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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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CTCF Binding Is Primarily Directed by Genetic Sequence and Is Highly Conserved; Western Blot Confirmation of CTCF RNAi and Tissue Specificity of Conserved CTCF Binding, Related to Figure 1(A) In the first column (Hs-chr21), ten kilobase windows around human CTCF-binding events were ordered, based whether a syntenic CTCF-binding event is present or not in mouse liver. In the second and third columns, CTCF binding in the Tc1 mouse has been shown for the human chromosome 21 (Tc1-Hs-chr21) and for the orthologous mouse sequences (Tc1-Mm-chr16, 17, 10). Most CTCF binding found on human chromosome 21 in human liver is recapitulated in the mouse liver.(B) Genome tracks displaying the CTCF binding found near the liver-expressed gene CLDN14 in human (red, Hs-chr21) and Tc1 mouse (blue, Tc1-Hs-chr21; green, Tc1-Mm-chr16).(C) Genomic occupancy of HNF4A, CEBPA (orange tracks), and CTCF (blue tracks) is shown around the liver gene APOA2 in human, mouse, and dog. Grey lines connect orthologous regions between species.(D) Binding events for CEBPA, HNF4A, and CTCF have been sorted, based on whether they occur in one, two, or three of the placental species from (C).(E) The fraction of binding events found only in human (human only) or shared among all placental mammals (five-way) were characterized by their tissue specificity. Few deeply shared CTCF-binding events are tissue specific in humans.(F) Western blot of nuclear extracts after CTCF RNAi, mock RNAi, and non-transfected (NT) human MCF-7 cells.(G) Read profiles of CTCF binding after CTCF (red lines) or mock RNAi (black lines) in MCF-7 cells. CTCF binding was separated into two groups: (1) human-specific binding events in liver that are also found in MCF-7 cells (human only binding events) and (2) five-way shared binding events in liver that overlap with CTCF binding in MCF-7 cells (five-way shared binding events).(H) The total numbers of CTCF-binding events (CTCF-bound regions) for the following data sets are shown: MCF-7 after mock RNAi (MCF-7), MCF-7 after CTCF RNAi (MCF-7 KD), human liver (Liver). The bottom two rows show the CTCF binding overlaps between MCF-7 versus Liver and MCF-7 KD versus Liver binding. Total CTCF-binding overlaps are indicated on the left and further split into three categories: five-way shared, human-specific, and all other CTCF binding.
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figs1: CTCF Binding Is Primarily Directed by Genetic Sequence and Is Highly Conserved; Western Blot Confirmation of CTCF RNAi and Tissue Specificity of Conserved CTCF Binding, Related to Figure 1(A) In the first column (Hs-chr21), ten kilobase windows around human CTCF-binding events were ordered, based whether a syntenic CTCF-binding event is present or not in mouse liver. In the second and third columns, CTCF binding in the Tc1 mouse has been shown for the human chromosome 21 (Tc1-Hs-chr21) and for the orthologous mouse sequences (Tc1-Mm-chr16, 17, 10). Most CTCF binding found on human chromosome 21 in human liver is recapitulated in the mouse liver.(B) Genome tracks displaying the CTCF binding found near the liver-expressed gene CLDN14 in human (red, Hs-chr21) and Tc1 mouse (blue, Tc1-Hs-chr21; green, Tc1-Mm-chr16).(C) Genomic occupancy of HNF4A, CEBPA (orange tracks), and CTCF (blue tracks) is shown around the liver gene APOA2 in human, mouse, and dog. Grey lines connect orthologous regions between species.(D) Binding events for CEBPA, HNF4A, and CTCF have been sorted, based on whether they occur in one, two, or three of the placental species from (C).(E) The fraction of binding events found only in human (human only) or shared among all placental mammals (five-way) were characterized by their tissue specificity. Few deeply shared CTCF-binding events are tissue specific in humans.(F) Western blot of nuclear extracts after CTCF RNAi, mock RNAi, and non-transfected (NT) human MCF-7 cells.(G) Read profiles of CTCF binding after CTCF (red lines) or mock RNAi (black lines) in MCF-7 cells. CTCF binding was separated into two groups: (1) human-specific binding events in liver that are also found in MCF-7 cells (human only binding events) and (2) five-way shared binding events in liver that overlap with CTCF binding in MCF-7 cells (five-way shared binding events).(H) The total numbers of CTCF-binding events (CTCF-bound regions) for the following data sets are shown: MCF-7 after mock RNAi (MCF-7), MCF-7 after CTCF RNAi (MCF-7 KD), human liver (Liver). The bottom two rows show the CTCF binding overlaps between MCF-7 versus Liver and MCF-7 KD versus Liver binding. Total CTCF-binding overlaps are indicated on the left and further split into three categories: five-way shared, human-specific, and all other CTCF binding.

Mentions: We used ChIP followed by sequencing (Table S1 available online) to determine CTCF binding in livers isolated from five eutherian mammals (human, macaque, mouse, rat, and dog) and the metatherian gray short-tailed opossum and confirmed that CTCF binding is mainly directed by genetic sequence rather than nuclear environment (Wilson et al., 2008) (Figures S1A and S1B).


