A Lamina-Associated Domain Border Governs Nuclear Lamina Interactions, Transcription, and Recombination of the Tcrb Locus

Abstract

SUMMARY Tcrb locus V(D)J recombination is regulated by positioning at the nuclear periphery. Here, we used DamID to profile Tcrb locus interactions with the nuclear lamina at high resolution. We identified a lamina-associated domain (LAD) border composed of several CTCF-binding elements that segregates active non-LAD from inactive LAD regions of the locus. Deletion of the LAD border causes an enhancer-dependent spread of histone H3 lysine 27 acetylation from the active recombination center into recombination center-proximal LAD chromatin. This is associated with a disruption to nuclear lamina association, increased chromatin looping to the recombination center, and increased transcription and recombination of recombination center-proximal gene segments. Our results show that a LAD and LAD border are critical components of Tcrb locus gene regulation and suggest that LAD borders may generally function to constrain the activity of nearby enhancers.

Lamin C regulates genome organization after mitosis

“…These silent heterochromatin regions, identified operationally as Lamina Associated Domains (LADs), correspond to the 'B' compartment identified via HiC and related chromatin mapping strategies [7][8][9] . Chromatin association with the lamina, and its opposite (dynamic release as active 'non-LAD' or A-compartment chromatin) are particularly important for developmentally-regulated genes needed to create or maintain cell-specific identity 8,[10][11][12] . 'Silent' histone modifications, including H3 lysine 9 methylation (H3K9me2/3) and H3 lysine 27 trimethylation (H3K27me3), are key components of LAD organization 6,[13][14][15][16] .…”

Inefficient V(D)J recombination underlies monogenic T cell receptor β expression

“…To achieve monogenic TCRβ assembly and expression, this RSS-based genetic mechanism might function with epigenetic processes that have been implicated to enforce monoallelic Vβ recombination. For example, it has been proposed that dynamic interactions of Vβ segments with the nuclear lamina lowers Vβ recombination efficiency by repressing Vβ chromatin accessibility and chromosome looping between Dβ–Jβ clusters and upstream Vβ segments ( 14 , 15 ). In this context, poor-quality Vβ RSSs could lower the likelihood that two Vβ rearrangements occur on an allele when V31 and an upstream Vβ segment are both accessible and the upstream Vβ is looped in proximity with Dβ–Jβ segments.…”

Poor Quality Vβ Recombination Signal Sequences Enforce TCRβ Allelic Exclusion by Limiting the Frequency of Vβ Recombination

“…In DN3 cells where RAG is re-expressed between DSB repair and S phase entry, poor Vβ RSSs limit the possibility of further Vβ recombination on the second allele. Additional factors, including inhibition of RC formation, Vβ accessibility, and locus contraction via stochastic interaction of alleles with nuclear lamina (Chan et al, 2013;Chen et al, 2018;Schlimgen et al, 2008), cooperate with poor Vβ RSSs to limit biallelic assembly as DN3 cells attempt Tcrb recombination. Finally, TCRβ signals promote genetic and epigenetic changes that silence Vβ recombination in DP cells where Tcra genes assemble (Jackson and Krangel, 2005;Liang et al, 2002;Majumder et al, 2015;Skok et al, 2007).…”

“…In the lymphocyte lineage and developmental stage that Tcrb, Igh, or Igk loci recombine, their individual alleles frequently reside in different nuclear locations with V(D)J-rearranged alleles underrepresented at transcriptionally repressive nuclear structures (Chan et al, 2013;Hewitt et al, 2009;Schlimgen et al, 2008;Skok et al, 2007). The positioning of an allele at these structures by deterministic or stochastic means could block V rearrangements by suppressing accessibility, RAG binding, and/or locus compaction (Chan et al, 2013;Chen et al, 2018;Hewitt et al, 2009;Schlimgen et al, 2008;Skok et al, 2007). Sequence features conserved among Vβ and V H RSSs, but not present in Dβ, J H , Vα, or Vκ RSSs, have been proposed to render Vβ and V H recombination inefficient, thereby stochastically lowering the likelihood of nearsimultaneous V rearrangements on both alleles (Liang et al, 2002).…”