Nucleosome positioning in human HOX gene clusters.
The distribution of nucleosomes along the genome is a significant aspect of chromatin structure and is thought to influence gene regulation through modulation of DNA accessibility. However, properties of nucleosome organization remain poorly understood, particularly in mammalian genomes. Toward this goal we used tiled microarrays to identify stable nucleosome positions along the HOX gene clusters in human cell lines. We show that nucleosome positions exhibit sequence properties and long-range organization that are different from those characterized in other organisms. Despite overall variability of internucleosome distances, specific loci contain regular nucleosomal arrays with 195-bp periodicity. Moreover, such arrays tend to occur preferentially toward the 3' ends of genes. Through comparison of different cell lines, we find that active transcription is correlated with increased positioning of nucleosomes, suggesting an unexpected role for transcription in the establishment of well-positioned nucleosomes.
Kharchenko
Peter V
PV
Harvard Partners Center for Genetics and Genomics, Boston, Massachusetts 02115, USA.
Woo
Caroline J
CJ
Tolstorukov
Michael Y
MY
Kingston
Robert E
RE
Park
Peter J
PJ
D002843:Chromatin / Q000378:metabolism; D005801:Genes, Homeobox; D006367:HeLa Cells; D018398:Homeodomain Proteins / Q000235:genetics*; D006801:Humans; D020014:K562 Cells; D009707:Nucleosomes / Q000737:chemistry / Q000378:metabolism*
D002843:Chromatin; D018398:Homeodomain Proteins; D009707:Nucleosomes