We report that human telomeres have an unusual chromatin structure characterized by diffuse micrococcal nuclease patterns. The altered chromatin manifested itself only in human telomeres that are relatively short (2 to 7 kb). In contrast, human and mouse telomeres with telomeric repeat arrays of 14 to 150 kb displayed a more canonical chromatin structure with extensive arrays of tightly packed nucleosomes. All telomeric nucleosomes showed a shorter repeat size than bulk nucleosomes, and telomeric mononucleosomal particles were found to be hypersensitive to micrococcal nuclease. However, telomeric nucleosomes were similar to bulk nucleosomes in the rate at which they sedimented through sucrose gradients. We speculate that mammalian telomeres have a bipartite structure with unusual chromatin near the telomere terminus and a more canonical nucleosomal organization in the proximal part of the telomere.Most eukaryotic telomeres are specialized nucleoprotein complexes with at least two functions (7,67 unstable (40, 47, 55). In part, the instability of broken ends is due to DNA damage control factors that monitor and repair lesions in the genome (55). Natural chromosome ends apparently go undetected by this system, most likely because they are effectively concealed by the telomeric nucleoprotein complex. Telomeres may have additional roles in mitotic and meiotic chromosomes, but these functions are still poorly defined.While the telomeric nucleotide sequences are known in representatives of most eukaryotic phyla, telomeric proteins have been identified in only a few species. The telomeres of Saccharomyces cerevisiae contain the double-stranded DNAbinding protein RAP1 (2,10,15,34,38). A different telomeric factor is found in several hypotrichous ciliates, whose telomere termini are encapsulated by a protein that recognizes the telomeric 3' overhang (26, 27, 50; for a review, see reference 51). Although recent experiments suggest a similar telomere terminus binding activity in Xenopus eggs (12), it remains to be determined whether telomeric proteins are evolutionarily conserved.Compelling evidence for stably bound telomeric proteins comes from the inspection of the overall chromatin structure of chromosome ends. In Tetrahymena thermophila macronuclear chromosomes, the terminal 400 bp are packaged in a large complex that does not resemble the nucleosomal chromatin (8,11 nuclease-resistant chromatin domain covering the 250-to 400-bp telomeric repeat region (66).The idea that interactions at the telomere profoundly alter the chromatin structure of chromosome ends is consistent with the influence of telomeres on neighboring genetic elements (for a review, see reference 56). In S. cerevisiae, subtelomeric genes and replication start sites are down-modulated apparently by long range effects of the telomeric nucleoprotein complex (22,25,36). Possibly, telomeric silencing involves spreading of an altered chromatin state into subtelomeric domains (24, 53).The nucleoprotein complex of vertebrate telomeres is still poorly defined....