Formation of the 3' end on U snRNAs requires at least three sequence elements

Structure of the catalytic core of the Integrator complex

The Integrator is a specialized 3' end-processing complex involved in cleavage and transcription termination of a subset of nascent RNA polymerase II transcripts, including small nuclear RNAs (snRNAs). We provide evidence of the modular nature of the Integrator complex by biochemically characterizing its two subcomplexes, INTS5/8 and INTS10/13/14. Using cryoelectron microscopy (cryo-EM), we determined a 3.5-Å-resolution structure of the INTS4/9/11 ternary complex, which constitutes Integrator's catalytic core. Our structure reveals the spatial organization of the catalytic nuclease INTS11, bound to its catalytically impaired homolog INTS9 via several interdependent interfaces. INTS4, a helical repeat protein, plays a key role in stabilizing nuclease domains and other components. In this assembly, all three proteins form a composite electropositive groove, suggesting a putative RNA binding path within the complex. Comparison with other 3' end-processing machineries points to distinct features and a unique architecture of the Integrator's catalytic module.

The 3' end formation in small RNAs

Small RNAs are a major class of RNAs along with transfer RNAs, ribosomal RNAs, and messenger RNAs. They vary in size from less than 100 nucleotides to several thousand nucleotides and have been identified and characterized both in prokaryotes and eukaryotes. Small RNAs participate in a variety of cellular functions including regulating RNA synthesis, RNA processing, guiding modifications in RNA, and in transport of proteins. Small RNAs are generated by a series of posttranscriptional processing steps following transcription. While RNA 5' end structure, 5' cap formation, and RNA processing mechanisms have been fairly well characterized, the 3' end processing is poorly understood. Recent data point to an emerging theme in small RNAs metabolism in which the 3' end processing is mediated by the exosome, a large multienzyme complex. In addition to removal of nucleotides by the exosome, there is simultaneous rebuilding of the 3' end of some small RNA by adenylation and/or uridylation. This review presents a picture of both degradative and rebuilding reactions operative on the 3' end of some small RNA molecules in prokaryotes and eukaryotes.

Non-mRNA 3' end formation: how the other half lives

The release of nascent RNA from transcribing RNA polymerase complexes is required for all further functions carried out by RNA molecules. The elements and processing machinery involved in 3' end formation therefore represent key determinants in the biogenesis and accumulation of cellular RNA. While these factors have been well-characterized for messenger RNA, recent work has elucidated analogous pathways for the 3' end formation of other important cellular RNA. Here, we discuss four specific cases of non-mRNA 3' end formation-metazoan small nuclear RNA, Saccharomyces cerevisiae small nuclear RNA, Schizosaccharomyces pombe telomerase RNA, and the mammalian MALAT1 large noncoding RNA-as models of alternative mechanisms to generate RNA 3' ends. Comparison of these disparate processing pathways reveals an emerging theme of evolutionary ingenuity. In some instances, evidence for the creation of a dedicated processing complex exists; while in others, components are utilized from the existing RNA processing machinery and modified to custom fit the unique needs of the RNA substrate. Regardless of the details of how non-mRNA 3' ends are formed, the lengths to which biological systems will go to release nascent transcripts from their DNA templates are fundamental for cell survival.

U1-like snRNAs lacking complementarity to canonical 5' splice sites

We have detected a surprising heterogeneity among human spliceosomal U1 small nuclear RNA (snRNA). Most interestingly, we have identified three U1 snRNA variants that lack complementarity to the canonical 5' splice site (5'SS) GU dinucleotide. Furthermore, we have observed heterogeneity among the identified variant U1 snRNA genes caused by single nucleotide polymorphism (SNP). The identified snRNAs were ubiquitously expressed in a variety of human tissues representing different stages of development and displayed features of functional spliceosomal snRNAs, i.e., trimethylated cap structures, association with Sm proteins and presence in nuclear RNA-protein complexes. The unanticipated heterogeneity among spliceosomal snRNAs could contribute to the complexity of vertebrates by expanding the coding capacity of their genomes.

