Small Nuclear RNA Molecules Research Articles

The Integrator complex: an emerging complex structure involved in the regulation of gene expression by targeting RNA polymerase II.

The Integrator complex is a multisubunit complex that participates in the processing of small nuclear RNA molecules in eukaryotic cells by cleaving the 3' end. In protein-coding genes, Integrator is a key regulator of promoter-proximal pausing, release, and recruitment of RNA polymerase II. Research on Integrator has revealed its critical role in the regulation of gene expression and RNA processing. Dysregulation of the Integrator complex has been implicated in a variety of human diseases including cancer and developmental disorders. Therefore, understanding the structure and function of the Integrator complex is critical to uncovering the mechanisms of gene expression and developing potential therapeutic strategies for related diseases.

Computational analysis of spliced leader trans-splicing in the regenerative flatworm Macrostomum lignano reveals its prevalence in conserved and stem cell related genes.

In eukaryotes, trans-splicing is a process of nuclear pre-mRNA maturation where two different RNA molecules are joined together by the spliceosomal machinery utilizing mechanisms similar to cis-splicing. In diverse taxa of lower eukaryotes, spliced leader (SL) trans-splicing is the most frequent type of trans-splicing, when the same sequence derived from short small nuclear RNA molecules, called SL RNAs, is attached to the 5’ ends of different non-processed pre-mRNAs. One of the functions of SL trans-splicing is processing polycistronic pre-mRNA molecules transcribed from operons, when several genes are transcribed as one pre-mRNA molecule. However, only a fraction of trans-spliced genes reside in operons, suggesting that SL trans-splicing must also have some other, less understood functions. Regenerative flatworms are informative model organisms which hold the keys to understand the mechanism of stem cell regulation and specialization during regeneration and homeostasis. Their ability to regenerate is fueled by the division and differentiation of the adult somatic stem cell population called neoblasts. Macrostomum lignano is a flatworm model organism where substantial technological advances have been achieved in recent years, including the development of transgenesis. Although a large fraction of genes in M. lignano were estimated to be SL trans-spliced, SL trans-splicing was not studied in detail in M. lignano before. Here, we performed the first comprehensive study of SL trans-splicing in M. lignano. By reanalyzing the existing genome and transcriptome data of M. lignano, we estimate that 30 % of its genes are SL trans-spliced, 15 % are organized in operons, and almost 40 % are both SL trans-spliced and in operons. We annotated and characterized the sequence of SL RNA and characterized conserved cis- and SL transsplicing motifs. Finally, we found that a majority of SL trans-spliced genes are evolutionarily conserved and significantly over-represented in neoblast-specific genes. Our findings suggest an important role of SL trans-splicing in the regulation and maintenance of neoblasts in M. lignano.

RNA Splicing in the Transition from B Cells to Antibody-Secreting Cells: The Influences of ELL2, Small Nuclear RNA, and Endoplasmic Reticulum Stress.

In the transition from B cells to Ab-secreting cells (ASCs) many genes are induced, such as ELL2, Irf4, Prdm1, Xbp1, whereas other mRNAs do not change in abundance. Nonetheless, using splicing array technology and mouse splenic B cells plus or minus LPS, we found that induced and "uninduced" genes can show large differences in splicing patterns between the cell stages, which could influence ASC development. We found that ∼55% of these splicing changes depend on ELL2, a transcription elongation factor that influences expression levels and splicing patterns of ASC signature genes, genes in the cell-cycle and N-glycan biosynthesis and processing pathways, and the secretory versus membrane forms of the IgH mRNA. Some of these changes occur when ELL2 binds directly to the genes encoding those mRNAs, whereas some of the changes are indirect. To attempt to account for the changes that occur in RNA splicing before or without ELL2 induction, we examined the amount of the small nuclear RNA molecules and found that they were significantly decreased within 18 h of LPS stimulation and stayed low until 72 h. Correlating with this, at 18 h after LPS, endoplasmic reticulum stress and Ire1 phosphorylation are induced. Inhibiting the regulated Ire1-dependent mRNA decay with 4u8C correlates with the reduction in small nuclear RNA and changes in the normal splicing patterns at 18 h. Thus, we conclude that the RNA splicing patterns in ASCs are shaped early by endoplasmic reticulum stress and Ire1 phosphorylation and later by ELL2 induction.

