Figure 1.
Total number of bases (coding versus conserved non-coding) in human that align to each species.
Species are ordered at progressively greater evolutionary distances. Placental mammal CNEs – placental mammal conserved non-coding elements.
Figure 2.
(A) Pattern of conservation of Bicores across the metazoan tree. Green checks denote conservation of sequence and gene synteny. Red crosses denote no detectable sequence conservation. (B) Characteristics of Bicores. CNS – central nervous system.
Figure 3.
Bicore1 is a bilaterian conserved enhancer.
(A) Multiple alignment of Bicore1. Above the alignment are mutations that reduce the cis-regulatory function of Bicore1 in response to Tgf-beta/Bmp signaling in a luciferase assay [20], [21], [24]. (B) Conservation profile of Bicore1 showing that conserved blocks in the alignment correspond to transcription factor binding preferences. (C) Each instance of Bicore1 (green oval) is syntenic to a conserved Id gene (blue gene structure). (D–G) Zebrafish transgenic assay showing (D) human, (E) zebrafish, (F) sea urchin, (G) owl limpet instances of Bicore1 drive expression in the central nervous system at 48 hours. (H) Whole-mount in situ hybridization of id1 in zebrafish shows expression throughout the central nervous system, courtesy of zfin.org. (I) A human genomic region containing Bicore1 drives expression in the forebrain, midbrain, hindbrain, neural tube, and eye of embryonic day 11.5 mice, courtesy of enhancer.lbl.gov. (J) A sea urchin genomic region drives expression in the aboral ectoderm (arrow) in the early pluteus stage sea urchin larva. (K) Pairwise percent identities of Bicore1 sequences. Green cells indicate a query sequence (row) that detected Bicore1 in the target (column). Red cells indicate query sequences that did not detect Bicore1 in the target.
Figure 4.
Bicore2 is a bilaterian conserved enhancer.
(A) Multiple alignment of Bicore2. (B) Conservation profile of Bicore2 showing that conserved blocks in the alignment correspond to transcription factor binding preferences. (C) Each instance of Bicore2 (green oval) is syntenic to a conserved instance of Znf503 (blue gene structure). (D–G) Zebfrafish transgenic enhancer assay showing (D) human, (E) zebrafish, (F) sea urchin, (G) tick instances of Bicore2 drive expression in the hindbrain at 48 hours. (H) Whole-mount in situ hybridization of Znf503 shows expression in the hindbrain, courtesy of zfin.org. (I) A human region containing Bicore2 drives expression in the hindbrain and the apical ectoderm of the limb in embryonic day 11.5 mice. (J) Pairwise percent identities of Bicore2 sequences. Green cells indicate a query sequence (row) that detected Bicore2 in the target (column). Red cells indicate query sequences that did not detect Bicore2 in the target.