Synthesis of U1 RNA in isolated mouse cell nuclei: initiation and 3'-end formation

Expression of histone-U1 snRNA chimeric genes: U1 promoters are compatible with histone 3' end formation

Chimeric genes which fuse the mouse histone H2a gene and the mouse U1b gene were constructed and introduced into CHO cells by cotransfection. In the UH genes, the U1b gene promoter and the start of the U1b gene were fused to the H2a gene in the 5' untranslated region. In the HU genes, the U1b 3' end was inserted into the 3' untranslated region of the H2a gene replacing the normal histone 3' end. Transcripts from the UH genes initiated at the start of the U1 gene and ended at the normal histone 3' end. Transcripts from the HU chimeric genes did not end at the U1 3' end but extended at least 80 nucleotides further and had heterogeneous 3' ends. Placing both a U1 snRNA promoter and a U1 snRNA 3' end around a histone coding region resulted in transcripts which initiate and terminate at the appropriate U1 ends. These results are consistent with previous reports that formation of the U1 3' ends require U1 promoters, but indicate that the histone 3' end can be formed on transcripts initiating at U1 promoters. The transcripts initiated at the U1 start site and ending at the histone 3' end are present on polyribosomes and show proper posttranscriptional regulation.

Pac1p, an RNase III homolog, is required for formation of the 3' end of U2 snRNA in Schizosaccharomyces pombe

Like its homologs in higher eukaryotes, the U2 snRNA in Schizosaccharomyces pombe is transcribed by RNA polymerase II and is not polyadenylated. Instead, an RNA stem-loop structure located downstream of the U2 snRNA coding sequence and transcribed as part of a 3' extended precursor serves as a signal for 3'-end formation. We have identified three mutants that have temperature-sensitive defects in U2 snRNA 3'-end formation. In these mutants, the synthesis of the major snRNAs is also affected and unprocessed rRNA precursors accumulate at the restrictive temperature. Two of these mutants contain the same G-to-A transition within the pac1 gene, whereas the third contains a lesion outside the pac1 locus, indicating that at least two genes are involved. The pac1+ gene is codominant with the mutant allele and can rescue the temperature-sensitive phenotype and the defects in snRNA and rRNA synthesis, if overexpressed. In vitro, Pac1p, an RNase III homolog, can cleave a synthetic U2 precursor within the signal for 3'-end formation, generating a product that is a few nucleotides longer than mature U2 snRNA. In addition, U2 precursors are cleaved and trimmed to the mature size in extracts made from wild-type S. pombe cells. However, extracts made from pac1 mutant cells are unable to do so unless they are supplemented with purified recombinant Pac1p. Thus, the 3' end of S. pombe U2 snRNA is generated by a processing reaction that requires Pac1p and an additional component, and can be dissociated from transcription in vitro.

Pac1p, an RNase III homolog, is required for formation of the 3' end of U2 snRNA in Schizosaccharomyces pombe

Like its homologs in higher eukaryotes, the U2 snRNA in Schizosaccharomyces pombe is transcribed by RNA polymerase II and is not polyadenylated. Instead, an RNA stem-loop structure located downstream of the U2 snRNA coding sequence and transcribed as part of a 3' extended precursor serves as a signal for 3'-end formation. We have identified three mutants that have temperature-sensitive defects in U2 snRNA 3'-end formation. In these mutants, the synthesis of the major snRNAs is also affected and unprocessed rRNA precursors accumulate at the restrictive temperature. Two of these mutants contain the same G-to-A transition within the pac1 gene, whereas the third contains a lesion outside the pac1 locus, indicating that at least two genes are involved. The pac1+ gene is codominant with the mutant allele and can rescue the temperature-sensitive phenotype and the defects in snRNA and rRNA synthesis, if overexpressed. In vitro, Pac1p, an RNase III homolog, can cleave a synthetic U2 precursor within the signal for 3'-end formation, generating a product that is a few nucleotides longer than mature U2 snRNA. In addition, U2 precursors are cleaved and trimmed to the mature size in extracts made from wild-type S. pombe cells. However, extracts made from pac1 mutant cells are unable to do so unless they are supplemented with purified recombinant Pac1p. Thus, the 3' end of S. pombe U2 snRNA is generated by a processing reaction that requires Pac1p and an additional component, and can be dissociated from transcription in vitro.

