Small RNA molecules related to the Alu family of repetitive DNA sequences

Heat shock increases lifetime of a small RNA and induces its accumulation in cells

4.5SH and 4.5SI RNA are two abundant small non-coding RNAs specific for several related rodent families including Muridae. These RNAs have a number of common characteristics such as the short length (about 100nt), transcription by RNA polymerase III, and origin from Short Interspersed Elements (SINEs). However, their stabilities in cells substantially differ: the half-life of 4.5SH RNA is about 20min, while that of 4.5SI RNA is 22h. Here we studied the influence of cell stress such as heat shock or viral infection on these two RNAs. We found that the level of 4.5SI RNA did not change in stressed cells; whereas heat shock increased the abundance of 4.5SH RNA 3.2-10.5 times in different cell lines; and viral infection, 5 times. Due to the significant difference in the turnover rates of these two RNAs, a similar activation of their transcription by heat shock increases the level of the short-lived 4.5SH RNA and has minor effect on the level of the long-lived 4.5SI RNA. In addition, the accumulation of 4.5SH RNA results not only from the induction of its transcription but also from a substantial retardation of its decay. To our knowledge, it is the first example of a short-lived non-coding RNA whose elongated lifetime contributes significantly to its accumulation in stressed cells.

Regulation of gene expression via retrotransposon insertions and the noncoding RNA 4.5S RNAH

Short interspersed elements (SINEs) comprise a significant portion of mammalian genomes and regulate gene expression through a variety of mechanisms. Here, we show that Myodonta clade-specific 4.5S RNAH (4.5SH), an abundant nuclear noncoding RNA that is highly homologous to the retrotransposon SINE B1, controls the expression of reporter gene that contains the antisense insertion of SINE B1 via nuclear retention. The depletion of endogenous 4.5SH with antisense oligonucleotides neutralizes the nuclear retention and changes the subcellular distribution of the reporter transcripts containing the antisense SINE B1 insertion. Importantly, endogenous transcripts with antisense SINE B1 were increased in the cytoplasm after knockdown of 4.5SH, leading to a decrease in cellular growth. We propose a tentative hypothesis that the amplification of the 4.5SH cluster in specific rodent species might delineate their evolutionary direction via the regulation of genes containing the antisense insertion of SINE B1.

Multiple Roles of Alu-Related Noncoding RNAs

Repetitive Alu and Alu-related elements are present in primates, tree shrews (Scandentia), and rodents and have expanded to 1.3 million copies in the human genome by nonautonomous retrotransposition. Pol III transcription from these elements occurs at low levels under normal conditions but increases transiently after stress, indicating a function of Alu RNAs in cellular stress response. Alu RNAs assemble with cellular proteins into ribonucleoprotein complexes and can be processed into the smaller scAlu RNAs. Alu and Alu-related RNAs play a role in regulating transcription and translation. They provide a source for the biogenesis of miRNAs and, embedded into mRNAs, can be targeted by miRNAs. When present as inverted repeats in mRNAs, they become substrates of the editing enzymes, and their modification causes the nuclear retention of these mRNAs. Certain Alu elements evolved into unique transcription units with specific expression profiles producing RNAs with highly specific cellular functions.

5'-flanking sequences can dramatically influence 4.5SH RNA gene transcription by RNA-polymerase III

4.5SH RNA is a 94 nt small nuclear RNA with an unknown function. Hundreds of its genes are present in the genomes of rodents of six families including Muridae. 4.5SH RNA genes contain an internal RNA-polymerase III promoter consisting of A and B boxes. Here we studied the influence of 5'-flanking sequences on the transcription of a mouse 4.5SH RNA gene. We found that replacement of the upstream sequence can dramatically change the 4.5SH RNA gene transcription efficiency. Various DNA fragments inserted immediately upstream from 4.5SH RNA gene completely inhibited its in vitro transcription, whereas others promoted it. The shortening of the native mouse 5'-flanking sequence of 4.5SH RNA gene to 42 bp resulted in the activation of an additional illegal transcription start site in upstream region. Transcription of the 4.5SH RNA gene with various upstream sequences in transfected HeLa cells revealed the differences between the tests performed in vivo and in vitro: in whole cells, only the construct with 5'-flanking native sequence could be transcribed. Apparently, at least some regions of the native 5'-flanking sequence of 4.5SH RNA genes have been selected during evolution for high transcription activity.

Mouse nucleolin binds to 4.5S RNAh, a small noncoding RNA

4.5S RNAh is a rodent-specific small noncoding RNA that exhibits extensive homology to the B1 short interspersed element. Although 4.5S RNAh is known to associate with cellular poly(A)-terminated RNAs and retroviral genomic RNAs, its function remains unclear. In this study, we analyzed 4.5S RNAh-binding proteins in mouse nuclear extracts using gel mobility shift and RNA-protein UV cross-linking assays. We found that at least nine distinct polypeptides (p170, p110, p93, p70, p48, p40, p34, p20, and p16.5) specifically interacted with 4.5S RNAhin vitro. Using anti-La antibody, p48 was identified as mouse La protein. To identify the other 4.5S RNAh-binding proteins, we performed expression cloning from a mouse cDNA library and obtained cDNA clones derived from nucleolin mRNA. We identified p110 as nucleolin using nucleolin-specific antibodies. UV cross-linking analysis using various deletion mutants of nucleolin indicated that the third of four tandem RNA recognition motifs is a major determinant for 4.5S RNAh recognition. Immunoprecipitation of nucleolin from the subcellular fractions of mouse cell extracts revealed that a portion of the endogenous 4.5S RNAh was associated with nucleolin and that this complex was located in both the nucleoplasm and nucleolus.

