Dissecting the functional relationship between DNA methylation and ATP dependent chromatin remodeler SMARCAD1

• Applicant: Jacqueline Mermoud, Ph.D.
• Subject Area: General Genetics and Functional Genome Biology
• Term: since 2021
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 464516164

In multicellular organisms the organisation of the genome into eu-and heterochromatin domains plays a crucial role in restricting lineage inappropriate gene expression and the activity of mobile elements, which comprise around 50% of the mammalian genome. Histone and DNA methylation underpin the stability of heterochromatin domains. How these modifications are maintained through cell division to ensure the faithful propagation of functional heterochromatin states is poorly understood. Yet failure to do so results in abnormal transcriptional programs and chromosomal instability. Identification and characterisation of the players and molecular events that drive the establishment and heritability of heterochromatin is therefore the aim of this proposal.Our focus in on an ATP dependent chromatin remodeling activity called SMARCAD1. We have previously shown that SMARCAD1 is required for the maintenance of histone modifications through replication and the repression of retrotransposons. Our preliminary data now implicates this remodeler in DNA methylation maintenance. SMARCAD1 deletion in mouse embryonic stem cells leads to reduced DNA methylation. A proteomic analysis identifies DNA methylation proteins as novel interactors of SMARCAD1, in particular NP95, an essential co-factor of DNA methyltransferase 1. We want to test the hypothesis that SMARCAD1, in concert with NP95, reinforces epigenetic instructions to ensure that silenced loci are correctly perpetuated in each replication cycle. To this end we will characterize the interaction of SMARCAD1 and NP95 in vitro and investigate its significance in vivo. One aim is to define the hierachy of SMARCAD1 interactions with the DNA methylation machinery at replication sites. We will also profile the DNA methylation targets of SMARCAD1 in mouse embryonic stem cells. Moreover, we will examine the mechanisms by which SMARCAD1 shapes the methylome and the functional consequences on the transcriptome. We will investigate how the separate catalytic and non-catalytic functions of SMARCAD1 govern DNA methylation. This program of research will provide insights into how DNA maintenance methylation is controlled and coordinated with chromatin replication, crucial for normal differentiation and development and our understanding of what triggers DNA methylation dysregulation associated with numerous pathologies.

• DFG Programme: Research Grants