The centromere-kinetochore complex can be divided into distinct domains bas
ed on structure and function. Previous work has used CREST auto-antibodies
with various microscopic techniques to map the locations of proteins within
the centromere-kinetochore complex and to analyze the maturation of prekin
etochores before mitosis, Here we have focused on the centromere-specific h
istone Centromere Protein (CENP)-A and its spatial relationship to other hi
stones and histone modifications found in condensed chromatin. We demonstra
te that the phosphorylation of histone H3 is essentially excluded from a sp
ecific region of centromeric chromatin, defined by the presence of CENP-A,
Interspersion of CENP-B with phosphorylated H3 in the inner centromere indi
cates that the exclusion of H3 modification is not a general property of cc
-satellite DNA, We also demonstrate that these regions are functionally dis
tinct by fragmenting mitotic chromatin into motile centromere-kinetochore f
ragments that contain CENP-A with little or no phosphorylated H3 and nonmot
ile fragments that contain exclusively phosphorylated H3, The sequence of C
ENP-A diverges from H3 in a number of key residues involved in chromosome c
ondensation and in transcription, potentially allowing a more specialized c
hromatin structure within centromeric heterochromatin, on which kinetochore
plates may nucleate and mature. This specialized centromere subdomain woul
d be predicted to have a very tight and static nucleosome structure as a re
sult of the absence of H3 phosphorylation and acetylation.