FIGURE 1.

Evolutionary profiles of well-conserved vertebrate miRNA genes. (A,B) Multispecies alignments of two miRNA genes that are conserved from humans to fish. (Green) Mature strands; (yellow) star strands; (red) nucleotides diverged with respect to human. (A) mir-20b is highly conserved; its mature product has sustained a few positions of divergence, but none involve its seed (nucleotides 1–8). On the other hand, miR-20b* has accumulated many more positions of divergence, including in seed nucleotides in its fish orthologs. (B) mir-18a is perfectly conserved along both miRNA and star arms among all vertebrates, from human to fish. Such extreme constraint is suggestive of conserved regulatory activities of both small RNAs produced by mir-18a. (C) Sequence divergence in 7-nt windows across 106 miRNA genes whose star arms sustained ≤3 diverged positions between human and chicken. We note three observations: (1) miRNA strands (green) are better conserved than star strands (yellow); (2) the ends of both miRNA and star strands are better conserved than their central regions; and (3) the 2–8 seed windows exhibit highest conservation along miRNA and star sequences (dotted reference line); the mature 1–7 and 2–8 windows had similar scores.