Structure-Function Relationships in Miscoding by Sulfolobus solfataricus DNA Polymerase Dpo4: GUANINE N2,N2-DIMETHYL SUBSTITUTION PRODUCES INACTIVE AND MISCODING POLYMERASE COMPLEXES

Structure-Function Relationships in Miscoding by Sulfolobus solfataricus DNA Polymerase Dpo4: GUANINE N2,N2-DIMETHYL SUBSTITUTION PRODUCES INACTIVE AND MISCODING POLYMERASE COMPLEXES

Roles of the U5 snRNP in spliceosome dynamics and catalysis

Most protein-coding genes in eukaryotes are interrupted by non-coding intervening sequences (introns), which must be precisely removed from primary gene transcripts (pre-mRNAs) before translation of the message into protein. Intron removal by pre-mRNA splicing occurs in the nucleus and is catalysed by complex ribonucleoprotein machines called spliceosomes. These molecular machines consist of several small nuclear RNA molecules and their associated proteins [together termed snRNP (small nuclear ribonucleoprotein) particles], plus multiple accessory factors. Of particular interest are the U2, U5 and U6 snRNPs, which play crucial roles in the catalytic steps of splicing. In the present review, we summarize our current understanding of the role played by the protein components of the U5 snRNP in pre-mRNA splicing, which include some of the largest and most highly conserved nuclear proteins.

Henry Kunkel, Stephanie Smith, clinical immunology, and split genes.

The York Avenue (New York) 'ecosystem' from the 1940s through the 1980s enabled Henry Kunkel to apply new scientific methodology to understanding human disease. Stephanie Smith, a young woman with lupus, was treated at the Rockefeller University Hospital in the 1960s. Studies of her antinuclear antibodies by Kunkel and Eng Tan led to the discovery of a precipitin line specific for lupus, and the responsible antigen was designated Sm (for 'Smith'). This review outlines the history of Sm antigen from an interesting precipitin line to the identification of small nuclear RNA molecules and small nuclear ribonucleoproteins, and subsequently the discovery of RNA splicing. The story illustrates Henry Kunkel's approach to science, emphasizing how 'accidental' clinical observations, in the hands of skilled investigators, can have unexpected and potentially momentous implications.

Life with 6000 genes.

The genome of the yeast Saccharomyces cerevisiae has been completely sequenced through a worldwide collaboration. The sequence of 12,068 kilobases defines 5885 potential protein-encoding genes, approximately 140 genes specifying ribosomal RNA, 40 genes for small nuclear RNA molecules, and 275 transfer RNA genes. In addition, the complete sequence provides information about the higher order organization of yeast's 16 chromosomes and allows some insight into their evolutionary history. The genome shows a considerable amount of apparent genetic redundancy, and one of the major problems to be tackled during the next stage of the yeast genome project is to elucidate the biological functions of all of these genes.

CDNA cloning of a human autoimmune nuclear ribonucleoprotein antigen.

Sera from patients with systemic lupus erythematosus and other autoimmune disorders contain antibodies against nuclear proteins. One such autoantibody system, known as Sm, reacts with antigens associated with small nuclear RNA molecules. In this paper we report the use of Sm autoantibodies to isolate a cDNA clone for the mRNA of one of these nuclear antigens. A HeLa cell cDNA library was screened by message selection followed by autoantibody reaction of cell-free translation products. This led to the identification of a cDNA clone, p281, containing sequences complementary to mRNA for an Sm autoantibody-reactive, 11,000 Mr protein. This cloned Sm antigen comigrated with the small nuclear RNA-associated protein known as "E" and reacted with four out of four Sm autoantibodies that precipitate E protein from total mRNA translation products. RNA gel blot hybridization with clone p281 DNA revealed a poly(A)+ mRNA of approximately equal to 600 nucleotides in human and marmoset (New World primate) cells. Southern blot hybridization of HeLa cell and human lymphocyte DNA indicated the presence of 6-10 copies of p281-homologous sequences. Similar copy numbers were observed with genomic DNA from baboon, cat, and mouse, indicating that the Sm antigen mRNA sequence represented in p281 is conserved across three classes of the Mammalia (primates, carnivores, and rodents). However, no cross-hybridization of p281 was observed with frog or Drosophila DNA. In light of existing evidence that the mammalian Sm antigen E is a weaker autoantigen than other small nuclear RNA-associated proteins, these results suggest a possible correlation between a protein's capacity to serve as an autoantigen during breakdown of the host's immunological tolerance and its extent of evolutionary conservation, whereas the inverse relationship applies to conventional immunity. We suspect, as have others, that this is a clue to the mechanism of autoimmunity.

