repetitive elements may comprise over two-thirds of the human genome重复的元素可能由超过三分之二的人类基因组.pdfVIP

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome 1 1¤ 1 2 1 A. P. Jason de Koning , Wanjun Gu , Todd A. Castoe , Mark A. Batzer , David D. Pollock * 1 Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, Colorado, United States of America, 2 Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America Abstract Transposable elements (TEs) are conventionally identified in eukaryotic genomes by alignment to consensus element sequences. Using this approach, about half of the human genome has been previously identified as TEs and low-complexity repeats. We recently developed a highly sensitive alternative de novo strategy, P-clouds, that instead searches for clusters of high-abundance oligonucleotides that are related in sequence space (oligo ‘‘clouds’’). We show here that P-clouds predicts .840 Mbp of additional repetitive sequences in the human genome, thus suggesting that 66%–69% of the human genome is repetitive or repeat-derived. To investigate this remarkable difference, we conducted detailed analyses of the ability of both P-clouds and a commonly used conventional approach, RepeatMasker (RM), to detect different sized fragments of the highly abundant human Alu and MIR SINEs. RM can have surprisingly low sensitivity for even moderately long fragments, in contrast to P-clouds, which has good sensitivity down to small fragment sizes (,25 bp). Although short fragments have a high intrinsic probability of being false positives, we performed a probabilistic annotation that reflects this fact. We further developed ‘‘element-specific’’ P-clouds (ESPs) to identify novel Alu and MIR SINE elements,