RT Journal
A1 Abyzov, Alexej
A1 Iskow, Rebecca
A1 Gokcumen, Omer
A1 Radke, David W.
A1 Balasubramanian, Suganthi
A1 Pei, Baikang
A1 Habegger, Lukas
A1 The 1000 Genomes Project Consortium
A1 Lee, Charles
A1 Gerstein, Mark
T1 Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division
JF Genome Research 
JO Genome Research 
YR 2013 
FD December 01 
VO 23 
IS 12 
SP 2042 
OP 2052 
DO 10.1101/gr.154625.113 
UL http://genome.cshlp.org/content/23/12/2042.abstract 
AB In primates and other animals, reverse transcription of mRNA followed by genomic integration creates retroduplications. Expressed retroduplications are either “retrogenes” coding for functioning proteins, or expressed “processed pseudogenes,” which can function as noncoding RNAs. To date, little is known about the variation in retroduplications in terms of their presence or absence across individuals in the human population. We have developed new methodologies that allow us to identify “novel” retroduplications (i.e., those not present in the reference genome), to find their insertion points, and to genotype them. Using these methods, we catalogued and analyzed 174 retroduplication variants in almost one thousand humans, which were sequenced as part of Phase 1 of The 1000 Genomes Project Consortium. The accuracy of our data set was corroborated by (1) multiple lines of sequencing evidence for retroduplication (e.g., depth of coverage in exons vs. introns), (2) experimental validation, and (3) the fact that we can reconstruct a correct phylogenetic tree of human subpopulations based solely on retroduplications. We also show that parent genes of retroduplication variants tend to be expressed at the M-to-G1 transition in the cell cycle and that M-to-G1 expressed genes have more copies of fixed retroduplications than genes expressed at other times. These findings suggest that cell division is coupled to retrotransposition and, perhaps, is even a requirement for it.