A simple immunoelectroblot technique for the rapid detection and sizing of capped small nuclear RNA molecules

We describe an immunoelectroblot procedure that allows the rapid detection and sizing of the capped small nuclear RNA molecules (U-RNAs). The procedure utilizes partial denaturation of total cellular RNA with formamide, electrophoresis of the RNA under partially denaturing conditions, electroblot transfer of the material to diethylaminoethyl (DEAE) membrane, and immunological detection of bound capped RNAs by interaction with iodinated anti-2,2,7-trimethylguanosine IgG. The technique, which in technical jargon would be called a “Northwestern,” offers several advantages over preparative immunoprecipitation since: 1) the potentially labile RNAs are fractionated by size prior to interaction with the IgG (and its endogenous nucleases); 2) the procedure utilizes tenfold less IgG (when the IgG is directly iodinated); 3) it provides information on the relative abundance of each U-RNA species without having to utilize in vivo-labeled RNA; and 4) it allows the detection of U-RNAs in the presence of excess ribosomal or transfer RNAs, even for invertebrate organisms where U-RNAs are ten- to 100-fold less abundant than in higher organisms. Glyoxal or formaldehyde-denatured RNA, required for the binding of RNA to the more widely used nitrocellulose membrane, gave a twofold weaker signal than formamide-denatured RNA in this assay, presumably due to disruption of the antigencity of the cap structure by these denaturants. The technique is demonstrated for the low abundance U-RNAs of the silkworm Bombyx mori. Possible future applications are discussed.

Polypeptide components of human small nuclear ribonucleoproteins.

Small nuclear RNA molecules (snRNAs) are associated with polypeptides in vivo, forming small nuclear ribonucleoprotein complexes (snRNPs). These snRNP complexes are targets for certain autoimmune antisera. Antisera of the type anti-Sm precipitate (and therefore define) a class including U1, U2, U4, U5, and U6 snRNAs, whereas antisera of the anti-RNP type precipitate only U1 snRNPs. We used these two types of autoimmune antisera (from patients with systemic lupus erythematosus) to study the polypeptide components in human cells. Sequential immunoprecipitation of the complexes from nuclear extracts with anti-RNP and anti-Sm antibodies, along with radioimmunoassay of protein transfers, identified four polypeptides of 14,000 (P14), 17,000 (P17), 26,000 (P26), and 27,000 (P27) daltons that are present on all members of this class, whereas a 68,000-dalton (P68) polypeptide is present only on U1 snRNPs. Based on the radioimmunoassay, three of these polypeptides, P17, P26, and P27, are also the antigens for anti-Sm antisera, whereas P68 is the antigen for anti-RNP antisera. Long-term phosphate labeling experiments show that the only detectably phosphorylated polypeptide is P68, which contains phosphoserine.

Transcription of repeated sequences of the mouse B1 family in friend erythroleukaemic cells: Intermolecular RNA-RNA duplex formation between polyadenylated and non-polyadenylated nuclear RNAs

It has been shown by previous workers that heterogeneous nuclear RNA in eucaryotic cells exists in the form of a complex with small nuclear RNA molecules, which are involved in RNA processing. It is demonstrated in this report that polyadenylated RNAs from the nuclei of Friend erythroleukaemic cells are isolated as complexes with a wide spectrum of non-polyadenylated RNAs. The associated non-polyadenylated RNAs are mainly of high molecular weight (15 to 30 S), but include the 4.5 S and 7 S RNA species. The complexes can be disrupted by denaturation with dimethyl sulphoxide, but also can be reconstituted by reannealing under appropriate stringency conditions. Saturation experiments involving unique DNA probes have shown that the associated non-polyadenylated RNA has a high base sequence complexity. It is shown that complexes involving poly(A) + nuclear RNA contain transcripts of the highly repeated mouse B1 family. The vast majority of these repetitive sequence transcripts are removed by processing within the nucleus and are barely detectable in poly(A) + polysomal RNA. Double-stranded RNA prepared from the nuclear complexes by digestion with ribonucleases contains sequences complementary to the mouse B1 family, suggesting that these may be involved in duplex formation between polyadenylated and non-polyadenylated RNAs. The possible role of interrnolecular RNA-RNA duplexes involving repetitive sequences in the folding of messenger RNA precursors prior to removal of introns and splicing is discussed.

