TY - JOUR
T1 - Locus folding mechanisms determine modes of antigen receptor gene assembly
AU - Allyn, Brittney M.
AU - Hayer, Katharina E.
AU - Oyeniran, Clement
AU - Nganga, Vincent
AU - Lee, Kyutae
AU - Mishra, Bikash
AU - Sacan, Ahmet
AU - Oltz, Eugene M.
AU - Bassing, Craig H.
N1 - Publisher Copyright:
© 2024 Allyn et al.
PY - 2024/2/5
Y1 - 2024/2/5
N2 - The dynamic folding of genomes regulates numerous biological processes, including antigen receptor (AgR) gene assembly. We show that, unlike other AgR loci, homotypic chromatin interactions and bidirectional chromosome looping both contribute to structuring Tcrb for efficient long-range V(D)J recombination. Inactivation of the CTCF binding element (CBE) or promoter at the most 5'Vβ segment (Trbv1) impaired loop extrusion originating locally and extending to DβJβ CBEs at the opposite end of Tcrb. Promoter or CBE mutation nearly eliminated Trbv1 contacts and decreased RAG endonuclease-mediated Trbv1 recombination. Importantly, Trbv1 rearrangement can proceed independent of substrate orientation, ruling out scanning by DβJβ-bound RAG as the sole mechanism of Vβ recombination, distinguishing it from Igh. Our data indicate that CBE-dependent generation of loops cooperates with promoter-mediated activation of chromatin to juxtapose Vβ and DβJβ segments for recombination through diffusion-based synapsis. Thus, the mechanisms that fold a genomic region can influence molecular processes occurring in that space, which may include recombination, repair, and transcriptional programming.
AB - The dynamic folding of genomes regulates numerous biological processes, including antigen receptor (AgR) gene assembly. We show that, unlike other AgR loci, homotypic chromatin interactions and bidirectional chromosome looping both contribute to structuring Tcrb for efficient long-range V(D)J recombination. Inactivation of the CTCF binding element (CBE) or promoter at the most 5'Vβ segment (Trbv1) impaired loop extrusion originating locally and extending to DβJβ CBEs at the opposite end of Tcrb. Promoter or CBE mutation nearly eliminated Trbv1 contacts and decreased RAG endonuclease-mediated Trbv1 recombination. Importantly, Trbv1 rearrangement can proceed independent of substrate orientation, ruling out scanning by DβJβ-bound RAG as the sole mechanism of Vβ recombination, distinguishing it from Igh. Our data indicate that CBE-dependent generation of loops cooperates with promoter-mediated activation of chromatin to juxtapose Vβ and DβJβ segments for recombination through diffusion-based synapsis. Thus, the mechanisms that fold a genomic region can influence molecular processes occurring in that space, which may include recombination, repair, and transcriptional programming.
UR - http://www.scopus.com/inward/record.url?scp=85182024482&partnerID=8YFLogxK
U2 - 10.1084/jem.20230985
DO - 10.1084/jem.20230985
M3 - Article
C2 - 38189780
AN - SCOPUS:85182024482
SN - 0022-1007
VL - 221
JO - The Journal of experimental medicine
JF - The Journal of experimental medicine
IS - 2
ER -