CHARACTERIZATION OF AN ENDONUCLEASE ACTIVITY WHICH PREFERENTIALLY CLEAVES THE G-RICH IMMUNOGLOBULIN SWITCH REPEAT SEQUENCES

B lymphocytes can alter selectively their immunoglobulin (Ig) isotype expression by deletional rearrangement of the first active immunoglobu lin heavy-chain (IgH) constant region (C mu) gene with one of six othe r constant region genes. Recombination breakpoints occur within highly repetitive ''switch'' (S) regions located upstream of each IgH consta nt region gene except C-delta. Analysis of rearranged switch DNA junct ions has not detected a consensus sequence, although the predominance of two pentamer motifs (TGGGG and TGAGC) at or near these breakpoints and throughout all murine S region sequences has led to their advocacy as the S recombination signals. In this paper, we describe the charac terization and partial purification of a lymphoid-specific endonucleas e activity which cleaves preferentially murine S region DNA. Enzyme ac tivity selectively produced single- and double-stranded breaks at TGAG C and TGGG motifs within murine Sp and S alpha DNA. Rare cryptic cleav age sites were detected also within non-switch sequences, although cle avage intensities at these sites were reduced greatly, relative to con sensus S region cleavages. Analogous activity was found in murine tiss ue extracts, although among the tissues assayed only spleen and thymus contained detectable activity. Subsequent biochemical characterizatio n of this activity demonstrated that the responsible enzyme (Endo-SR) represented a previously unreported tissue-specific mammalian endonucl ease. Endo-SR-specific activity could be enhanced by addition of Mg2or Ca2+ and inhibited by addition of Zn2+. Maximal specific activity w as detected at pH 5.5 and sharply declined within +/- 0.5 pH units. In view of this enzyme's sequence- and tissue-specificity, we propose th at Endo-SR is a strong candidate for an endonuclease activity associat ed with the switch recombination process.