Long noncoding RNAs: Impact on Gene Regulatory Networks

Project Information

lncImpact

Grant agreement ID: 863589

DOI

10.3030/863589

Project closed

EC signature date 24 January 2020

Start date 1 June 2020

End date 31 May 2026

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 000 000,00

EU contribution

€ 2 000 000,00

Coordinated by

WEIZMANN INSTITUTE OF SCIENCE
Israel

Periodic Reporting for period 3 - lncImpact (Long noncoding RNAs: Impact on Gene Regulatory Networks)

Reporting period: 2023-12-01 to 2025-05-31

Summary of the context and overall objectives of the project

We are studying the biology of long noncoding RNAs (lncRNAs). Recently, it has been appreciated that major parts of the human genome are transcribed into RNA molecules. While some of these molecules go on to produce proteins that carry out many important cellular functions, and have been heavily studied for decades, many of the RNAs are not producing such proteins. A major fraction of these produces long RNA molecules that closely resemble on the molecular level those that lead to protein production, and these are collectively called lncRNAs. The actions of these lncRNAs have now been implicated in all major cellular processes and in many different human diseases, but how they carry out their functions remains unclear as is the focus of the lncIMPACT proposal. Understanding the modes of action of lncRNAs is key both for understanding which and how mutations in these genes affect our physiology and health and for designing potential therapeutic modalities that can change lncRNA function with potential health benefits. In the proposal, we identified three key types of lncRNAs: those that enhance the activity of other genes found elsewhere on the same chromosome as the lncRNA gene, those that act specifically at beginnings of other genes found close to the lncRNA; an, those that act independently of the lncRNA genomic position by scaffolding and affecting protein activity. We aim to understand the importance of key lncRNAs in each group and decipher their modes of action.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Since the beginning of the project, we've made substantial progress in all three aims, shining light on the mechanisms underlying the activities of several lncRNAs from each type. We studied the Silc1 lncRNA that we previously found to be induced and important during regeneration in neurons, in the context of memory formation in the hippocampus and found that without Silc1 the process of memory acquisition is significantly impaired and this occurs because the induction of Sox11, a gene found on the same chromosome as Silc1 but separated from it by ~200,000 DNA bases is lost in specific regions of the hippocampus. For another lncRNA, Meteor, we found that different elements within the gene are important for different aspects of early embryonic development, acting through the Eomes gene, which is important for the development of the heart and related tissues. To understand the second type of lncRNAs, we are mainly focused on the Chaserr lncRNA, which represses Chd2, a gene found immediately near it, on the same chromosome. Mutations in Chd2 lead to epilepsy and autism, and we are exploring targeting Chaserr as a potential treatment for Chd2 haploinsufficiency. We made substantial progress in understanding how Chaserr acts, which opens new avenues for its inhibition. In the first aim of the project, we made progress in understand the way the NORAD lncRNA folds and how this folding helps it to be very efficient in its activities, principles which we now use for the design of new potent lncRNAs.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

In the first part of the project, we already made an intriguing observation about the mode of action of the Chaserr lncRNA which allowed us to try additional ways for inhibiting its function and increasing expression of its target gene. We also were able to understand much better how NORAD long noncoding RNAs uses a particular structural organization to inhibit the activity of Pumilio proteins, and which can be extended to inhibit the activities of other RNA-binding proteins similarly. We expect that further interrogations in the second part of the project will allow us to understand how to bring over the insights we gained into the biology of specific lncRNAs to the hundreds and thousands of lncRNAs that remain completely obscure.