The U8 snoRNA gene family: identification and characterization of distinct, functional U8 genes in Xenopus

U8 snoRNA is the RNA component of a small nucleolar ribonucleoprotein (U8 snoRNP) required for accumulation of mature 5.8S and 28S rRNAs, components of the large ribosomal subunit. We have identified two putative U8 genes in Xenopus laevis. Sequence analysis of the coding regions of these two genes indicate that both differ at several positions from the previously characterized U8 RNA and that the two differ from each other. Functional analysis of these genes indicates that both are transcribed in vivo, produce stable U8 transcripts, and are capable of facilitating pre-rRNA processing in vivo. These data demonstrate that natural sequence variation exists among the U8 snoRNA genes in Xenopus. Alignment of these three Xenopus U8 sequences with the previously described mammalian U8 homologues in mouse, rat and human has provided information about evolutionarily conserved sequence and structural elements in U8 RNA. Identification and functional characterization of these naturally occurring variants in Xenopus has helped identify regions in U8 RNA that may be critical for function.

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.

U1 snRNA is cleaved by RNase III and processed through an Sm site-dependent pathway

Core snRNP proteins bind snRNA through the conserved Sm site, PuA(U)n>/=3GPu. While yeast U1 snRNA has three matches to the Sm consensus, the U1 3'-terminal Sm site was found to be both necessary and sufficient for U1 function. Mutation of this site inhibited pre-mRNA splicing, blocked cell division and resulted in the accumulation of two 3'-extended forms of the U1 snRNA. Cells which harbor the Sm site mutation lack mature U1 RNA (U1alpha) but have a minor polyadenylated species, U1gamma, and a prominent, non-polyadenylated species, U1beta. Metabolic depletion of the essential Sm core protein, Smd1p, also resulted in the increased accumulation of U1beta and U1gamma. In vitro, synthetic U1 precursors were cleaved by Rnt1p (RNase III) very near the U1beta 3'-end observed in vivo. We propose that U1beta is an Rnt1p-cleaved intermediate and that U1 maturation to the U1alpha form occurs through an Sm-sensitive step. Interestingly, both U1alpha and a second, much longer RNA, U1straightepsilon, were produced in an rnt1 mutant strain. These results suggest that yeast U1 snRNA processing may progress through Rnt1p-dependent and Rnt1p-independent pathways, both of which require a fun-ctional Sm site for final snRNA maturation.

Alternative 3'-end processing of U5 snRNA by RNase III

The cellular components required to form the 3' ends of small nuclear RNAs are unknown. U5 snRNA from Saccharomyces cerevisiae is found in two forms that differ in length at their 3' ends (U5L and U5S). When added to a yeast cell free extract, synthetic pre-U5 RNA bearing downstream genomic sequences is processed efficiently and accurately to generate both mature forms of U5. The two forms of U5 are produced in vitro by alternative 3'-end processing. A temperature-sensitive mutation in the RNT1 gene encoding RNase III blocks accumulation of U5L in vivo. In vitro, alternative cleavage of the U5 precursor by RNase III determines the choice between the two multistep pathways that lead to U5L and U5S, one of which (U5L) is strictly dependent on RNase III. These results identify RNase III as a trans-acting factor involved in 3'-end formation of snRNA and show how RNase III might regulate alternative RNA processing pathways.

Functional characterization of ribozymes expressed using U1 and T7 vectors for the intracellular cleavage of ANF mRNA

Hammerhead ribozymes targeted to various GUC or GUA sites on rat atrial natriuretic factor (ANF) mRNA were developed. The catalytic activity of ribozymes to four of these sites, synthesized by transcription off synthetic oligodeoxynucleotide duplexes, was studied in detail. In vitro, ribozyme-mediated cleavage was highly Mg(2+)-dependent, and at concentrations approaching those found intracellularly, the rate but not the extent of cleavage was markedly reduced. To test for cellular activity, synthetic genes encoding the ribozymes were cloned between the initiation and termination sequences of the U1snRNA gene or between the T7RNA polymerase promoter and terminator sequences in pSP64. Both constructs had defined initiation and termination sequences to minimize transcript size and for message stability. In vitro the addition of T7 or U1 terminator sequences had variable effects on catalytic activity, presumably due to structural interactions between the ribozyme and the added sequence. The ribozyme-encoding plasmids were cotransfected with an expression plasmid containing a rat ANF cDNA into COS-1 cells using a liposome method, which provided high-level transfection efficiency. Quantitation of ANF mRNA by RNase protection showed marked decreases in ANF transcript levels with both the U1- and the T7-expressed ribozymes directed at three of the four sites on ANF mRNA. With all constructs, target accessibility, determined in vitro, was a more important determinant of intracellular ANF mRNA cleavage than catalytic activity per se. ANF mRNA cleavage was not merely due to an antisense effect, since a mutant construct that was catalytically inactive but could still bind produced less cleavage than the corresponding wild-type ribozyme construct. These findings indicate that both U1 and T7 vector systems provide efficient ribozyme expression for the intracellular cleavage of target mRNA.

