team

Chromatin and Genome Silencing

Team manager: Di Stefano Luisa & Mattout Anna

Presentation

Precise regulation of gene expression is critical for life. Indeed, in certain conditions, some genes need to be expressed into functional molecules such as proteins, and in other conditions, those or other genes need to be silenced to guarantee the proper functions of cells and organisms during development and in response to the environment. Misregulation of gene expression can lead to developmental defects and diseases.

In addition to genes, a considerable portion of many eukaryotic genomes is made of repetitive elements, derived from the Transposable Elements. Transposable Elements (TE) are mobile genetic elements that have or once had the ability to move within the genome threatening genome stability. Therefore, limiting TE expression is crucial for genome integrity.

Regulation of gene and TE expression relies on three main levels, the transcriptional (DNA>RNA), post-transcriptional level (RNA regulation), and translational (protein level regulation).

In the lab, we are interested in the epigenetics mechanisms underlying genome silencing at the transcriptional and post-transcriptional levels and the consequences of disrupting them at a multiscale level (chromatin organization, subcellular transcript production and localization, immune response, soma-germline communication, organogenesis, developmental rate, fertility).

Our favorite model organisms are Drosophila and C. elegans, but we also work on mammalian cells including human and primary murine cells when necessary. Our main approaches are a combination of microscopy, biochemical, molecular biology, genetics and genomics analysis.

Project 1

Transposable Elements silencing

Finely tuned gene transcription requires a dynamic regulation of chromatin structure, and the precise role of histone marks in this process is a subject of intense study. In particular, little is known about the role of chromatin factors in Transposable Element (TE) regulation. TEs are major components of the genome, constituting approximately 20% of the Drosophila genome and up to 50% in humans. TEs are genetic elements that threaten genomic stability through their capability to move throughout the genome. Strict regulation of TE expression appears essential for normal development but also for the normal physiology of somatic adult tissues, and their aberrant regulation is linked to infertility, cancer and neurodegenerative diseases. Understanding how transposable elements are regulated within the genome is thus a fundamental question in biology. Although it is known that the heterochromatin machinery is implicated in TE silencing, the mechanistic aspects of this regulation have not been fully established.

Our research focuses on the chromatin mediated mechanisms implicated in the control of gene and transposable element transcription through the study of chromatin modulation by the highly conserved histone demethylase, LSD1 and its co-factors. By combining genomic and proteomic approaches with genetic analysis and genome editing in the model organism Drosophila melanogaster we aim to:

1) Dissect the mechanisms by which dLsd1 and its cofactors act to transcriptionally regulate TEs

2) Determine where/when this regulation occurs and how it impacts genome stability and normal development

3) Identify novel chromatin factors involved in TE silencing

Project 2

Heterochromatin and Polycomb-marked gene Silencing by RNA decay

We have recently discovered that the highly conserved LSM2-8 complex mediates a mechanism of RNA degradation that selectively targets H3K27me3-marked genes in C. elegans, revealing that in animals heterochromatin, the compact compartment of the genome can be silenced by specific degradation of heterochromatic transcripts, and not only by transcriptional repression. Therefore, we are interested to focus our research on post-transcriptional mechanism(s) involved in heterochromatin silencing in general in higher eukaryotes. We expect that this research will deepen our understanding of regulation of gene expression in normal animal development and in response to the environment by integrating this novel RNA silencing regulation. In a longer perspective, our goal is to better understand the crosstalk between RNA and chromatin implicated in gene regulation, the initial targeting of the Polycomb H3K27me3 mark to the genome in C. elegans and mammals and ultimately to inflect abnormal gene expression in pathological contexts.

All our cells have the same genome, with the same genes, but different combinations of genes are expressed or repressed/silenced to create different cell types and to adapt to the environment. The expressed genes (DNA) are transcribed into RNA molecules and, in most cases, translated into proteins. The regulation of the expression of genes into RNA and proteins is essential for life.
The formation of heterochromatin, which is the condensed compartment of the genome, often accumulates as cells differentiate, and correlates with silencing of the expression of genes found in it. A chemical mark called “H3K27me3” or the “Polycomb mark” is found on some of the heterochromatin regions and this mark plays a major role in decisions about cell differentiation and maintenance of cellular identity. Misregulation of H3K27me3 levels contributes to many types of cancer (leukemia, lymphoma and others), as well as to genetic diseases.

Until our recent findings, silencing of genes associated with H3K27me3 had been explained exclusively by transcriptional repression which implies that those genes/DNA sequences are not transcribed into RNA. However, many H3K27me3-marked genes are actually transcribed and we have discovered that there is another type of regulation at the post-transcriptional level that specifically degrades RNA arising from those genes, enriched in H3K27me3. The RNA binding complex “LSM2-8” and the exoribonuclease “XRN-2” are involved in this process.

Therefore, we will investigate this novel mechanism of heterochromatic RNA degradation via the LSM2-8 complex and aim to understand the detailed mechanism of the LSM2-8 mediated silencing mechanism, the contribution of the transcriptional versus post-transcriptional repression; the feedback mechanism on the epigenetic state; and the conservation of this mechanism and level of regulation in mammals.

Currently, we aim particularly to:

1) Characterize LSM-8 and the LSM2-8 mediated silencing mechanism

2) Study the implication of this pathway in C. elegans development, fertility and innate immunity

3) Determine the conservation and the role of the LSM2-8 complex in murine Embryonic stem (ES) cells and CD4+ T cells differentiation

Altogether, this will allow a better understanding of this post-transcriptional regulation and its contribution to human health. In a longer term, this could be crucial for the development of innovative therapeutic targeting.

If you are interested to discuss Science or to join the team, please do not hesitate to contact us directly!