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We  identified two lamina associated domain subsets through their differential  nuclear lamina versus nucleolar positioning in different cell lines which showed  distinctive patterns of DNA replication timing and gene expression across all  cell lines. Unexpectedly, active, nuclear speckle-associated genomic regions were  found near typically repressive nuclear compartments, which is attributable to  the close proximity of nuclear speckles and nucleoli in some cell types, and  association of centromeres with nuclear speckles in hESCs. 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