Alternative promoter usage of the Fos-responsive gene Fit-1 generates mRNA isoforms coding for either secreted or membrane-bound proteins related to the IL-1 receptor

Fit-1 has been identified previously as a Fos-responsive gene of rat fibroblasts. Here we show that Fit-1 is directly regulated by the estrogen-inducible transcription factor Fos-ER and that it belongs to the family of delayed early genes. Two different mRNA isoforms are expressed from the Fit-1 gene. The Fit-1M mRNA isolated from spleen codes for a membrane-bound protein which is most closely related in its extracellular, transmembrane and intracellular domains to the type I interleukin-1 (IL-1) receptor. The Fit-1S mRNA of fibroblasts directs, instead, the synthesis of a secreted protein consisting of only the extracellular domain. Analysis of the exon-intron structure of the Fit-1 gene indicated that the Fit-1S and Fit-1M mRNAs are transcribed from two different promoters and that the sequence differences at their 3' ends result from alternative 3' processing. Northern blot analysis with specific 5' and 3' probes directly demonstrated tight coupling between alternative promoter usage and 3' processing of the Fit-1 transcripts. The orthologous gene of the mouse (known as T1 or ST2) is expressed during ontogeny first in the fetal liver of the embryo and then in lung and hematopoietic tissues of the adult. The mRNA coding for the membrane-bound protein is more abundantly expressed in all of these tissues, while the transcript for the secreted form predominates in fibroblasts and mammary epithelial cells. Differential regulation of two distinct promoters is thus used to determine the ratio between secreted and membrane-bound forms of Fit-1 (T1/ST2) which may modulate signaling in response to IL-1.

A transcriptional analysis of the gene encoding mouse U7 small nuclear RNA

Expression of the U7 gene, encoding mouse U7 snRNA, following microinjection into Xenopus oocytes is both accurate and efficient, giving rise to mature U7 snRNA and a precursor with an 8-nucleotide (nt) 3' extension. The mouse U7 gene promoter, which is similar to that of the vertebrate major U genes comprising a DSE, a PSE and a 3' box, with the same spatial arrangement, is as efficient as the Xenopus U2 gene promoter in this assay. A deletion analysis of the mouse U7 gene identified sequences downstream from the 3' box, within the region (nt +74 to +196), which seem to have a negative regulatory effect upon the frequency of transcription initiation and are also required for accurate 3' end formation. Sequences in the nt -1699 to -431 region also seemed to have a negative effect on the level of transcription. In addition, sequences upstream from the PSE, within the nt -65 to -421 region, are necessary for accurate and efficient synthesis of mature U7 snRNA. Finally, the mouse U7 snRNA may not form a functional snRNP in Xenopus oocytes due to defective snRNP assembly and/or nuclear import.

A mutation in a single gene of Schizosaccharomyces pombe affects the expression of several snRNAs and causes defects in RNA processing

A bank of temperature sensitive (ts-) mutants of Schizosaccharomyces pombe was screened for snRNA expression mutants using an oligodeoxynucleotide that recognizes U2 RNA. One mutant with a novel phenotype was identified that has reduced steady-state levels of the spliceosomal snRNAs U1, U2, U4, U5 and U6. In addition, the mutant exhibits a temperature-dependent accumulation of aberrant U2 and U4 transcripts elongated at their 3' end. The steady-state concentration of the RNA component of RNase P is also reduced in the mutant, whereas the amount of U3 RNA, 7SL RNA, tRNA, rRNA and mRNA are the same as wild-type. Pre-mRNA, pre-tRNA and U6 RNA precursor processing are impaired in the mutant. Genetic analysis demonstrates that the snRNA defects are tightly linked to the ts- growth defect and are recessive. We have named this mutant snm1 to indicate a defect in snRNA maintenance. The data on snm1 suggest that a single trans-acting factor is essential for the maintenance of steady-state levels of several snRNAs and for proper 3' end formation of U2 and U4 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.

