Induction of a chromatin boundary in vivo upon insertion of a TAD border

Abstract

Mammalian genomes are partitioned into sub-megabase to megabase-sized units of preferential interactions called topologically associating domains or TADs, which are likely important for the proper implementation of gene regulatory processes. These domains provide structural scaffolds for distant cis regulatory elements to interact with their target genes within the three-dimensional nuclear space and architectural proteins such as CTCF as well as the cohesin complex participate in the formation of the boundaries between them. However, the importance of the genomic context in providing a given DNA sequence the capacity to act as a boundary element remains to be fully investigated. To address this question, we randomly relocated a topological boundary functionally associated with the mouse HoxD gene cluster and show that it can indeed act similarly outside its initial genomic context. In particular, the relocated DNA segment recruited the required architectural proteins and induced a significant depletion of contacts between genomic regions located across the integration site. The host chromatin landscape was re-organized, with the splitting of the TAD wherein the boundary had integrated. These results provide evidence that topological boundaries can function independently of their site of origin, under physiological conditions during mouse development.

3D chromatin remodeling potentiates transcriptional programs driving cell invasion

“…CCCTC-binding factor (CTCF) is a multifunctional epigenetic regulatory protein critical for the establishment and maintenance of TAD boundaries 18 . The loss of CTCF binding is known to cause the loss of insulation of TAD/subTAD boundaries, resulting in chromatin domain shift or fusion.…”

“…Considering the central role of CTCF in maintenance of genomic TADs ( 12 ), it is not surprising that CTCF knockout (KO) leads to lethality at very early stages of embryonic development ( 13 ). Although not lethal, the loss of heterozygosity at the CTCF locus is also detrimental to cellular homeostasis ( 14 ), and CTCF appears to act as an haploinsufficent tumor suppressor gene ( 15 , 16 ), with its loss impacting hematopoietic tumor initiation in CTCF hemizygous mice ( 15 ).…”

Structural Variation at a Disease Mutation Hotspot: Strategies to Investigate Gene Regulation and the 3D Genome

“…Such a disease mechanism is relatively understudied, however a recent investigation by Willemin and others (2021) has provided valuable insights. After generating a transgenic mouse line whereby a TAD boundary element usually located on chromosome two was inserted into a large TAD on chromosome 10, the authors observed splitting of the host TAD into two smaller regulatory domains which was associated with tissue specific changes in local gene expression (Willemin et al, 2021).…”

CTCF shapes chromatin structure and gene expression in health and disease

“…Recent data show that both boundary‐encoded, and locus intrinsic features shape the capacity of CBS to sustain insulator functions (Fig 2). When inserted into an unrelated genomic locus, both an artificial construct containing three CBS and a TAD boundary separating the HoxD locus into two domains retain their insulator functions at the ectopic site (Redolfi et al , 2019; Willemin et al , 2021). In contrast, the CTCF‐enriched TAD boundary intersecting the long‐noncoding RNA locus Firre , exerts no overt effect on chromatin structure at an ectopic locus (Barutcu et al , 2018).…”