Immunoglobulin heavy chain (IgH) locus-associated G-rich long noncoding RNA (SμGLT) is important for physiological and pathological B cell DNA recombination. We demonstrate that the METTL3 enzyme-catalyzed N6-methyladenosine (m6A) RNA modification drives recognition and 3′ end processing of SμGLT by the RNA exosome, promoting class switch recombination (CSR) and suppressing chromosomal translocations. The recognition is driven by interaction of the MPP6 adaptor protein with nuclear m6A reader YTHDC1. MPP6 and YTHDC1 promote CSR by recruiting AID and the RNA exosome to actively transcribe SμGLT. Direct suppression of m6A modification of SμGLT or of m6A reader YTHDC1 reduces CSR. Moreover, METTL3, an essential gene for B cell development in the bone marrow and germinal center, suppresses IgH-associated aberrant DNA breaks and prevents genomic instability. Taken together, we propose coordinated and central roles for MPP6, m6A modification, and m6A reader proteins in controlling long noncoding RNA processing, DNA recombination, and development in B cells. Display omitted •N6-methyladenosine (m6A) guides IgH lncRNA SμGLT 3′ end processing by RNA exosome•M6A RNA modification is important for IgH class switch recombination•M6A RNA modification is important for genomic stability of B cells•YTHDC1 and MPP6 guide m6A recognition of G-rich SμGLT B-lymphocytes generate a vast number of antibodies to neutralize pathogenic insults. Somatic mutations of antibody genes are important for antibody diversity but also cause lymphomagenesis. Here, Nair et al. demonstrate that N6-methyladenosine modification of the SμGLT long noncoding RNA expressed from antibody gene locus drives somatic mutations but suppresses lymphomagenic genomic alterations.