Human centromeric chromatin is a dynamic chromosomal domain that can spread over noncentromeric DNA

• DOI: 10.1073/pnas.0507947103
• Publication Date: 2006-03-07T01:34:02Z
• Authors: Ai Leen Lam; Christopher D. Bo...; Caitlin F. Bonney; M. Katharine Rudd; Beth A. Sullivan
• Keywords: 0301 basic medicine; Transcription, Genetic; Chromosomal Proteins, Non-Histone; Centromere; DNA; DNA, Satellite; Autoantigens; Polymerase Chain Reaction; Chromatin; Chromosomes, Artificial, Human; Cell Line; 03 medical and health sciences; Heterochromatin; Chromosomes, Human; Humans; Immunoprecipitation; Centromere Protein A; In Situ Hybridization, Fluorescence

Human centromeres are specialized chromatin domains containing the centromeric histone H3 variant CENP-A. CENP-A nucleosomes are interspersed with nucleosomes containing histone H3 dimethylated at lysine 4, distinguishing centromeric chromatin (CEN chromatin) from flanking heterochromatin that is defined by H3 lysine 9 methylation. To understand the relationship between chromatin organization and the genomic structure of human centromeres, we compared molecular profiles of three endogenous human centromeres, defined by uninterrupted higher-order α-satellite DNA, with human artificial chromosomes that contain discontinuous blocks of higher-order α-satellite DNA and noncentromeric DNA. The underlying sequence did not correlate with chromatin states, because both higher-order α-satellite DNA and noncentromeric DNA were enriched for modifications that define CEN chromatin, euchromatin, and heterochromatin. Human artificial chromosomes were also organized into distinct domains. CENP-A and heterochromatin were assembled over noncentromeric DNA, including the gene blasticidin, into nonoverlapping domains. Blasticidin transcripts were enriched at sites of CENP-A binding but not at H3 methylated at lysine 9, indicating that formation of CEN chromatin within a repetitive DNA environment does not preclude gene expression. Finally, we tested the role of centric heterochromatin as a centromeric boundary by increasing CENP-A dosage to expand the CEN domain. In response, H3 lysine 9 dimethylation, but not trimethylation, was markedly decreased at all centromeres examined. We propose that human centromere regions normally exist in a dynamic state in which a regional boundary, defined by H3 lysine 9 dimethylation, separates CEN chromatin from constitutive heterochromatin.