Dictyostelium small nuclear RNA D2 is homologous to rat nucleolar RNA U3 and is encoded by a dispersed multigene family.

We have cloned and partially sequenced a 3.9 kb Bgl II restriction fragment from the genome of the cellular slime mold Dictyostelium discoideum which encodes D2, the most abundant small nuclear RNA (snRNA) in vegetative amoebae. The D2 gene is colinear with the mature snRNA and is surrounded by extremely A + T rich DNA for at least 61 nucleotides 5' to the coding region and 218 nucleotides in the 3' direction. D2 is the only small stable RNA encoded by the cloned DNA fragment. Although D2 RNA is homogeneous in length, a comparison of the RNA and DNA sequencing data indicates that C/U or A/G heterogeneity is present in at least three positions within the D2 RNA sequence. Such minor heterogeneity implies that D2 is encoded by multiple genes, and indeed five different restriction fragments complementary to D2 RNA can be detected when genomic blots are probed with labeled fragments derived from the cloned D2 coding region. Further hybridizaton experiments using the cloned flanking sequences as probes suggest that sequences outside the RNA coding region are not detectably conserved between the five dispersed loci. The D2 RNA sequence is more tha 40% homologous to the small nucleolar RNA U3B from rat Novikoff hepatoma, and the implications of this evolutionary conservation are discussed.