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Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages.

Schmidt D, Schwalie PC, Wilson MD, Ballester B, Gonçalves A, Kutter C, Brown GD, Marshall A, Flicek P, Odom DT - Cell (2012)

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.

View Article: PubMed Central - PubMed

Affiliation: Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.

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Intermittent Repeat Expansions Can Lead to Conserved, Lineage-Specific, and Species-Specific CTCF Binding in MammalsA CTCF-binding site found within an ancient transposon shows conserved binding in placental and nonplacental mammals (left data inset) and must have been present in the mammalian ancestor (ur-Mammal). In contrast, a CTCF-binding site generated in the eutherian ancestor (ur-Placental) shows conserved binding across placental mammals but is absent in marsupials (right data inset). More recent CTCF-binding expansions lead to increasingly lineage- and species-specific CTCF binding. For example, the expansions of B2 repeats in the mouse and rat ancestor (ur-Rodent) created CTCF binding that is highly shared between mouse and rat, whereas the continued B2 expansions along both lineages also generated species-specific CTCF-binding sites (see Figure 4C). See also Table S3.
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fig5: Intermittent Repeat Expansions Can Lead to Conserved, Lineage-Specific, and Species-Specific CTCF Binding in MammalsA CTCF-binding site found within an ancient transposon shows conserved binding in placental and nonplacental mammals (left data inset) and must have been present in the mammalian ancestor (ur-Mammal). In contrast, a CTCF-binding site generated in the eutherian ancestor (ur-Placental) shows conserved binding across placental mammals but is absent in marsupials (right data inset). More recent CTCF-binding expansions lead to increasingly lineage- and species-specific CTCF binding. For example, the expansions of B2 repeats in the mouse and rat ancestor (ur-Rodent) created CTCF binding that is highly shared between mouse and rat, whereas the continued B2 expansions along both lineages also generated species-specific CTCF-binding sites (see Figure 4C). See also Table S3.

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).


Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages.

Schmidt D, Schwalie PC, Wilson MD, Ballester B, Gonçalves A, Kutter C, Brown GD, Marshall A, Flicek P, Odom DT - Cell (2012)

Intermittent Repeat Expansions Can Lead to Conserved, Lineage-Specific, and Species-Specific CTCF Binding in MammalsA CTCF-binding site found within an ancient transposon shows conserved binding in placental and nonplacental mammals (left data inset) and must have been present in the mammalian ancestor (ur-Mammal). In contrast, a CTCF-binding site generated in the eutherian ancestor (ur-Placental) shows conserved binding across placental mammals but is absent in marsupials (right data inset). More recent CTCF-binding expansions lead to increasingly lineage- and species-specific CTCF binding. For example, the expansions of B2 repeats in the mouse and rat ancestor (ur-Rodent) created CTCF binding that is highly shared between mouse and rat, whereas the continued B2 expansions along both lineages also generated species-specific CTCF-binding sites (see Figure 4C). See also Table S3.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368268&req=5

fig5: Intermittent Repeat Expansions Can Lead to Conserved, Lineage-Specific, and Species-Specific CTCF Binding in MammalsA CTCF-binding site found within an ancient transposon shows conserved binding in placental and nonplacental mammals (left data inset) and must have been present in the mammalian ancestor (ur-Mammal). In contrast, a CTCF-binding site generated in the eutherian ancestor (ur-Placental) shows conserved binding across placental mammals but is absent in marsupials (right data inset). More recent CTCF-binding expansions lead to increasingly lineage- and species-specific CTCF binding. For example, the expansions of B2 repeats in the mouse and rat ancestor (ur-Rodent) created CTCF binding that is highly shared between mouse and rat, whereas the continued B2 expansions along both lineages also generated species-specific CTCF-binding sites (see Figure 4C). See also Table S3.
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).

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.

View Article: PubMed Central - PubMed

Affiliation: Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.

Show MeSH