Increasing the distance between the snRNA promoter and the 3' box decreases the efficiency of snRNA 3'-end formation

Chimeric genes which contained the mouse U1b snRNA promoter, portions of the histone H2a or globin coding regions and the U1b 3'-end followed by a histone 3'-end were constructed. The distance between the U1 promoter and the U1 3' box was varied between 146 and 670 nt. The chimeric genes were introduced into CHO cells by stable transfection or into Xenopus oocytes by microinjection. The efficiency of utilization of the U1 3' box, as measured by the relative amounts of transcripts that ended at the U1 3' box and the histone 3'-end, was dependent on the distance between the promoter and 3'-end box. U1 3'-ends were formed with >90% efficiency on transcripts shorter than 200 nt, with 50-70% efficiency on transcripts of 280-400 nt and with only 10-20% efficiency on transcripts >500 nt. Essentially identical results were obtained after stable transfection of CHO cells or after injecting the genes into Xenopus oocytes. The distance between the U1 promoter and the U1 3' box must be <280 nt for efficient transcription termination at the U1 3' box, regardless of the sequence transcribed.

Methylated cap structures in eukaryotic RNAs: structure, synthesis and functions

There are more than twenty capped small nuclear RNAs characterized in eukaryotic cells. All the capped RNAs appear to be involved in the processing of other nuclear premessenger or preribosomal RNAs. These RNAs contain either trimethylguanosine (TMG) cap structure or methylated gamma phosphate (Mppp) cap structure. The TMG capped RNAs are capped with M7G during transcription by RNA polymerase II and trimethylated further post-transcriptionally. The Mppp-capped RNAs are transcribed by RNA polymerase III and also capped post-transcriptionally. The cap structures improve the stability of the RNAs and in some cases TMG cap is required for transport of the ribonucleoproteins from cytoplasm to the nucleus. Where tested, the cap structures were not essential for their function in processing other RNAs.

A 7 bp mutation converts a human RNA polymerase II snRNA promoter into an RNA polymerase III promoter

The human U2 snRNA promoter directs the formation of a specialized RNA polymerase II transcription complex that recognizes the snRNA gene 3' box as a signal for RNA 3' end formation. In contrast, the human U6 promoter is recognized by RNA polymerase III and transcription terminates in a run of Ts. We show that transcription from the U6 promoter is dependent on a sequence similar to the U2 proximal element and on an AT-rich element centered around position -27. Mutation of the AT-rich element induces RNA polymerase II transcription from the U6 promoter, whereas insertion of this element within the U2 promoter converts it into a predominantly RNA polymerase III promoter. The site of transcription termination always correlates with the nature of the transcribing polymerase: the 3' box with RNA polymerase II and a run of Ts with RNA polymerase III. Thus, a single element determines the RNA polymerase specificity of snRNA promoters and hence the site of transcription termination.

Effect of ultraviolet light on the expression of genes for human U1 RNA

Two types of UV-light-induced inhibitions of the synthesis of small nuclear RNA species U1, U2, U3, U4, and U5 were described previously: an immediate inhibition and a separate, delayed suppression that requires 1-2 hr of postirradiation cell incubation and UV doses that are about tenfold lower. In the present report, U1 RNA transcription in isolated nuclei from HeLa cells, assayed by RNAase T1 protection, reproduced the delayed inhibition. The sizes of the protected RNA fragments suggest that it is the initiation of U1 RNA transcription that is blocked during this inhibition. Transient expression of a marked human U1 RNA gene that contains 425 and 92 nucleotides of the 5' and 3' flanking sequences, respectively, showed delayed, but not immediate inhibition (while the endogenous U1 RNA genes exhibited immediate suppression). This indicates that continuity of the U1 gene flanking sequences beyond those segments and/or chromosomal integration of the U1 gene are not needed for the delayed inhibition, but may be required for the immediate inhibition. Irradiation of a U1 RNA gene, followed by its injection into Xenopus laevis oocyte nuclei, did not reproduce the immediate or delayed inhibitions. This suggests that direct UV radiation damage to DNA in the U1 RNA gene region is not the critical lesion in either the immediate or delayed UV-light-induced inhibitions of U1 RNA synthesis. In addition, the RNAase T1 protection pattern of transcripts synthesized in isolated nuclei from nonirradiated HeLa cells suggests that these cells may produce small amounts of U1 RNA molecules with variant nucleotide sequences in the mature region of the transcript.