CTCF mediates allele-specific 3D domain structure at paternally imprinted gene loci
Daan Noordermeer (I2BC, Gif-sur-Yvette, France)
NOTE THE NEW LOCATION (due to renovation work at LPS)
Imprinted genes are mammalian genes where only one copy (allele) is active, depending on whether it is inherited from the mother or the father. This selective activity is determined by allele-specific DNA methylation at defined sites in the genome, so-called Imprinting Control Regions (ICRs). Recent microscopy studies by the group of Robert Feil (IGM-Montpellier, France) have revealed that imprinted genes are differently organized in the cell nucleus, depending on their parental origin (Kota et al., 2014). We have used high-resolution 4C-seq studies (Circular Chromosome Conformation Capture) to dissect the mechanisms and dynamics of this differential organization at the Dlk1-Dio3 and Igf2-H19 loci.
Recent studies have revealed that mammalian genomes are organized into Topologically Associating Domains (TADs) that demarcate ‘gene regulatory neighborhoods’ (Dixon et al., 2012). These physical domains are formed through a mechanism of ‘loop extrusion’ of the DNA fiber, with borders that are demarcated by opposing binding sites of the architectural CTCF protein (Fudenberg et al., 2016). I will show that the imprinted Dlk1-Dio3 and Igf2-H19 loci are organized into different DNA domains, determined by allele specific CTCF binding.
Both the Dlk1-Dio3 and Igf2-H19 loci are contained within large, invariant Topologically Associating Domains (TADs). The presence of the CTCF protein at the unmethylated ICRs on the maternal allele allows the establishment of new loops within the TADs. This result in the formation of a domain that acts like a cage, thereby shielding regulatory elements from nearby genes.
At the paternal alleles, DNA methylation at the ICR inhibits CTCF binding. As a result, the paternal Igf2-H19 allele displays little specific organization within the TAD. In contrast, at the paternal Dlk1-Dio3 locus, loops are formed between more distant unmethylated CTCF sites. The paternal allele therefore forms a much larger subdomain that is contained within the TAD.
Our work, for the first time, shows that constitutive TADs can have a markedly different allele-specific internal domain organization. Moreover, it shows that methylation-dependent DNA binding of the CTCF protein at ICRs guides the process of loop extrusion, thereby change the 3D structure of chromatin domains. We speculate that the imprinted patterns of gene expression at these loci are mostly imposed by the maternal 3D architecture, supporting previous genetic studies.