METTL3-mediated m6A modification controls Tcra recombination center formation and thymic T cell development

N6-methyladenosine (m6A) is the most prevalent internal modification of RNA, and METTL3 functions as the catalytic core of the methyltransferase complex. While m6A regulates T cell activation and differentiation, whether this RNA modification participates in antigen receptor V(D)J recombination remains unknown. Using conditional Mettl3 knockout mice and multi-omic profiling, we examined m6A function in thymocyte development and Tcra rearrangement. Mettl3 deficiency reduced thymic cellularity by about 20-30%, substantially decreased double-positive (DP) thymocytes, diminished peripheral CD8+ T cells, and selectively impaired Tcra but not Tcrb rearrangement. Mechanistically, m6A specifically decorated TEA germline transcripts and maintained recombination center architecture. METTL3 loss abolished m6A enrichment at TEA, diminished Eα-TEA chromatin looping, and reduced germline transcription. Concurrently, rearranged Tcra translation efficiency fell to about 40% of wild-type levels, significantly reducing TCR-CD3 surface expression on DP, CD4 SP, and CD8 SP cells. Mettl3 knockout further upregulated DNA repair genes such as Lig4, Fignl1, and Rad51ap1, activated the interferon pathway, and increased γH2A.X DNA double-strand break markers and double-stranded RNA accumulation in DP thymocytes. Collectively, these results establish RNA m6A modification as a previously unrecognized regulatory layer of V(D)J recombination that controls recombination center formation and preserves genomic integrity during Tcra gene rearrangement.