Abundant pseudogenes for small nuclear RNAs are dispersed in the human genome.

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Abstract
Loci (24) from the human genome which are complementary to U1, U2, or U3, the 3 major species of small nuclear RNA (smRNA) in HeLa cells, were cloned and characterized. When compared to the known U1 (human) and U2 (rat) snRNA sequences, the DNA sequences for the complementary regions from 2 of the clones, U1.11 and U2.7, reveal the presence of truncated and divergent gene copies. Most if not all of the 24 cloned loci contain gene copies that are significantly divergent from the homologous HeLa snRNA species; DNA from every recombinant phage, except U1.7 and U1.15, proved unable to form snRNA.cntdot.DNA hybrids which protect full-length HeLa snRNA from mild digestion with ribonuclease T1. These loci are referred to as snRNA pseudogenes. In both clones U1.11 and U2.7, an element of the dominant middle repetitive DNA sequence family in the human genome, the Alu family, is located upstream from the snRNA pseudogene and in the same orientation. Alu elements in the same location and orientation relative to bona fide genes have previously been found in the human .beta.-globin gene cluster. The significance of these findings in relation to the nature of snRNA multigene families and other reported examples of pseudogenes are discussed.