Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages.
Bottom Line: To gain insight into how these DNA elements are conserved and spread through the genome, we defined the full spectrum of CTCF-binding sites, including a 33/34-mer motif, and identified over five thousand highly conserved, robust, and tissue-independent CTCF-binding locations by comparing ChIP-seq data from six mammals.We discovered fossilized repeat elements flanking deeply conserved CTCF-binding regions, indicating that similar retrotransposon expansions occurred hundreds of millions of years ago.Repeat-driven dispersal of CTCF binding is a fundamental, ancient, and still highly active mechanism of genome evolution in mammalian lineages.
Affiliation: Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.Show MeSH
Mentions: Taking a more targeted approach that exploited our six species' in vivo experimental data, we looked for evidence in any genome of repeat element survival within the set of partially—or fully—shared CTCF-binding events. We found just over 100 CTCF-binding events (Table S3), often very deeply conserved, which had fossilized repeat sequences surrounding them in one or more of the mammals we profiled (Figure 5).
Affiliation: Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.