the subcellular localisation between mutated and wild type cells, I will identify which domains are responsible for subcellular localization. Finally, I will use CRISPR-Locate to create a map of lncRNA domains, an invaluable resource linking sequence to function, and bring us a step closer to unlocking the potential of 10^4 novel genes in medicine and biology.
Original text from CORDIS.
Participants
- UNIVERSITY COLLEGE DUBLIN, NATIONAL UNIVERSITY OF IRELAND, DUBLIN · DublinCoordinatorIreland
- UNIVERSITAET BERN · BernSwitzerland
Links
Data: CORDIS, © European Union