Body maps on the human genome
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RESEARCH
Open Access
Body maps on the human genome Christopher Cherniak* and Raul Rodriguez-Esteban
Abstract Background: Chromosomes have territories, or preferred locales, in the cell nucleus. When these sites are taken into account, some large-scale structure of the human genome emerges. Results: The synoptic picture is that genes highly expressed in particular topologically compact tissues are not randomly distributed on the genome. Rather, such tissue-specific genes tend to map somatotopically onto the complete chromosome set. They seem to form a “genome homunculus”: a multi-dimensional, genome-wide body representation extending across chromosome territories of the entire spermcell nucleus. The antero-posterior axis of the body significantly corresponds to the head-tail axis of the nucleus, and the dorso-ventral body axis to the central-peripheral nucleus axis. Conclusions: This large-scale genomic structure includes thousands of genes. One rationale for a homuncular genome structure would be to minimize connection costs in genetic networks. Somatotopic maps in cerebral cortex have been reported for over a century. Keywords: Somatotopic map, Homunculus, Tissue-specific gene, Chromosome territory, Connection optimization
Background The human genome may show “little evidence of organization” [1] and be in “an alarming state of disarray” [2], but it seems to have a global landscape, with largescale patterns encompassing all chromosomes together. One key to revealing this structure is chromosome territories, that is, their sites in the cell nucleus. Tissuespecific genes of the adult human body then appear to map somatotopically onto the genome, in multiple dimensions. The holistic arrangement of tissue gene-positions in the complete chromosome set significantly mirrors the antero-posterior, and dorso-ventral, configuration of the tissue-locations in the body. Unlike hox complexes [3] or collinearity phenomena [4], this anatomical mapping includes thousands of genes in the entire chromosome set of the genome. Such a multi-chromosomal bodymap may help as a navigation guide in uncovering genes involved in pathologies of corresponding tissues. There appears to be little prior study of this extensive structure. Danchin et al. [5] discussed such a mapping idea for the prokaryotic chromosome. Caron et al. [6] described clustering on individual human chromosomes of highly expressed genes into regions of increased gene * Correspondence: [email protected] Committee for Philosophy and the Sciences, Department of Philosophy, University of Maryland, College Park, MD 20742, USA
expression. In a survey of gene expression in human tissues, Shyamsundar et al. [7] reported clustering according to anatomic locations or types of tissues (e.g., “lymphoid tissues”, including thymus, spleen, etc.); but not any higher-order pattern of whole-organism, or whole-genome, mapping. The map results here are based on combining published data about chromosome territory locations in the nucleus, and about tissue-specific gene expression levels.
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