Function of the mammalian La protein: evidence for its action in transcription termination by RNA polymerase III

We have tested the hypothesis that the mammalian La protein, which appears to be required for accurate and efficient RNA polymerase III transcription, is a transcription termination factor. Our data suggest that 3' foreshortened transcripts generated in La's absence are components of a novel transcription intermediate containing a paused polymerase. These transcripts are produced by fractionated transcription complexes, are synthesized with kinetics different from full-length transcripts, and are chasable to completion from the stalled transcription complexes. Together, these findings argue that termination by RNA polymerase III requires auxilliary factor(s) and implicate La as such a factor. Since La appears to facilitate transcript completion and release and also binds the resulting RNA product, it may be a regulator of RNA polymerase III transcription.

Sequences linked to prokaryotic promoters can affect the efficiency of downstream termination sites

The efficiency of transcription termination at certain well-defined prokaryotic rho-independent terminators depends on the promoter unit from which transcription is initiated. Some promoter units allow substantial readthrough of strong termination signals, a phenomenon we term "factor-independent antitermination". This observation is not easily explained by current models for prokaryotic terminator function that consider the terminator to be a "cassette" involving only sequences and RNA transcript structures in the immediate region of the terminator or directly upstream. When transcription is carried out in vitro employing only purified Escherichia coli RNA polymerase, up to 20 times as many RNA polymerase molecules pass through a particular terminator when transcription is initiated from the E. coli tac promoter unit, as compared to transcription initiated from the T7A1 or rrnB P2 promoters. This effect cannot be attributed to antitermination factors separate from the core RNA polymerase. Similar differences in termination efficiency are found for the same promoters in vivo. These termination differences are affected by sequences just downstream from the start site for transcription, including those in the +25 region of the nascent transcript. These early transcribed sequences can confer factor-independent antitermination onto a heterologous promoter, but only when the sequences are precisely positioned relative to the start site for transcription. We have considered several possible models to explain how early transcribed sequences might affect termination, including those in which the 5' end of the transcript interacts with either the terminator RNA or the polymerase. We favor an alternative model in which these sequences interact with the core RNA polymerase to convert the enzyme from a termination-proficient state (T-state) to a conformation resistant to termination (R-state). Such enzyme conformations may be an important component of factor-dependent antitermination systems.

Two conserved domains of yeast U2 snRNA are separated by 945 nonessential nucleotides

Yeast U2 snRNA (1175 nucleotides) is six times larger than its mammalian counterpart (188 nucleotides). Using deletion analysis, we show that the molecule can be divided into three phenotypically distinct domains. As expected, the highly conserved 5' domain (approximately 120 nucleotides) is absolutely essential for viability. Surprisingly, however, deletion of the central 945 nucleotides has no effect on growth rate. In contrast, removal of sequences in the 3' terminal 110 nucleotides results in low numbers of slow-growing colonies; these cells contain U2 with altered 3' ends. This domain can be folded into a secondary structure that strongly resembles the 3' terminal stem-loop IV of human U2. We conclude that yeast U2 contains two functionally important elements. While the 5' domain is known to be directly involved in the splicing reaction, the 3' domain may function primarily in the generation of stable small nuclear ribonucleoprotein particles.

Three types of rat U1 small nuclear RNA genes with different flanking sequences are induced to express in vivo

There are about 50 copies of U1 RNA genes/pseudogenes in the rat genome. To date, we have isolated so far 25 phage clones carrying a U1 RNA gene/pseudogene from two rat genomic libraries. The 12 clones were selected by hybridization with the U1 RNA coding region under a stringent condition, and were mapped and sequenced. Here, we report three types of U1 RNA genes with different flanking sequences, all of which were shown to be induced to express in vivo by transfection with their polylinker-inserted maxi U1 RNA genes into cultured rat cells. Although these three classes of U1 RNA genes have few homologous flanking sequences, they provide both upstream and downstream of the genes two conserved blocks, which may possibly play an important role in U1 RNA expression.

