Gómez-Marín et al., 2015 - Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders. Proceedings of the National Academy of Sciences of the United States of America   112(24):7542-7 Full text @ Proc. Natl. Acad. Sci. USA

Fig. 2

All four zebrafish six clusters are divided in two different 3D compartments. (A–D) 4C-seq on whole zebrafish embryos at 24 hpf from the different six genes at each cluster (black triangles). Border regions are indicated by an asterisk, and the two 3D compartments are shaded in red and blue. Contact percentages for each gene on the two 3D compartments are shown. Expression patterns of each gene at 24 hpf are shown for each gene below the 4C-seq tracks. (A) six3a/six2a cluster. (B) six3b/six2b cluster. (C) six6a/six1a/six4a cluster. (D) sixba/six1b/six4b cluster.

Fig. 3

Conserved subdivision of Six clusters in two 3D compartments along deuterostome evolution. (A–C) 4C-seq in whole mouse (A and B) or sea urchin (C) embryos from the different Six genes as viewpoints. Border regions are indicated by an asterisk, and the two 3D compartments are shaded in red and blue. Contact percentages for each gene on the two 3D compartments is shown. In murine clusters, HiC data from mouse ES cells is shown below. HiC data show that clusters are divided into the two TADs also defined by 4C-seq. Border regions identified by 4C-seq coincide in both clusters with TADs borders. (Right) Expression patterns of the different genes. (D) Transient transgenic fish embryos injected with the full six2a-GFP/six3a-mCherry BAC (Left) or a TAD-deleted version (Δ18kb) of the same BAC (Right) at 72 h hpf. Arrowheads point to the brain expression domain characteristic of the six3a gene.

Acknowledgments:
ZFIN wishes to thank the journal Proceedings of the National Academy of Sciences of the United States of America for permission to reproduce figures from this article. Please note that this material may be protected by copyright. Full text @ Proc. Natl. Acad. Sci. USA