Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

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Abstract
The architecture of human chromosomes within the nucleus is still a mystery. The nuclear lamina is thought to anchor specific DNA elements to help organize the genome within the nucleus. Van Steensel and colleagues report a high-resolution map of the sites of the human genome that contact the nuclear lamina. The map shows that interactions with the lamina occur via large yet sharply demarcated genomic domains. This domain structure is linked to the epigenetic and transcriptional profile of the genome. Many domain borders are marked by specific sequence elements, indicating that the higher-order folding of chromosomes is in part encoded in the genome itself. The architecture of human chromosomes in interphase nuclei is still largely unknown. Microscopy studies have indicated that specific regions of chromosomes are located in close proximity to the nuclear lamina (NL)1,2,3. This has led to the idea that certain genomic elements may be attached to the NL, which may contribute to the spatial organization of chromosomes inside the nucleus. However, sequences in the human genome that interact with the NL in vivo have not been identified. Here we construct a high-resolution map of the interaction sites of the entire genome with NL components in human fibroblasts. This map shows that genome–lamina interactions occur through more than 1,300 sharply defined large domains 0.1–10 megabases in size. These lamina-associated domains (LADs) are typified by low gene-expression levels, indicating that LADs represent a repressive chromatin environment. The borders of LADs are demarcated by the insulator protein CTCF, by promoters that are oriented away from LADs, or by CpG islands, suggesting possible mechanisms of LAD confinement. Taken together, these results demonstrate that the human genome is divided into large, discrete domains that are units of chromosome organization within the nucleus.