Functional analysis of the sea urchin U7 small nuclear RNA

U7 small nuclear RNA (snRNA) is an essential component of the RNA-processing machinery which generates the 3' end of mature histone mRNA in the sea urchin. The U7 small nuclear ribonucleoprotein particle (snRNP) is classified as a member of the Sm-type U snRNP family by virtue of its recognition by both anti-trimethylguanosine and anti-Sm antibodies. We analyzed the function-structure relationship of the U7 snRNP by mutagenesis experiments. These suggested that the U7 snRNP of the sea urchin is composed of three important domains. The first domain encompasses the 5'-terminal sequences, up to about nucleotides 7, which are accessible to micrococcal nuclease, while the remainder of the RNA is highly protected and hence presumably bound by proteins. This region contains the sequence complementarities between the U7 snRNA and the histone pre-mRNA which have previously been shown to be required for 3' processing (F. Schaufele, G. M. Gilmartin, W. Bannwarth, and M. L. Birnstiel, Nature [London] 323:777-781, 1986). Nucleotides 9 to 20 constitute a second domain which includes sequences for Sm protein binding. The complementarities between the U7 snRNA sequences in this region and the terminal palindrome of the histone mRNA appear to be fortuitous and play only a secondary, if any, role in 3' processing. The third domain is composed of the terminal palindrome of U7 snRNA, the secondary structure of which must be maintained for the U7 snRNP to function, but its sequence can be drastically altered without any observable effect on snRNP assembly or 3' processing.

A common octamer motif binding protein is involved in the transcription of U6 snRNA by RNA polymerase III and U2 snRNA by RNA polymerase II

The structure of a Xenopus U6 gene promoter has been investigated. Three regions in the 5'-flanking sequences of the gene that are important for U6 expression are defined. Deletion of the first, between positions -156 and -280 relative to the site of transcription initiation, reduces transcription to roughly 5% of its original level. Deletion of the second, between -60 and -77, abolishes transcription. These regions contain not only functional but also sequence homology to the previously defined distal and proximal sequence elements (DSE and PSE) of the Xenopus U2 promoter, although U2 is transcribed by RNA polymerase II and U6 by RNA polymerase III. Competition experiments show that at least the distal sequence elements of the two promoters bind to a common factor both in vivo and in vitro. Part of the sequence recognized by this factor is the octamer motif (ATG-CAAAT). A sequence similar to the common RNA polymerase II TATA box is also shown to have an effect, albeit minor, on U6 transcription. The U6 coding region contains a good match to the A box, part of all previously characterized RNA polymerase III promoters. Deletion of this region has no apparent effect on the efficiency or accuracy of U6 transcription.

Identification of intrinsic termination sites in vitro for RNA polymerase II within eukaryotic gene sequences

We have identified and mapped several DNA sequences within a human histone gene (H3.3) at which in-vitro transcription by highly purified RNA polymerase II is efficiently terminated. Since transcription in our system involves only RNA polymerase II acting on a linear DNA template, these sequences contain "intrinsic" termination signals recognized by the polymerase protein itself. The existence of such signals within a gene suggests that efficient antitermination systems probably exist for mammalian transcription units. Alternatively, there could be a high frequency of premature transcription termination, or "polarity" for genes such as H3.3. Intrinsic transcription termination sites in H3.3 are located in sequences of consecutive thymidylate residues (5 to 8 nucleotides) on the non-transcribed DNA strand (T-runs), from which it is likely that such T-runs are elements of the intrinsic termination signal for RNA polymerase II. However, transcription proceeds without significant termination through many similar T-runs, from which it follows that these intrinsic termination signals include other elements. Since transcription is also terminated efficiently at these sites when the transcript remains bound along its full length as a DNA-RNA hybrid, it is unlikely that formation of specific RNA secondary structures in the transcript is a general element of the intrinsic termination signal. Although DNA sequences downstream from the coding portion of the mouse beta-globin gene have been implicated as sites of transcription termination in vivo, these regions do not contain strong intrinsic termination signals, and transcription in vitro proceeds through these regions almost undiminished. Transcriptional termination in this region in vivo may depend on the presence of termination factors or other intracellular elements, and there may be multiple classes of DNA signals that control eukaryotic termination.