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
Related in: MedlinePlus
Mentions: The CTCF antibody 07-729 (Milipore) was used for all experiments except the opossum ones, which were performed using a custom antibody as described and validated in Figure S5. The custom opossum CTCF antibody is available upon request. The STAG1 antibody used for validation of the opossum results and the H2AK5ac antibody were both purchased from abcam, ab4457 and ab1764, respectively.
Affiliation: Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.