Human centromeric chromatin is a dynamic chromosomal domain that can spread over noncentromeric DNA.
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 alpha-satellite DNA, with human artificial chromosomes that contain discontinuous blocks of higher-order alpha-satellite DNA and noncentromeric DNA. The underlying sequence did not correlate with chromatin states, because both higher-order alpha-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.
Department of Genetics and Genomics, Boston University School of Medicine, Boston, MA 02118, USA.
Ai Leen
AL
Lam
Christopher D
CD
Boivin
Caitlin F
CF
Bonney
M Katharine
MK
Rudd
Beth A
BA
Sullivan
D001324:Autoantigens / Q000737:chemistry / Q000378:metabolism; D002460:Cell Line; D002503:Centromere / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D000076247:Centromere Protein A; D002843:Chromatin / Q000737:chemistry* / Q000378:metabolism; D002868:Chromosomal Proteins, Non-Histone / Q000737:chemistry / Q000378:metabolism; D022222:Chromosomes, Artificial, Human / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D002877:Chromosomes, Human / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004276:DNA, Satellite / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D006570:Heterochromatin / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D047468:Immunoprecipitation; D017404:In Situ Hybridization, Fluorescence; D016133:Polymerase Chain Reaction; D014158:Transcription, Genetic
D001324:Autoantigens; C000619700:CENPA protein, human; D000076247:Centromere Protein A; D002843:Chromatin; D002868:Chromosomal Proteins, Non-Histone; D004276:DNA, Satellite; D006570:Heterochromatin; D004247:DNA