A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions

ABSTRACT: A variety of self-interacting domains, defined at different levels of resolution, have been described in mammalian genomes. These include Chromatin Compartments (A and B), Topologically Associated Domains (TADs), contact domains, sub-TADs, insulated neighborhoods and frequently interacting regions (FIREs). Whereas many studies have found the organisation of self-interacting domains to be conserved across cell types, some do form in a lineage-specific manner. However, it is not clear to what degree such tissue-specific structures result from processes related to gene activity such as enhancer-promoter interactions or whether they form earlier during lineage commitment and are therefore likely to be prerequisite for promoting gene expression. To examine these models of genome organisation in detail, we used a combination of high-resolution chromosome conformation capture, a newly-developed form of quantitative fluorescence in-situ hybridisation and super-resolution imaging to study a 70 kb self-interacting domain containing the mouse alpha-globin locus. To understand how this self-interacting domain is established, we studied this structure when the genes are inactive and during erythroid differentiation when the genes are progressively switched on. In contrast to many current models of long-range gene regulation, we show that an erythroid-specific, decompacted self-interacting domain, delimited by convergent CTCF/cohesin binding sites, forms prior to the onset of robust gene expression. Using previously established mouse models we also show that formation of the self-interacting domain does not rely on interactions between the alpha-globin genes and their enhancers or on tissue-specific changes in CTCF binding. Rather, formation of the domain simply depends on the presence of activated lineage-specific cis-elements driving a transcription-independent mechanism for opening chromatin throughout the 70 kb region to create a permissive environment for gene expression. These findings are consistent with a model of loop-extrusion in which all segments of chromatin within a region delimited by CTCF boundary elements contact each other. Our findings suggest that activation of tissue-specific element(s) within such a self-interacting region is sufficient to influence all chromatin within such a domain.

ORGANISM(S): Mus musculus

PROVIDER: GSE107675 | GEO | 2021/04/04

REPOSITORIES: GEO