Transposable elements, also known as mobile DNA, are present all over the tree of life. They play a major role in the biology of prokaryotes and eukaryotes, have implications in agriculture and medicine and are useful biotechnology tools. Due to their fascinating capacity to jump around, and their structural and functional impact on the genomes in which they reside, a large palette of research is dedicated to them, tackling a broad spectrum of organisms using a wide variety of biological processes and methodologies. From April 20 to 23, 2024, 310 transposable element aficionados gathered in Saint Malo, France at the International Congress on Transposable Elements (ICTE) 2024, to present their most recent discoveries and exchange ideas and techniques. The themes covered diverse fields such as evolution, epigenetics, biochemistry, structural biology, ecology, genomics, bioinformatics, plant biology, microbiology, neurobiology, aging research, and oncology. ICTE is organized every four years since 2008, except in 2020 when the edition was cancelled. This year, 77% of the participants, of 50 different nationalities and at various stages of their careers, were coming for the first time. The overall conference fostered many new collaborations that hopefully will be present at the next 2028 ICTE edition. Finally, following the vote of all participants, three poster prizes were awarded from among the 300 poster presenters: the biography of Barbara McClintock (“A Feeling for the organism”) and a PeerJ interview.

ICTE 2024 organizing committee.

 

Thomas Balan PhD Candidate at the Jacques Monod Institute, Paris, France.

Can you tell us a bit about yourself and your research interests?

I am a PhD candidate at the Jacques Monod Institute in the team of Sandra Duharcourt. My work focuses on understanding the role of repressive histone modifications, particularly the methylation of lysine 27 on histone H3 (H3K27me3). My research interests lie in the field of epigenetics and its role in gene expression and genome stability. I am especially interested in unravelling the mechanisms that act downstream of chromatin modifications using the unicellular eukaryote Paramecium as a model organism.

What first interested you in this field of research?

I have always been fascinated by the complexity of gene regulation. During my studies, I became intrigued by the role of epigenetics in these processes. The fact that changes in gene expression can be inherited without alterations in the DNA sequence was particularly captivating. This led me to focus on understanding the mechanisms that control histone modifications, which play a crucial role in epigenetic regulation during development.

Can you briefly explain the research you presented at ICTE 2024?

At ICTE 2024, I presented my research on the identification and characterization of an uncharacterized protein that is required for the accumulation of H3K27me3 in Paramecium. I am currently investigating its mode of action through a combination of genetics, genomics, cellular and biochemical approaches. This research will provide a better understanding of the mechanisms that act downstream of the deposition of chromatin modifications, whose regulation is crucial for a proper development.

How will you continue to build on this research?

The next steps in my research is to continue using Paramecium as a model organism to unravel the mechanisms involved in the role of histone modifications. I then wish to continue investigating these questions of genome regulation during the next steps of my career by doing a post-doc.

 

Clément Goubert Senior bioinformatician, University of Arizona, USA

Can you tell us a bit about yourself and your research interests?

I am an evolutionary biologist by training. I am a French national and did all my university training, from undergrad to PhD in France. During my PhD with Matthieu Boulesteix and Cristina Vieira, I specialized in population genetics working on the genetic basis of adaptation to temperate environments in the invasive Asian tiger mosquito. My PhD lab specialized in the population genetics of Transposable Elements (TEs), and I developed genetic markers based on the insertion polymorphism of TEs between individuals. At the same time, I progressively familiarized myself with bioinformatics, in order to predict which TE families (group of homologous TE copies) were abundant and polymorphic in my species of interest. This ignited a strong interest in the development of bioinformatic methods, and in particular those dedicated to study TEs. Later during my postdoc with Cédric Feschotte (Cornell University), I studied how TE insertion polymorphisms can affect gene regulatory networks in the human population. Our approach relied on using high-quality TE genotypes, which we correlated with gene expression (TE-expression QTL). I then realized that some efforts could be made to improve genotyping methods, and while continuing to study how TEs shape the evolution genomes, I worked on different projects related to TE annotation and genotyping. At the same time, I am an active member of the TE Hub, a consortium dedicated to ease researcher’s access to bioinformatic methods and training. We regularly organize workshops, our latest being dedicated to create a community-based benchmark for methods related to TE annotation. You can learn more about the TE Hub on our website: tehub.org.

What first interested you in this field of research?

I’ve always been fascinated by evolution. In particular the wide array of evolutionary strategies displayed in nature, at every level of organization: populations, individuals, cells and genes and molecules themselves. TEs are the archetype of the “selfish gene”, these self-replicating sequences can be seen as genomic parasites that need to reach an equilibrium between invading genomes and avoiding complete extinction by killing their hosts before reproduction. They walk a fine line, between evading silencing mechanisms for their own survival, and being domesticated by the host genomes, sometimes becoming “regular genes”. It’s quite fun to explain to someone that half of their DNA is made of these parasites, or that some part of their immune system stems from the capture of such elements. Furthermore, while this field is consistently becoming more popular, our community is rather small, and hasn’t reached the methodological maturity that other fields in genomics may benefit from. I like to take on this challenge, both in my approach to developing new methods but also organizing the community through the TE hub consortium.

Can you briefly explain the research you presented at ICTE 2024?

In 2020 I went to work at the Genome Centre of McGill University in Montréal, Canada, in the lab of Guillaume Bourque, an expert in comparative genomics and pangenomic approaches. There, I worked closely with a talented graduate student (now owner of a PhD!), Cristian Groza, who has an acute knowledge of all the bioinformatic methods related to pangenomes and structural variation. Pangenomics, or the study of many genomes at once, offers new methods that allow the representation and interrogation of genomic diversity, by stepping out of the reign of the “reference genome”, instead using data structures such as graph-genomes. These graph-genomes represent shared segments of the DNA as shared paths, while individual variants including SNPs, indels, insertions, deletion, inversions, etc… are displayed as alternate paths, creating “bubbles” in the graph. TEs, by jumping around genomes, create new copies sometimes found in a genome but not another. These are not really different from any other structural variants through the lense of a graph-genome. In pangenomes, polymorphic TE insertion will create bubbles that we can search and annotate. The research presented at ICTE24 pertains to the use of graph-genomes and other pangenomic tools to detect and genotypes such TE polymorpshims. Our method, called GraffiTE, first searches for structural variants between genomic assemblies or long-read datasets and a given reference genome (the “backbone” of a pangenome). We then filter the discovered variants to retain only TEs, and create a genome-graph, where TE polymorphisms form bubbles. In a final step, we can map reads (long or short) to this TE-graph-genome, and infer the allelic frequencies of each insertion polymorphism with higher accuracy than traditional, reference-based, methods.

How will you continue to build on this research?

We just submitted the revisions of our paper for GraffiTE, so I’m currently crossing all my fingers! I would like to obtain further funding to keep the project alive. The first reason is being able to maintain user support. GraffiTE is developed with non-expert users in mind, which requires providing quick and thorough responses to those requesting assistance. Also, I see GraffiTE as a genomic toolbox, which I hope we can enrich regularly with the latest algorithms available. I would also like to explore other questions that can be answered by TE-graph-genomes, such as mapping RNA-seq or epigenetic data to TE polymorphisms. These tasks are currently done using linear reference genomes, and often exclude or miss events related to TE polymorphisms. Currently, I am working on diverses project using GraffiTE in humans (investigating the link between TE and health), arthropods (looking at the role of TEs in the evolution of endosymbiosis) and bacteria (contribution of bacterial TE to genomic diversity and adaptation).