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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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Custom Opossum CTCF Antibody Design and Validation, Related to Experimental Procedures(A) Alignment of parts of CTCF's protein sequences in multiple mammals. The peptides used to generate the commercial (human, rhesus, mouse, rat, dog) and custom (opossum) antibodies are highlighted.(B) Wiggle tracks of CTCF and cohesin (STAG1/SA1) binding in opossum liver around the APP1 gene. The binding event highlighted with a star is in the orthologous location of the human binding event used for DNase I footprinting (Quitschke et al., 2000).(C) Violin plots of raw read counts in opossum CTCF binding events for both replicates and cohesin validating that most opossum CTCF-binding events show strong cohesin enrichment.(D) Scatter and Bland-Altman plots comparing the opossum CTCF to the opossum cohesin replicates. Spearman correlations are indicated.
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figs5: Custom Opossum CTCF Antibody Design and Validation, Related to Experimental Procedures(A) Alignment of parts of CTCF's protein sequences in multiple mammals. The peptides used to generate the commercial (human, rhesus, mouse, rat, dog) and custom (opossum) antibodies are highlighted.(B) Wiggle tracks of CTCF and cohesin (STAG1/SA1) binding in opossum liver around the APP1 gene. The binding event highlighted with a star is in the orthologous location of the human binding event used for DNase I footprinting (Quitschke et al., 2000).(C) Violin plots of raw read counts in opossum CTCF binding events for both replicates and cohesin validating that most opossum CTCF-binding events show strong cohesin enrichment.(D) Scatter and Bland-Altman plots comparing the opossum CTCF to the opossum cohesin replicates. Spearman correlations are indicated.

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.


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)

Custom Opossum CTCF Antibody Design and Validation, Related to Experimental Procedures(A) Alignment of parts of CTCF's protein sequences in multiple mammals. The peptides used to generate the commercial (human, rhesus, mouse, rat, dog) and custom (opossum) antibodies are highlighted.(B) Wiggle tracks of CTCF and cohesin (STAG1/SA1) binding in opossum liver around the APP1 gene. The binding event highlighted with a star is in the orthologous location of the human binding event used for DNase I footprinting (Quitschke et al., 2000).(C) Violin plots of raw read counts in opossum CTCF binding events for both replicates and cohesin validating that most opossum CTCF-binding events show strong cohesin enrichment.(D) Scatter and Bland-Altman plots comparing the opossum CTCF to the opossum cohesin replicates. Spearman correlations are indicated.
© Copyright Policy
Related In: Results  -  Collection

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

figs5: Custom Opossum CTCF Antibody Design and Validation, Related to Experimental Procedures(A) Alignment of parts of CTCF's protein sequences in multiple mammals. The peptides used to generate the commercial (human, rhesus, mouse, rat, dog) and custom (opossum) antibodies are highlighted.(B) Wiggle tracks of CTCF and cohesin (STAG1/SA1) binding in opossum liver around the APP1 gene. The binding event highlighted with a star is in the orthologous location of the human binding event used for DNase I footprinting (Quitschke et al., 2000).(C) Violin plots of raw read counts in opossum CTCF binding events for both replicates and cohesin validating that most opossum CTCF-binding events show strong cohesin enrichment.(D) Scatter and Bland-Altman plots comparing the opossum CTCF to the opossum cohesin replicates. Spearman correlations are indicated.
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.

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
Related in: MedlinePlus