Evolution of Gene Deserts in the Human Genome


‘Gene deserts’ are improbably large regions of the human genome that contain no genes. The evolutionary origin of these regions is still unknown, but experimental and computational evidence suggests there are multiple classes of gene deserts in the human genome, each with different evolutionary origins and functional associations.

Keywords: gene desert; genome architecture; gene regulation

Figure 1.

Gene desert on human chromosome 1 flanked by LPHN2 and TTLL7. The orthologous gene desert on mouse chromosome 3 is one of two gene deserts that were deleted in mice with no observable phenotypic consequences (by Nóbrega et al.). View from UCSC Genome Browser (Kent et al., ).

Figure 2.

Region on human chromosome 13 showing DACH1 and the two gene deserts that flank it. The nine highly conserved regions that tested for enhancer activity by Nobrega et al. in 2003 are shown, along with the seven regions that tested positive. View from UCSC Genome Browser (Kent et al., ).

Figure 3.

Region of human chromosome 13 containing four gene clusters separated and surrounded by gene deserts. The homologous region on mouse chromosome 14 was examined by Shopland et al. in 2006, who suggest a relationship between the cluster/desert architecture of this region with higher order chromatin structure and nuclear positioning.

Figure 4.

Region of human chromosome 13 containing a gene desert that corresponds to a large ancient duplication (LAD) identified by Itoh et al. The top portion of the plot is a view from the UCSC Genome Browser (Kent et al., ) showing the location of genes, the gene desert and genome‐wide chained human self‐alignments. The bottom portion shows a dotplot generated from Blastz (Schwartz et al., ) alignments of this human region with itself (each line corresponds to a local alignment). This representation clearly shows multiple large low‐similarity duplications corresponding to the position of this gene desert.



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Further Reading

Itoh T, Toyoda A, Taylor TD, Sakaki Y and Hattori M (2005) Identification of large ancient duplications associated with human gene deserts. Nature Genetics 37(10): 1041–1043.

Nobrega MA, Ovcharenko I, Afzal V and Rubin EM (2003) Scanning human gene deserts for long‐range enhancers. Science 302(5644): 413.

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Shopland LS, Lynch CR, Peterson KA et al. (2006) Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence. Journal of Cell Biology 174(1): 27–38.

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Taylor, James(Mar 2008) Evolution of Gene Deserts in the Human Genome. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0020830]