Multiple, dispersed human U6 small nuclear RNA genes with varied transcriptional efficiencies

• Published in: Nucleic acids research Vol. 31; no. 9; pp. 2344 - 2352
• Main Authors: Domitrovich, Angela M., Kunkel, Gary R.
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.05.2003; Oxford Publishing Limited (England)
• Subjects: Acetylation; Base Sequence; Cell Line; Chromatin - metabolism; Chromosome Mapping; Genome, Human; Histones - metabolism; Humans; Multigene Family - genetics; Promoter Regions, Genetic - genetics; Protein Binding; RNA, Small Nuclear - genetics; Sequence Homology, Nucleic Acid; TATA-Box Binding Protein - metabolism; Transcription Factors - genetics; Transcription Factors - metabolism; Transcription, Genetic - genetics; Transfection
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkg331

Vertebrate U6 small nuclear RNA (snRNA) gene promoters are among the founding members of those recognized by RNA polymerase III in which all control elements for initiation are located in the 5′‐flanking region. Previously, one human U6 gene (U6‐1) has been studied extensively. We have identified a total of nine full‐length U6 loci in the human genome. Unlike human U1 and U2 snRNA genes, most of the full‐length U6 loci are dispersed throughout the genome. Of the nine full‐length U6 loci, five are potentially active genes (U6‐1, U6‐2, U6‐7, U6‐8 and U6‐9) since they are bound by TATA‐binding protein and enriched in acetylated histone H4 in cultured human 293 cells. These five all contain OCT, SPH, PSE and TATA elements, although the sequences of these elements are variable. Furthermore, these five genes are transcribed to different extents in vitro or after transient transfection of human 293 cells. Of the nine full‐length U6 loci, only U6‐7 and U6‐8 are closely linked and contain highly conserved 5′‐flanking regions. However, due to a modest sequence difference in the proximal sequence elements for U6‐7 and U6‐8, these genes are transcribed at very different levels in transfected cells.