Not one but many: adopting structural flexibility in the analysis of the evolution of lncRNAs.

Project Information

MULTI_FOLDS

Grant agreement ID: 793699

DOI

10.3030/793699

Project closed

EC signature date 23 March 2018

Start date 1 April 2018

End date 26 May 2020

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 170 121,60

EU contribution

€ 170 121,60

Coordinated by

BARCELONA SUPERCOMPUTING CENTER CENTRO NACIONAL DE SUPERCOMPUTACION
Spain

Periodic Reporting for period 1 - MULTI_FOLDS (Not one but many: adopting structural flexibility in the analysis of the evolution of lncRNAs.)

Reporting period: 2018-04-01 to 2020-03-31

Summary of the context and overall objectives of the project

Long non-coding RNAs (lncRNAs) are abundant in mammalian transcriptomes. However, it remains unclear how many of them are functional and how their functions are performed. LncRNAs seem to be poorly conserved at the sequence level, but some of them share conserved structural elements and are present at syntenic genomic locations in different species. A recent study revealed that secondary structure constrains sequence variation in lncRNAs. This is in contrast with previous analyses that dismissed relationships between structure and sequence evolution in lncRNAs. A crucial difference in the previous study is that the considered structural feature, accessibility, is computed from an ensemble of thermodynamically stable structures.
Our group recently developed a novel Illumina-based implementation of in-vitro parallel probing of RNA structures called nextPARS. Using this technique, we observed that many lncRNA sites exhibit positive signals for both single- and double-strand specific enzymes, suggesting several structures may coexist. Based on this, we argue that the difficulty of identifying links between sequence and structure in lncRNAs results in part from limitations imposed by assuming a single, stable structure. To solve this, we developed a computational framework that enables the reconstruction of co-existing lncRNA structures from nextPARS or similar empirical data, and the comparison of such reconstructed ensembles from different species.
The main goal of my research project is to study lncRNAs structures from animals and fungi. Using the model that enables the reconstruction of co-existing structures, I’ve investigated lncRNAs from different species for which experimental data from RNA structure probing has been obtained. I found that lncRNAs in different species share common structural elements, despite high sequence divergence, suggesting that lncRNAs may rely on short functional elements rather than long stretches of conserved sequences. This novel multidisciplinary approach establishes a framework for understanding the evolution of lncRNAs and should help to fill the gap between the structure and function of lncRNAs in different species.

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

Using a new paradigm which states that an ensemble of structures may coexist in a given lncRNA, I’ve contributed with major breakthroughs in the study of lncRNAs evolution, function and structure, with potential impacts on both basic and clinical studies. I’ve developed a method to predict a combination of secondary structures using RNA probing experimental data. I’ve performed experiments at different temperatures to analyze the stability of RNA secondary structures depending on thermodynamical characteristics. Furthermore, I’ve designed nextPARS experiments in synthetic RNAs introducing mutations that force some constraints on secondary structure conformation. Moreover, I’ve studied in detail the structural profiles from lncRNAs in nematodes to determine structural regions and shared structural motifs. In addition, I’ve observed that NORAD lncRNA regions of repeats units are less variable at different temperatures than other areas of the same lncRNA. Finally, I’ve shown that using the possible structures that may coexist within a given lncRNA is better than using only the most stable one, to study the evolution of lncRNAs.
Furthermore, I’ve presented my research project by participating in national and international conferences such as Keystone Symposia on Noncoding RNA (Whistler, Canada), 25th Annual Meeting of the RNA Society, XIV Symposium on Bioinformatics (Granada, Spain) and EMBO RNA: Structure meets function (Stockholm, Sweden). Moreover, I’ve published part of the results for this project in the journals NAR, RNA Biology and a book chapter in Springer Nature and I hope to publish other results soon. Furthermore, I’ve participate in outreach activities and communication activities, like CNN radio, TN international tv show, Border periodismo blog, PRBB Open Day and with several posts on twitter.

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)

The central aim of this proposal was to study in detail lncRNAs structures from animals and fungi. By combining computational approaches, high-throughput structure probing techniques and molecular biology experiments the project created a wealth of original information by unraveling novel, uncharacterized structure conservation for lncRNAs in animals and fungi.
Thus, I hope that the computational approach developed here will help the scientific community to identify conserved structures in different species for other long RNAs that were missed with the current available methods. Consequently, this project will likely further our understanding of evolution in lncRNAs, with potential impacts on both basic and clinical studies.
Finally, the proposed project strongly contributed to European excellence and competitiveness due not only to the breaking-edge results to understand the function and evolution of lncRNAs, but also to the extensive competences acquired during the training in the host laboratory. This has enhanced my reputation in the research communities and will provide a strong foundation for a permanent and productive research career.
Address (URL) of the project's public website

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