Genomic Imprinting : From regulation to Function

Regulation of Imprinting Loci in Neural Lineages (Contacts: F. Court, P. Arnaud)

Genomic imprinting restricts the expression of nearly 150 mammalian genes to a single parental allele. These genes play key roles in growth control and brain function. At the molecular level, they are organized into about twenty genomic domains, each regulated by an imprinting control region (ICR) and the coordinated action of multiple regulatory layers. However, the mechanisms that orchestrate this multi-scale regulation and enable the ICR to remotely control the monoallelic expression of genes during cellular identity acquisition remain poorly understood. Our goal is to identify these mechanisms and the key players involved in neural identity acquisition.

To achieve this, we need to simultaneously assess the dynamics of multiple regulatory levels during cellular identity acquisition. To this end, we have developed an integrated approach that combines multi-scale experimental studies with functional analyses using 2D and 3D (organoids)  in vitro corticogenesis systems that recapitulate imprinting patterns observed in the early (Bouschet et al., Cereb Cortex, 2017) and postnatal brain, respectively. This animal-reduced system relies on the controlled differentiation of reciprocal hybrid murine embryonic stem (ES) cells, enabling the dynamic and allelic study of molecular signatures.

Our strategy integrates comprehensive molecular (DNA methylation, gene expression, histone modifications, and regulatory factors), 3D chromatin conformation, and bioinformatics analyses. This has allowed us to generate a high-resolution map providing an integrative, allelic, and dynamic view of both the linear molecular signatures and 3D chromatin organization associated with ICR regions during murine neural lineage formation. This framework uniquely enables us to dissect the regulatory mechanisms of multiple imprinting loci, which we are functionally testing using CRISPR-based approaches.

Function of Imprinting Loci: The H13/Mcts2 Locus (Contacts: B. Montibus,P. Arnaud)

Disruptions in the transcriptional regulation of genomic imprinting, including alterations in allele-specific isoform production, can lead to imprinting disorders (IDs)—a group of rare congenital conditions affecting growth and neurodevelopment. Identifying the genetic causes and pathophysiological mechanisms underlying IDs remains a major challenge.

A striking example is Mulchandani–Bhoj–Conlin syndrome (MBCS), a disorder characterized by fetal and postnatal growth restriction, short stature, failure to thrive, and developmental delay. Evidence suggests that dysregulated expression of the imprinted HM13/Mcts2 locus contributes to MBCS. To test this hypothesis, our project aims to elucidate the regulatory mechanisms and functional roles of the H13/Mcts2 locus to assess its impact on MBCS pathogenesis.

To achieve this, we employ a combination of phenotypic analyses and molecular studies at both the transcriptional and translational levels in mouse models and cell lines. Our approach integrates descriptive and functional studies to uncover the roles of allele-specific and isoform expression during development and the consequences of their deregulation in disease.

Glioma: study of chimeric transcripts from LINE L1 elements  

(Contacts: C. Vaurs-Barriére; P Arnaud)

This project was initiated to identify the mechanisms that coordinate different levels of epigenetic regulation by investigating the causes and consequences of their alteration in malignant glioma, one of the most common types of brain tumors. Collaborations with clinical teams allow us to carry out this study on samples from the Auvergne Glioma Tumorotheque and glioblastoma initiating cell lines (GIC). An exhaustive molecular study allowed us to reveal that the majority of transcriptional defects in gliomas are not related to DNA methylation defects but rather due to an alteration in the control of H3K27me3 (here). The search for the causes of this alteration leads us to study in more detail the (de)regulation of HOX genes, for which we have established that the alteration is a signature of the most aggressive gliomas.

To identify new candidates we have undertaken, in a parallel approach, to explore the link between deregulation of transposable elements and alteration of H3K27me3 in cancer cells. Our original hypothesis is that antisense transcription from L1 repeats can induce aberrant expression of adjacent genes, in the form of so-called LINE-1 chimeric transcripts (LCTs), which in turn influence the dynamics of the H3K27me3 mark. We have previously developed the CLIFinder bioinformatics tool to identify these chimeric transcripts from RNA seq data (here). With this tool, we have, for the first time, established the panorama of LCTs in aggressive gliomas and undertaken to characterise the altered genes in CIGs.