Central tolerance plays a critical role in eliminating self-reactive T cells specific for peripheral antigens. Here we show that central tolerance of MHC class I-restricted T cells specific for classic myelin basic protein (MBP), a component of the myelin sheath, is mediated by both bone marrow (BM)-derived and nonBM-derived cells. Unexpectedly, BM-derived cells induce tolerance directly by using classic MBP that they synthesize, whereas nonBM-derived cells mediate tolerance by crosspresenting classic MBP acquired from an exogenous source. Thus, tolerance to tissue-specific antigens can involve multiple cell types and mechanisms in the thymus, which may account for the limited spectrum of autoimmune syndromes observed when expression of tissue-specific antigens is impaired only in thymic epithelial cells.autoimmunity ͉ EAE ͉ multiple sclerosis D efining the mechanisms that maintain tolerance to tissuespecific antigens (TSAs) is critical for understanding the pathogenesis of organ-specific autoimmune diseases such as multiple sclerosis (MS). Tolerance of many TSAs occurs in the thymus and is facilitated by medullary thymic epithelial cells (mTECs) that promiscuously express a broad range of TSAs (1). TSAs synthesized and presented by mTECs can induce tolerance in the MHC class I and II pathways (2, 3). In addition, bone marrow (BM)-derived cells can acquire TSAs from mTECs and induce both CD4 ϩ and CD8 ϩ T cell tolerance (2, 4). However, in vivo studies indicate that, under physiological conditions, only BM-derived cells acquire sufficient TSA from exogenous sources to negatively select MHC class II-restricted T cells (3,5).We investigated the mechanisms that induce central tolerance to myelin basic protein (MBP), which is believed to be targeted by self-reactive T cells in MS. The genetic organization of the MBP locus may influence how tolerance is induced to this self-antigen. The MBP locus encodes two separate protein families that are transcribed by using different promoters, both of which generate multiple isoforms via alternative splicing (6). One family consists of MBP isoforms that are incorporated into myelin (classic MBP) and are considered TSAs because of their restricted expression in myelin-forming cells. Proteins in the other family (golli MBP) modulate calcium influx (7,8) and are expressed in the nervous system, thymus, and peripheral lymphoid tissues (6). Although the two families differ functionally, classic and golli MBP are immunologically related because they contain stretches of identical amino acid sequence because of exon sharing (6). Thus, expression of golli MBP in the thymus could mediate negative selection of many classic MBP-specific T cells.We sought to define tolerance mechanisms for CD4 ϩ and CD8 ϩ MBP-specific T cells because both subsets mediate autoimmunity (5, 9, 10). We previously found that CD4 ϩ MHC class II-restricted T cells specific for MBP121-140, an epitope present in classic but not golli MBP, undergo central tolerance mediated by BM-derived cells that acquire classic ...