A functional overlap between actively transcribed genes and insulator elements [RNA-seq]

Mammalian genomes are subdivided into large (50-2000 kb) regions of chromatin referred to as Topologically Associating Domains (TADs or sub-TADs). Chromatin within an individual TAD contacts itself more frequently than with regions in surrounding TADs thereby directing enhancer-promoter interactions. In many cases, the borders of TADs are defined by convergently orientated boundary elements associated with CCCTC-binding factor (CTCF), which stabilises the cohesin complex on chromatin and prevents its translocation. This delimits chromatin loop extrusion which is thought to underlie the formation of TADs. However, not all CTCF-bound sites act as boundaries and, importantly, not all TADs are flanked by convergent CTCF sites. Here, we examined the CTCF binding sites within a ~70 kb sub-TAD containing the duplicated mouse a-like globin genes and their five enhancers (5'-R1-R2-R3-Rm-R4-a1-a2-3'). The 5' border of this sub-TAD is defined by a pair of CTCF sites. Surprisingly, we show that deletion of the CTCF binding sites within and downstream of the a-globin locus leaves the sub-TAD largely intact. The predominant 3' border of the sub-TAD is defined by a steep reduction in contacts: this corresponds to the transcribed a2-globin gene rather than the CTCF sites at the 3'-end of the sub-TAD. Insertion of actively transcribed fragments of the a-globin gene between the enhancers and native genes leads to a reduction in native a-globin expression and accumilation of cohesin at the insertion site. Together, these observations provide direct evidence that actively transcribed genes can behave as insulator elements. Overall design: Fragments of the alpha globin gene were introduced in a region between the super enhancer and the native alpha globin genes in mESCs with a Hba-a1:mVenus fusion. These mESCs also carried a large deletion spanning the locus alpha globin on the other allele, hence these cells are hemizygous. CD71+ erythroid cells were generated from edited mESC using an in vitro embryoid body differentiation protocol. To determine the transcriptional output from the inserts, PolyA(+) and PolyA(-) RNA was collected from CD71+ and prepared for sequencing.