Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1

Jeong Do Kim, Christopher Faulk, Joomyeong Kim

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YY1 is a DNA-binding transcription factor found in both vertebrates and invertebrates. Database searches identified 62 YY1 related sequences from all the available genome sequences ranging from flying insects to human. These sequences are characterized by high levels of sequence conservation, ranging from 66% to 100% similarity, in the zinc finger DNA-binding domain of the predicted proteins. Phylogenetic analyses uncovered duplication events of YY1 in several different lineages, including flies, fish and mammals. Retroposition is responsible for generating one duplicate in flies, PHOL from PHO, and two duplicates in placental mammals, YY2 and Reduced Expression 1 (REX1) from YY1. DNA-binding motif studies have demonstrated that YY2 still binds to the same consensus sequence as YY1 but with much lower affinity. In contrast, REX1 binds to DNA motifs divergent from YY1, but the binding motifs of REX1 and YY1 share some similarity at their core regions (5′-CCAT-3′). This suggests that the two duplicates, YY2 and REX1, although generated through similar retroposition events have undergone different selection schemes to adapt to new roles in placental mammals. Overall, the conservation of YY2 and REX1 in all placental mammals predicts that each duplicate has co-evolved with some unique features of eutherian mammals.

Original languageEnglish (US)
Pages (from-to)3442-3452
Number of pages11
JournalNucleic acids research
Issue number10
StatePublished - May 2007

Bibliographical note

Funding Information:
The authors would like to thank Dr Lisa Stubbs for helpful discussions and Jennifer M. Huang for providing help in cloning and sequencing. This study was supported by NIH grant GM66225 (to J.K.). Funding to pay the Open Access publication charges for this article was provided by NIH grant GM66225.


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