Worm Breeder's Gazette 10(2): 13
These abstracts should not be cited in bibliographies. Material contained herein should be treated as personal communication and should be cited as such only with the consent of the author.
The C. elegans genome contains about 12 U2 snRNA genes, and we have cloned and at least partially sequenced ten of them. Seven of the genes are identical in sequence or differ by only a single base pair, and these genes occur in three clusters of two or three U2 genes per lambda clone. Three remaining U2 genes we sequenced are not closely linked to other U2 genes, and they differ from the majority class by one, five and six base pairs. The gene sequence is 66% identical to the human U2 sequence and can be folded into a very similar secondary structure. All sequence alterations are consistent with this structure, and all but one of the changes in stem regions are conservative with respect to base-pairing. We have also determined the sequence of the 5' flanking DNA of all ten genes. We find a remarkable degree of conservation from position -64 to the start site of transcription. There is a consensus base for nearly every position within this region and most genes differ from the consensus sequence by fewer than ten bases. Further upstream there is little resemblance between the ten sequences. Thus we believe the region between -64 and the cap site is likely to contain the cis-acting sequences involved in activation of the U2 genes. Within this region are sequences that are similar to sequence elements shown to function in vertebrate U2, U1 and U4 gene transcription. We have also begun analysis of U4 and U6 snRNAs and the genes that encode them. We have obtained one lambda clone that contains two U4 genes, another that contains a single U4 gene, and a third that contains two U6 genes. The gene sequences of the two U4 genes are identical to each other and have 75% similarity to human U4. The U6 genes are also identical in sequence and are 88% similar to their human homolog. There is good evidence from other organisms that the U4 and U6 snRNAs interact by base-pairing and C. elegans has conserved complementarity between the regions implicated in this interaction. In contrast to the U4 coding regions, and in contrast to the U2 5' flanking regions, the U4 5' flanking regions are highly diverged from each other. The only easily recognizable similarity between all three upstream regions is a sequence from -65 to -41 which also resembles the sequence found at this position in the worm U2 gene promoter. The three U4 genes share no similarity downstream of their 3' ends. The U6 5' flanking regions are nearly identical to each other to the extent we sequenced (-160), presumably reflecting a recent duplication.