Immunoglobulin class switch recombination (CSR) plays critical roles in controlling infections and inflammatory tissue injuries. Here, we show that
AFF3
, a candidate gene for both rheumatoid arthritis and type 1 diabetes, is a molecular facilitator of CSR with an isotype preference.
Aff3
-deficient mice exhibit low serum levels of immunoglobulins, predominantly immunoglobulin G2c (IgG2c) followed by IgG1 and IgG3 but not IgM. Furthermore,
Aff3
-deficient mice show weak resistance to
Plasmodium yoelii
infection, confirming that
Aff3
modulates immunity to this pathogen. Mechanistically, the AFF3 protein binds to the IgM and IgG1 switch regions via a C-terminal domain, and
Aff3
deficiency reduces the binding of AID to the switch regions less efficiently. One
AFF3
risk allele for rheumatoid arthritis is associated with high mRNA expression of
AFF3
,
IGHG2
, and
IGHA2
in human B cells. These findings demonstrate that AFF3 directly regulates CSR by facilitating the recruitment of AID to the switch regions.