Human U1 small nuclear RNA pseudogenes do not map to the site of the U1 genes in 1p36 but are clustered in 1q12-q22.

Abstract

Human U1 small nuclear RNA is encoded by approximately 30 gene copies. All of the U1 genes share several kilobases of essentially perfect flanking homology both upstream and downstream from the U1 coding region, but remarkably, for many U1 genes excellent flanking homology extends at least 24 kilobases upstream and 20 kilobases downstream. Class I U1 RNA pseudogenes are abundant in the human genome. These pseudogenes contain a complete but imperfect U1 coding region and possess extensive flanking homology to the true U1 genes. We mapped four class I pseudogenes by in situ hybridization to the long arm of chromosome 1, bands q12-q22, a region distinct from the site on the distal short arm of chromosome 1 to which the U1 genes have been previously mapped (Lund et al., Mol. Cell. Biol. 3:2211-2220, 1983; Naylor et al., Somat. Cell Mol. Genet. 10:307-313, 1984). We confirmed our in situ hybridization results by genomic blotting experiments with somatic cell hybrid lines with translocation products of human chromosome 1. These experiments provide further evidence that class I U1 pseudogenes and the true U1 genes are not interspersed. The results, along with those published elsewhere (Bernstein et al., Mol. Cell. Biol. 5:2159-2171, 1985), suggest that gene amplification may be responsible for the sequence homogeneity of the human U1 gene family.

Differentially expressed, variant U1 snRNAs regulate gene expression in human cells

“…However, wherever studied, it seems that the inability to produce a protein does not necessarily imply nonfunctionality, as recent studies have demonstrated that pseudogenes often exert their activity through RNA-based mechanisms, generating antisense transcripts that either interfere with translation of real genes or sense transcripts that act as miRNA decoys or compete for mRNA stabilizing factors (Korneev et al 1999;Chiefari et al 2010;Poliseno et al 2010;Muro et al 2011). For the past 30 yr, the class I U1 snRNA pseudogenes were also considered to be nonfunctional since they would encode imperfect or incomplete copies of the U1 snRNA (Denison et al 1981;Lindgren et al 1985). However, the results presented here challenge this notion and suggest that these ''imperfect'' copies have a biological function.…”

“…The U1 snRNA class I pseudogenes, in contrast, have considerable 59 and 39 flanking sequence homology with the U1 snRNA genes and retain good homology with the two essential promoter elements, the distal sequence element (DSE), and proximal sequence element (PSE) (Denison and Weiner 1982). The pseudogenes map to a separate location on the long arm of chromosome 1 (1q12-21) (Lindgren et al 1985). The term ''pseudogene'' has been assigned to gene sequences that resemble real genes but contain base changes, deletions, and/or insertions that disrupt their ability to encode a functional protein (Balakirev and Ayala 2003;Zheng et al 2007).…”

Analysis of the human immunodeficiency virus-1 RNA packageome

“…For example, some reads originated from 3 ′ extended forms of the spliceosomal U1 snRNA. Human U1 snRNAs are encoded by a multicopy gene family located on the short arm of chromosome 1, while some pseudogenes and variant genes cluster on the long arm at 1q12-21 (Lindgren et al 1985;O'Reilly et al 2013). Our data set contained reads derived from both "wild-type" U1 genes (RNU1-1) and a variant locus (RNvU6-8) (Fig.…”

Adenovirus Type 12-Induced Fragility of the Human RNU2 Locus Requires U2 Small Nuclear RNA Transcriptional Regulatory Elements

“…Since these four sites are not preferential targets for adenoviral integration (reference 32, but see reference 52), virally inducible fragility must be an intrinsic property of the underlying chromosomal regions, perhaps reflecting some unusual aspect of chromatin structure, gene organization, transcription, or DNA replication. Remarkably, three of the four sites appear to colocalize with large tandem arrays of genes encoding small, abundant, ubiquitously expressed structural RNAs-the RNU1 locus encoding U1 small nuclear RNA (snRNA) at 1p36 (23,35), the RNU2 locus encoding U2 snRNA at 17q21-22 (14,22), and the RN5S locus encoding 5S rRNA at 1q42-43 (47,48). The fourth fragile site colocalizes with the PSU1 locus at 1q21 (23), an old and highly divergent family of U1 snRNA genes that are no longer expressed as stable U1 snRNA (24) but which may still retain active transcriptional regulatory elements.…”