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)

CTCF Binding Is Primarily Directed by Genetic Sequence and Is Highly Conserved; Western Blot Confirmation of CTCF RNAi and Tissue Specificity of Conserved CTCF Binding, Related to Figure 1(A) In the first column (Hs-chr21), ten kilobase windows around human CTCF-binding events were ordered, based whether a syntenic CTCF-binding event is present or not in mouse liver. In the second and third columns, CTCF binding in the Tc1 mouse has been shown for the human chromosome 21 (Tc1-Hs-chr21) and for the orthologous mouse sequences (Tc1-Mm-chr16, 17, 10). Most CTCF binding found on human chromosome 21 in human liver is recapitulated in the mouse liver.(B) Genome tracks displaying the CTCF binding found near the liver-expressed gene CLDN14 in human (red, Hs-chr21) and Tc1 mouse (blue, Tc1-Hs-chr21; green, Tc1-Mm-chr16).(C) Genomic occupancy of HNF4A, CEBPA (orange tracks), and CTCF (blue tracks) is shown around the liver gene APOA2 in human, mouse, and dog. Grey lines connect orthologous regions between species.(D) Binding events for CEBPA, HNF4A, and CTCF have been sorted, based on whether they occur in one, two, or three of the placental species from (C).(E) The fraction of binding events found only in human (human only) or shared among all placental mammals (five-way) were characterized by their tissue specificity. Few deeply shared CTCF-binding events are tissue specific in humans.(F) Western blot of nuclear extracts after CTCF RNAi, mock RNAi, and non-transfected (NT) human MCF-7 cells.(G) Read profiles of CTCF binding after CTCF (red lines) or mock RNAi (black lines) in MCF-7 cells. CTCF binding was separated into two groups: (1) human-specific binding events in liver that are also found in MCF-7 cells (human only binding events) and (2) five-way shared binding events in liver that overlap with CTCF binding in MCF-7 cells (five-way shared binding events).(H) The total numbers of CTCF-binding events (CTCF-bound regions) for the following data sets are shown: MCF-7 after mock RNAi (MCF-7), MCF-7 after CTCF RNAi (MCF-7 KD), human liver (Liver). The bottom two rows show the CTCF binding overlaps between MCF-7 versus Liver and MCF-7 KD versus Liver binding. Total CTCF-binding overlaps are indicated on the left and further split into three categories: five-way shared, human-specific, and all other CTCF binding.
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figs1: CTCF Binding Is Primarily Directed by Genetic Sequence and Is Highly Conserved; Western Blot Confirmation of CTCF RNAi and Tissue Specificity of Conserved CTCF Binding, Related to Figure 1(A) In the first column (Hs-chr21), ten kilobase windows around human CTCF-binding events were ordered, based whether a syntenic CTCF-binding event is present or not in mouse liver. In the second and third columns, CTCF binding in the Tc1 mouse has been shown for the human chromosome 21 (Tc1-Hs-chr21) and for the orthologous mouse sequences (Tc1-Mm-chr16, 17, 10). Most CTCF binding found on human chromosome 21 in human liver is recapitulated in the mouse liver.(B) Genome tracks displaying the CTCF binding found near the liver-expressed gene CLDN14 in human (red, Hs-chr21) and Tc1 mouse (blue, Tc1-Hs-chr21; green, Tc1-Mm-chr16).(C) Genomic occupancy of HNF4A, CEBPA (orange tracks), and CTCF (blue tracks) is shown around the liver gene APOA2 in human, mouse, and dog. Grey lines connect orthologous regions between species.(D) Binding events for CEBPA, HNF4A, and CTCF have been sorted, based on whether they occur in one, two, or three of the placental species from (C).(E) The fraction of binding events found only in human (human only) or shared among all placental mammals (five-way) were characterized by their tissue specificity. Few deeply shared CTCF-binding events are tissue specific in humans.(F) Western blot of nuclear extracts after CTCF RNAi, mock RNAi, and non-transfected (NT) human MCF-7 cells.(G) Read profiles of CTCF binding after CTCF (red lines) or mock RNAi (black lines) in MCF-7 cells. CTCF binding was separated into two groups: (1) human-specific binding events in liver that are also found in MCF-7 cells (human only binding events) and (2) five-way shared binding events in liver that overlap with CTCF binding in MCF-7 cells (five-way shared binding events).(H) The total numbers of CTCF-binding events (CTCF-bound regions) for the following data sets are shown: MCF-7 after mock RNAi (MCF-7), MCF-7 after CTCF RNAi (MCF-7 KD), human liver (Liver). The bottom two rows show the CTCF binding overlaps between MCF-7 versus Liver and MCF-7 KD versus Liver binding. Total CTCF-binding overlaps are indicated on the left and further split into three categories: five-way shared, human-specific, and all other CTCF binding.
Mentions: We used ChIP followed by sequencing (Table S1 available online) to determine CTCF binding in livers isolated from five eutherian mammals (human, macaque, mouse, rat, and dog) and the metatherian gray short-tailed opossum and confirmed that CTCF binding is mainly directed by genetic sequence rather than nuclear environment (Wilson et al., 2008) (Figures S1A and S1B).

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