Class switch recombination (CSR) allows B cells to make effective protective antibodies. CSR involves the replacement of the constant region with one of the downstream constant regions by recombination between the donor and recipient switch (S) regions. Although histone H3 hyperacetylation in recipient S regions was recently reported to coincide with CSR, the relative histone H3 and H4 acetylation status of the donor and recipient S regions and the relationship between the generation of mutations and histone hyperacetylation in S regions have not been addressed. Here we report that histone H3 and H4 were constitutively hyperacetylated in the donor S region before and after different mitogen and cytokine treatments. We observed an increased frequency of mutations in hyperacetylated S␥ DNA segments immunoprecipitated with anti-acetyl histone antibodies. Furthermore, time course experiments revealed that the pattern of association of RNA polymerase II with S regions was much like that of H3 hyperacetylation but not always like that of H4 hyperacetylation. Collectively, our data suggest that H3 and H4 histone hyperacetylation in different S regions is regulated differently, that RNA polymerase II distribution and H3 hyperacetylation reflect the transcriptional activity of a given S region, and that transcription, hyperacetylation, and mutation are not sufficient to guarantee CSR. These findings support the notion that there are additional modifications and͞or factors involved in the complex process of CSR.H igh-affinity IgG, IgA, and IgE antibodies protect higher organisms from infection by pathogenic organisms and other environmental threats. The generation of effective protective antibodies requires B cells to carry out somatic hypermutation (SHM) and class switch recombination (CSR), two related but quite different DNA transactions (1). SHM introduces many point mutations in the variable (V) regions of the Ig heavy and light chain genes that encode the antigen-binding site of the antibody molecule (2). In contrast to SHM, CSR is a region-specific recombinationdeletion process that requires the generation of double-stranded DNA breaks (DSB) (3). These DSB are generated in the donor switch (S) region that is just upstream of the constant (C) region gene and in a downstream recipient ␥, , or ␣ S region (4, 5). Recombination then brings one of those downstream C regions into proximity to the V region. This allows the mutated heavy chain V region to be expressed with one of the C regions so that each antigen-binding site will be able to mediate different effector functions and be distributed throughout the body.Despite the different outcomes of SHM and CSR, activationinduced cytidine deaminase (AID) is required for both processes (6) presumably because of its ability to deaminate deoxycytidine to deoxyuridine on single-stranded DNA (ssDNA) (7-11). Both SHM and CSR require transcription (12), suggesting that the ssDNA substrate for AID is created by the generation of transcription bubbles (7) and͞or perhaps triplex RNA...