Position-dependent function of a B block promoter element implies a specialized chromatin structure on the S.cerevisiae U6 RNA gene, SNR6.
The Saccharomyces cerevisiae U6 RNA gene, SNR6, is transcribed by RNA polymerase III (Pol III), but lacks the intragenic B block promoter element found in most other Pol III transcription units. Rather, the SNR6 B block element is located 120 bp downstream of the terminator. In contrast, the Schizosaccharomyces pombe U6 RNA gene has an intragenic B block sequence in a short intron. We show that the S.pombe U6 intron, when inserted into SNR6, can functionally replace the downstream B block in vitro but not in vivo. The in vivo expression defect is caused by at least three different effects of the insertion: (i) the S.pombe intron is inefficiently spliced in S.cerevisiae due to the short distance between the 5' splice site and branchpoint; (ii) the S.pombe B block sequence is suboptimal for S.cerevisiae; and (iii) a B block does not function well within the context of the SNR6 intron, especially when the gene is present at its normal chromosomal locus rather than on a plasmid. This last observation suggests that the chromatin structure of the SNR6 locus favors utilization of a downstream B block element. We also provide evidence that splicing of U6 RNA reduces its activity, presumably due to alterations in U6 RNA structure, localization and/or assembly into the spliceosome.
Kaiser
Michael W
MW
Department of Biomolecular Chemistry, University of Wisconsin Medical School, Madison, WI 53706-1532, USA.
Chi
Jing
J
Brow
David A
DA
D000483:Alleles; D001483:Base Sequence; D002843:Chromatin / Q000648:ultrastructure; D015825:Chromosomes, Fungal; D005800:Genes, Fungal; D007438:Introns; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D012322:RNA Precursors / Q000378:metabolism; D022821:RNA Splice Sites; D012326:RNA Splicing; D012331:RNA, Fungal / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012342:RNA, Small Nuclear / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012045:Regulatory Sequences, Nucleic Acid; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D012568:Schizosaccharomyces / Q000235:genetics; D014158:Transcription, Genetic
D002843:Chromatin; D012322:RNA Precursors; D022821:RNA Splice Sites; D012331:RNA, Fungal; D012342:RNA, Small Nuclear; C405486:U6 small nuclear RNA