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Chicken Special/Letter

Evolution and functional classification of vertebrate gene deserts

¹ Energy, Environment, Biology, and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, California 94550, USA ² Genome Biology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA ³ Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA ⁴ Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA ⁵ Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA ⁶ Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA

Large tracts of the human genome, known as gene deserts, are devoid of protein-coding genes. Dichotomy in their level of conservation with chicken separates these regions into two distinct categories, stable and variable. The separation is not caused by differences in rates of neutral evolution but instead appears to be related to different biological functions of stable and variable gene deserts in the human genome. Gene Ontology categories of the adjacent genes are strongly biased toward transcriptional regulation and development for the stable gene deserts, and toward distinctively different functions for the variable gene deserts. Stable gene deserts resist chromosomal rearrangements and appear to harbor multiple distant regulatory elements physically linked to their neighboring genes, with the linearity of conservation invariant throughout vertebrate evolution.

⁷ Corresponding author
E-mail ovcharenko1{at}llnl.gov; fax (925) 422-2099.

[Supplemental material is available online at www.genome.org.]

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