During the developmental progression of lymphoid progenitors, antigen receptor loci are assembled from variable (V), diversity (D), and joining (J) gene segments. In precursor B cells, the immunoglobulin heavy chain (Igh) locus undergoes ordered gene segment rearrangement with DHJH joining preceding VH to DHJH rearrangement. Similarly, in progenitor T lineage cells, the T cell receptor β chain is assembled from V, D, and J elements, whereas the TCRα chain is generated from the joining of V and J elements. The ordered rearrangement of the Igh locus is controlled by an insulator element, characterized by two CTCF binding sites, named the intergenic control region 1 (IGCR1), located between the VH and DHJH region. The IGCR1 helps to equalize antibody repertoires by suppressing transcription of proximal VH regions and their recombination with DH elements that have not yet joined with JH regions. Likewise, the Vκ regions are segregated from the Jκ regions by regulatory elements, named Cer and Sis, which antagonize transcription across the proximal Vκ regions and suppress proximal VκJκ recombination.
In this issue, Majumder et al. provide new mechanistic insights into how regulatory elements help mediate appropriate long-range rearrangements between V elements and DJ regions involving the TCRβ locus. The authors dissect a genomic region separating the TCR Vβ from the DβJβ elements. They identify two elements within the insulator: a distally located high affinity CTCF biding site and a more proximal region characterized by relatively weak CTCF binding. They found that the most distally located CTCF-containing element functions as an anchor to promote looping of distal Vβ regions to the DβJβ region, essentially promoting locus contraction. The second element, located most proximally to the DβJβ region, acts as a barrier to prevent the spreading of active chromatin associated with the DβJβ region into the CTCF anchor. However, removal of the proximal element interferes with the ability of the distal element to promote locus contraction. Thus, these findings point to a separation of function for binding sites associated with insulator elements: anchors that promote long-range contraction must be protected from transcriptionally active chromatin by boundary elements.
The data presented by Majumder et al. indicate that the presence of a bifunctional insulator-anchoring element ensures an equal playing field for the Vβ repertoire. Such bifunctional elements are not restricted to the TCRβ locus. The IGCR1 element separating the VH cluster from the DHJH region and the Cer and Sis elements located in the Igκ locus may perform similar functions. Thus, a common mechanism is now emerging that underpins the generation of diverse antigen receptor repertoires for both B- and T lineage cells. Now, it will be important to unravel the mechanistic underpinnings of the bifunctional insulator-anchoring elements. For instance, how does the distally located anchor promote long-range contraction, and how does the proximally positioned boundary protect the anchor from active chromatin spreading in the DJ region? Further molecular analyses should reveal the mechanisms by which pairs of insulator-anchoring elements operate. It will be particularly interesting to examine whether and how trajectories adopted by the V and DJ regions across antigen receptor loci are controlled by the insulator-anchoring elements and how alterations in the paths taken by the chromatin fibers affect genomic encounters. Finally, the regulation of long-range genomic interactions—as described by this group and others—is not likely to be restricted to antigen receptor loci only. Rather, these studies will very likely serve as a paradigm for locus region encounters involving regulatory elements across genomes of both animal and plant kingdoms.