Small nuclear RNA molecules that regulate nuclease accessibility in specific chromatin regions of meiotic cells

One of the factors regulating the accessibility of specific DNA sequences to endonuclease nicking during meiosis is a group of small nuclear RNA molecules, 125 nucleotides in length and transcribed by RNA polymerase III. These molecules (referred to as PsnRNA) are synthesized during meiotic prophase, when chromosomes are undergoing homologous pairing or are already paired. Accessibility to the meiotically active DNA sequences (P DNA) depends on an as-yet-undefined alteration in chromatin structure. PsnRNA is a critical factor in the alteration; it cannot be replaced by other forms of RNA. The specificity of the chromatin sites altered by PsnRNA appears to be a function of sequence complementarity between it and P DNA. Under in vivo conditions the effective action of PsnRNA depends on homologous chromosome pairing. Chromatin sites housing P-DNA sequences in nuclei isolated from cells lacking homologous pairing are not affected by meiotic endonuclease or DNAase II. Accessibility to these sites can be effected by incubation of the nuclei with PsnRNA, but only if the nuclei are from zygotene-pachytene cells. Analyses of pachytene nuclei preincubated with PsnRNA indicate that PsnRNA renders chromatin accessible to at least two endonucleases, meiotic endonuclease and DNAase II, and that it also limits such accessibility to regions housing the complementary P-DNA sequences.

Antibodies to small nuclear RNAs complexed with proteins are produced by patients with systemic lupus erythematosus

Patients with systemic lupus erythematosus often possess antibodies against two nuclear antigens called Sm and RNP (ribonucleoprotein). We have established the molecular identity of these antigens by analyzing immune precipitates of nuclear extracts from mouse Ehrlich ascites cells labeled with (32)P and (35)S. Anti-Sm serum selectively precipitates six small nuclear RNA molecules (snRNAs); anti-RNP serum reacts with only two of these; and a third serum, characterized as mostly anti-RNP, precipitates a subset of three snRNA bands. Three of the six RNAs are identified by fingerprint analysis as the previously characterized and highly abundant nucleoplasmic snRNA species U1a (171 nucleotides), U1b, and U2 (196 nucleotides). The other three RNAs (U4, U5, and U6) likewise are uridine rich and contain modified nucleotides, but they are smaller, with lengths of about 145, 120, and 95 residues, respectively. Each of the six snRNAs is complexed with and apparently antigenic by virtue of association with specific proteins. All three sera precipitate an identical complement of seven different polypeptides ranging in molecular weight from 12,000 to 35,000; these proteins are abundant in nuclear extracts, but are neither histones nor the major polypeptides comprising the 30S heterogeneous nuclear RNP particles of mammalian nuclei. Our data argue that each of the six snRNAs exists in a separate small nuclear ribonucleoprotein (snRNP) complex with a total molecular weight of about 175,000. We find that human antisera also precipitate snRNAs from a wide range of vertebrate species and from arthropods. We discuss the antigenic snRNPs in relation to the published literature on snRNAs and nuclear RNPs and consider possible functions of snRNPs in nuclear processes.

Small nuclear RNA molecules in nuclear ribonucleoprotein complexes from mouse erythroleukemia cells.

Small nuclear RNA molecules in nuclear ribonucleoprotein complexes from mouse erythroleukemia cells.

A new class of small nuclear RNA molecules synthesized by a type I RNA polymerase in hela cells

A new class of previously undetected small RNA molecules with a range of discrete sizes between 6S and 10S has been identified in HeLa cell nuclei. They differ in size and location from the previously described small nuclear RNA species (snRNA). These RNA molecules were initially found by selective RNA labeling in vitro in isolated nuclei. The in vitro products migrate in gel electrophoresis in the region from 6–10S with predominant components between 8S and 10S. They are labeled in the presence of very high concentrations of α-amanitin (150–400 μg/ml), suggesting they are synthesized by a type I polymerase. Unlike the major polymerase I product, ribosomal precursor RNA, however, these molecules are found in the nucleoplasm and their labeling is not affected by pretreatment of cells with low concentrations of actinomycin D (0.04 μg/ml). Their formation by a presumptive polymerase I type of enzyme is the basis of their tentative designation as small nuclear polymerase I (snPI) RNAs. The snPI RNA molecules appear to be associated with chromatin and the nuclear matrix. They can be selectively eluted from nuclei leaving most of hnRNA behind. This association is used as the basis of fractionation procedures which separate these molecules from hnRNA and permit the demonstration of the synthesis of at least the most predominant of these RNA molecules in vivo. w