CTCF modulates allele-specific sub-TAD organization and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains

David Llères (1) , Benoît Moindrot (2) , Rakesh Pathak (1) , Vincent Piras (2) , Mélody Matelot (2) , Benoît Pignard (1) , Alice Marchand (1) , Mallory Poncelet (2) , Aurélien Perrin (1) , Virgile Tellier (2) , Robert Feil (1) , Daan Noordermeer (2)

1 IGMM - Institut de Génétique Moléculaire de Montpellier
2 I2BC - Institut de Biologie Intégrative de la Cellule

BACKGROUND: Genomic imprinting is essential for mammalian development and provides a unique paradigm to explore intra-cellular differences in chromatin configuration. So far, the detailed allele-specific chromatin organization of imprinted gene domains has mostly been lacking. Here, we explored the chromatin structure of the two conserved imprinted domains controlled by paternal DNA methylation imprints-the Igf2-H19 and Dlk1-Dio3 domains-and assessed the involvement of the insulator protein CTCF in mouse cells. RESULTS: Both imprinted domains are located within overarching topologically associating domains (TADs) that are similar on both parental chromosomes. At each domain, a single differentially methylated region is bound by CTCF on the maternal chromosome only, in addition to multiple instances of bi-allelic CTCF binding. Combinations of allelic 4C-seq and DNA-FISH revealed that bi-allelic CTCF binding alone, on the paternal chromosome, correlates with a first level of sub-TAD structure. On the maternal chromosome, additional CTCF binding at the differentially methylated region adds a further layer of sub-TAD organization, which essentially hijacks the existing paternal-specific sub-TAD organization. Perturbation of maternal-specific CTCF binding site at the Dlk1-Dio3 locus, using genome editing, results in perturbed sub-TAD organization and bi-allelic Dlk1 activation during differentiation. CONCLUSIONS: Maternal allele-specific CTCF binding at the imprinted Igf2-H19 and the Dlk1-Dio3 domains adds an additional layer of sub-TAD organization, on top of an existing three-dimensional configuration and prior to imprinted activation of protein-coding genes. We speculate that this allele-specific sub-TAD organization provides an instructive or permissive context for imprinted gene activation during development.

Mots clés: Igf2; Meg3; TADs; 3D genome organization; CTCF; Development; Dlk1; DNA methylation; Genomic imprinting; Topologically associating domains

Domaines: Sciences du Vivant [q-bio]

David Llères, Benoît Moindrot, Rakesh Pathak, Vincent Piras, Mélody Matelot, et al.. CTCF modulates allele-specific sub-TAD organization and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains. Genome Biology, 2019, 20 (1), pp.272. ⟨10.1186/s13059-019-1896-8⟩. ⟨hal-02413890⟩