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Human Genome Ultraconserved Elements Are Ultraselected

Sol Katzman,^1* Andrew D. Kern,^2* Gill Bejerano,² Ginger Fewell,³ Lucinda Fulton,³ Richard K. Wilson,³ Sofie R. Salama,^2,4 David Haussler^1,2,4

Ultraconserved elements in the human genome are defined as stretches of at least 200 base pairs of DNA that match identically with corresponding regions in the mouse and rat genomes. Most ultraconserved elements are noncoding and have been evolutionarily conserved since mammal and bird ancestors diverged over 300 million years ago. The reason for this extreme conservation remains a mystery. It has been speculated that they are mutational cold spots or regions where every site is under weak but still detectable negative selection. However, analysis of the derived allele frequency spectrum shows that these regions are in fact under negative selection that is much stronger than that in protein coding genes.

¹ Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA.
² Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA.
³ Genome Sequencing Center, Washington University School of Medicine, St. Louis, MO 63108, USA.
⁴ Howard Hughes Medical Institute, University of California, Santa Cruz, CA 95064, USA.

^* These authors contributed equally to this work.

Present address: Department of Developmental Biology and Department of Computer Science, Stanford University, Stanford, CA 94305, USA.

To whom correspondence should be addressed. E-mail: haussler{at}soe.ucsc.edu

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