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CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation

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Science  27 Feb 2015:
Vol. 347, Issue 6225, pp. 1017-1021
DOI: 10.1126/science.1262088
  • Fig. 1 CTCF localizes to a HoxA chromatin boundary in motor neurons.

    (A) Heat map of HoxA relative expression (log2) between WT ESCs and MNs. (B) Normalized chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) read densities for the indicated proteins and histone modifications in ESCs and MNs from two merged biological replicates. Genes that are activated during differentiation are annotated in green; repressed genes are shown in red. (C) Zoomed-in view of H3K4me3 and H3K27me3 boundaries, along with CTCF peaks and their underlying binding motifs. Blue highlights nucleotides that diverge from the consensus motif. The guide RNA used to target C5|6 is shown. (D) Sequencing chromatogram of the Δ5|6 line depicts a 9-bp deletion overlapping the CTCF core motif. (E) Normalized ChIP-seq read densities for CTCF in WT and Δ5|6 MNs from two merged biological replicates. The deleted CTCF binding site (C5|6) is boxed, as well as the neighboring site (C6|7).

  • Fig. 2 The chromatin boundary is disrupted upon deletion of the C5|6 CTCF motif.

    (A) RNA-seq MA plot of WT versus Δ5|6 ESCs (left) and MNs (4 days after RA/SAG, right). MN data are representative of two biological replicate experiments; ESC data represent one experiment. Mean abundance is plotted on the x axis and enrichment is plotted on the y axis. Hb9 is a marker of motor neurons. (B) Normalized ChIP-seq read densities for the indicated protein and histone modifications along the HoxA cluster in ESCs and MNs (4 days after RA/SAG) from two biological replicates.

  • Fig. 3 Loss of CTCF alters topological architecture of the HoxA locus.

    (A to C) Normalized ChIP-seq read densities for CTCF and 4C contact profiles in WT and Δ5|6 ESCs (A) and MNs [(B) and (C)] using a viewpoint (red) in either the rostral [(B), 4C.Hoxa5-A] or caudal [(A) and (C), 4C.Hoxa10] segment of the cluster. The ChIP signal is merged across two biological replicates and the 4C signal across three replicates. The median and 20th and 80th percentiles of sliding 5-kb windows determine the main trend line. Color scale represents enrichment relative to the maximum attainable 12-kb median value. Dotted lines highlight the region between C6|7 and C7|9.

  • Fig. 4 Compound C5|6:7|9 deletion causes a further caudal spread of active transcription within the HoxA locus.

    (A) RNA-seq MA plot of WT versus ∆5|6:7|9 MNs. Mean abundance is plotted on the x axis, and enrichment is plotted on the y axis. (B) Heat map of HoxA relative expression in MNs (day 4) versus EBs (embryoid bodies) (day 0) across two biological replicates (single replicate in the ∆5|6:7|9 line). (C) Normalized ChIP-seq read densities for CTCF and 4C contact profiles in WT and Δ5|6:7|9 MNs using the 4C.Hoxa5-B viewpoint (red) from two biological replicates. The median and 20th and 80th percentiles of sliding 5-kb windows determine the main trend line. The color scale represents enrichment relative to the maximum attainable 12-kb median value. Dotted lines highlight the region between C6|7 and C10|11. (D) Normalized ChIP-seq read densities for the indicated proteins and histone modifications along the HoxA cluster in MNs (4 days after RA/SAG). A magnified view of the boxed region is presented on the right.

Supplementary Materials

  • CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation

    Varun Narendra, Pedro P. Rocha, Disi An, Ramya Raviram, Jane A. Skok, Esteban O. Mazzoni, Danny Reinberg

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