Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus

Abstract

Three-dimensional genome structure plays an important role in gene regulation. Globally, chromosomes are organized into active and inactive compartments while, at the gene level, looping interactions connect promoters to regulatory elements. Topologically associating domains (TADs), typically several hundred kilobases in size, form an intermediate level of organization. Major questions include how TADs are formed and how they are related to looping interactions between genes and regulatory elements. Here we performed a focused 5C analysis of a 2.8 Mb chromosome 7 region surrounding CFTR in a panel of cell types. We find that the same TAD boundaries are present in all cell types, indicating that TADs represent a universal chromosome architecture. Furthermore, we find that these TAD boundaries are present irrespective of the expression and looping of genes located between them. In contrast, looping interactions between promoters and regulatory elements are cell-type specific and occur mostly within TADs. This is exemplified by the CFTR promoter that in different cell types interacts with distinct sets of distal cell-type-specific regulatory elements that are all located within the same TAD. Finally, we find that long-range associations between loci located in different TADs are also detected, but these display much lower interaction frequencies than looping interactions within TADs. Interestingly, interactions between TADs are also highly cell-type-specific and often involve loci clustered around TAD boundaries. These data point to key roles of invariant TAD boundaries in constraining as well as mediating cell-type-specific long-range interactions and gene regulation.

YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment

“…5D, lower red boxes on both axes, consensus orientation not shown). We hypothesized that a subset of constitutive CTCF sites might form loops that create a preexisting topological framework ,within which critical developmentally dynamic chromatin interactions form (Symmons et al 2014;Tang et al 2015;Smith et al 2016). Constitutive topological frameworks may be critical for proper gene expression because they create insulated neighborhoods around coregulated genes and enhancers that will interact during subsequent differentiation steps (Dowen et al 2014).…”

“…Finally, at the sub-megabase scale within TADs, two classes of highly dynamic architectural features exist: (1) small-scale contact domains termed sub-TADs (Phillips-Cremins et al 2013;Dowen et al 2014;Rao et al 2014), and (2) loops (Rao et al 2014). Looping interactions and sub-TADs often link genes to developmentally regulated enhancers and are markedly reorganized between cellular states (Tolhuis et al 2002;Sanyal et al 2012;Phillips-Cremins et al 2013;Dowen et al 2014;Smith et al 2016). Thus, the emerging model is that mammalian genomes are arranged into a nested hierarchy of unique structural features, of which the finer, sub-megabase scale configurations within TADs are critical for the proper activation and inactivation of genes during development.…”

SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells

“…Chromosomes are positioned in distinct volumes forming the chromosome territories (Cremer et al 2006), which consist of open (A-type) and closed (Btype) genomic compartments (Lieberman-Aiden et al 2009). The genomic compartments are further folded into sub-megabasescaled structures called topologically associating domains (TADs) (Dixon et al 2012;Nora et al 2012Nora et al , 2013, where local looping interactions between promoters and enhancers occur (Sanyal et al 2012;Symmons et al 2014;Tang et al 2015;Smith et al 2016).…”

Controlling gene expression by DNA mechanics: emerging insights and challenges

“…TADs partition chromosomes into blocks of DNA at scales of hundreds of kilobases to megabases of DNA and are frequently bounded at inverted CTCF-binding sites, suggesting that CTCF-mediated loops comprise a major organizing principle for the genome (Cook and Gove 1992;Dekker and Heard 2015;Dekker and Misteli 2015;Dixon et al 2012;Guo et al 2015;Ji et al 2016;Pope et al 2014;Smith et al 2016;Tang et al 2015;Valton and Dekker 2016). CTCF and cohesin are enriched at TAD boundaries (Guo et al 2015;Ji et al 2016;Katainen et al 2015;Rao et al 2015;Sofueva et al 2013;Tang et al 2015;Xiao et al 2011;Zuin et al 2014).…”