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Ultraconserved Elements in the Human Genome

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Science  28 May 2004:
Vol. 304, Issue 5675, pp. 1321-1325
DOI: 10.1126/science.1098119
  • Fig. 1.

    Locations of the 481 ultraconserved elements on the 24 human chromosomes. Each partly exonic element is represented by a thin blue tick mark extending above the chromosome, each non-exonic element by a green tick mark extending below the chromosome, and each possibly exonic element by a black tick mark centered on the chromosome. Purple boxes represent centromeres. By joining two elements into a cluster when they are separated by less than 675 kb, we obtained 89 local clusters of two or more elements, each of which is boxed and named. Names are taken from a prominent gene or gene family co-located with the cluster or from a Drosophila ortholog or mRNA entry if no Human Genome Organization (HUGO)–named gene was available. Among the cluster representatives, there is a distinct enrichment for non-exonic elements and for developmental genes, suggesting that many of these clusters may be part of distal enhancers or “global control loci” analogous to those studied in association with HOXD (38) or DACH (21). One possible such cluster, near the ARX gene, is shown in more detail in the inset at the bottom of the figure. There known genes are shown in blue (tall boxes for coding exons, shorter boxes for UTRs, and hatched lines for introns), and ultraconserved elements are shown below them.

  • Fig. 2.

    Annotation enrichment in type I and type II genes. In the top half of the figure, the maroon bars (“observed”) give the numbers of type I genes that are annotated in the GO database (19) with molecular function “RNA binding” or “DNA binding” or biological process “RNA splicing” or “transcription regulation,” or are annotated in InterPro (20) as containing the domains “RNA recognition motif” or “homeobox.” The blue bars (“expected”) give the number of genes that one would expect to obtain if the same number of genes (111 genes for type I) were chosen at random among all genes annotated in the relevant database. The bottom half of the figure gives similar information for type II genes. It is apparent that type I genes are enriched for RNA-related functions, whereas type II genes are not. Both types are enriched for DNA-related functions, but the type II genes are more enriched.

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    Ultraconserved Elements in the Human Genome
    Gill Bejerano, Michael Pheasant, Igor Makunin, Stuart Stephen, W. James Kent, John S. Mattick, David Haussler

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