Deletion mapping of tumor promotion-susceptibility gene pro1 implicates an RNA polymerase III transcription unit

The murine gene pro1 has been cloned from JB6 epidermal cell lines that are sensitive to neoplastic transformation by tumor promoters. Insensitive JB6 variants acquire susceptibility to neoplastic transformation by tumor promoters when transfected with pro1. The repetitive nature of pro1 was indicated by sequence and Southern analysis. In contrast, northern analysis of RNA from promotion-sensitive cells revealed the presence of a small pro1-hybridizing transcript. Strand-specific RNA probes implicated an RNA polymerase III (RNAPIII) coding domain in pro1 as the source of this hybridization signal. Ribonuclease protection of gel-purified pro1 RNA from JB6 variant cell lines identified a 130-nucleotide transcript. The size of this transcript is compatible with in vitro RNAPIII transcription of pro1. Deletion mapping of pro1 by exonuclease III demonstrated that the biologically active domain included the RNAPIII transcription unit. RNA probes map pro1 RNA within the activity domain. These results delineate an activity domain of 597 nucleotides and suggest that a small RNA is the product of promotion-sensitivity gene pro1.

Molecular markers of endometrial epithelial cell mitogenesis mediated by the Sp/Krüppel-like factor BTEB1

Basic transcription element binding (BTEB1) protein is one of at least 20 Sp/KLF family members that function as transcriptional activators or repressors by binding to GC/GT-rich sequences within target genes to influence cellular homeostasis in mammals. Previously, we demonstrated that increased expression of BTEB1 in a human endometrial epithelial cell line Hec-1-A resulted in serum dependent-enhanced proliferation, which was accompanied by heightened expression of cell cycle- and growth-associated genes. In the present study, we examined the mechanism underlying the altered proliferative potential associated with BTEB1 by the identification of additional BTEB1 downstream gene targets and by the demonstration of BTEB1 transactivation of promoters for a number of growth-associated genes. Using mRNA differential display in the analysis of RNA populations from Hec-1-A sublines with high (4S, 9S) and low (2As, 3As) BTEB1 cellular content, we identified 10 distinct differentially expressed transcripts, nine of which had higher levels in S than in As sublines. The expression levels of two of these cDNAs, Axl receptor tyrosine kinase and mitosin, whose encoded products are implicated in cellular proliferation, were modestly induced by serum, albeit in a BTEB1-independent manner. Moreover, insulin-like growth factor-I, a mitogen present in serum, had no significant effect on their expression in either subline. In transient reporter assays, the basal activities of the Axl gene promoter and those for two other growth-regulatory genes, namely p21(WAF1) and IGFBP-2, were increased by serum and were significantly higher in 4S than in 2As lines. However, while BTEB1 and its ubiquitous family member Sp1 increased basal p21(WAF1) and IGFBP-2 transcription when added as expression constructs in the parental Hec-1-A cell line, only Sp1 activated Axl transcription, despite the presence in all three gene promoters of GC-enriched regions that presumably can bind BTEB1 and Sp1 with similar affinities. To elucidate intracellular signaling pathways that might involve BTEB1, inhibitors of specific kinase-dependent transducers were used in transient transfection assays involving the IGFBP-2 gene promoter in 4S and 2As sublines. While inhibitors of the MAPK, PI-3K, and PKA pathways elicited similar effects on the IGFBP-2 gene promoter activity, irrespective of cellular BTEB1 content, that for JNK had a more pronounced effect on Hec-1-A sublines exhibiting higher BTEB1 expression levels. Taken together, the results suggest that BTEB1 mediates the expression of growth-associated genes through direct and indirect transactivation mechanisms, one of which may involve the participation of a JNK family member.

The signal recognition particle and related small cytoplasmic ribonucleoprotein particles

Recently, a number of novel small cytoplasmic ribonucleoprotein particles have been identified that comprise RNA and protein subunits related to the signal recognition particle (SRP). Here we discuss the latest results on the structure and functions of SRP together with the structures and putative functions of the novel SRP-related ribonucleoprotein particles.

Emergence of master sequences in families of retroposons derived from 7sl RNA

The past few years have brought new insight into the evolution of families of retroposons. These are composed of a very small number of master sequences able to duplicate, and a large majority of copies that are inactive for retroposition. During the course of time, successive replacements of master sequences have produced waves of amplification that are recognizable as subfamilies. In the Alu and the B1 families, one can distinguish two evolutionary periods. The first involves only monomeric elements that are now extinguished (fossil elements) and is characterized by deep remodeling of the sequences. This period ends, in primates, with the fusion of a free left and a free right Alu monomer, producing the first modern Alu dimeric element; in rodents it ends with a tandem duplication of 29 bp to create the first modern B1 element. The second period is characterized by a great stability of the master sequences. The observed turn-over of master sequences is still an enigma. However, analysis of the contemporary master sequences and of the oldest master sequences provide some clues. Here, we review the very first stages of the appearance of the Alu and the B1 families in mammalian genomes.

Sequence organization of variant mouse 4.5 S RNA genes and pseudogenes

The rodent 4.5 S RNA is an RNA polymerase III product with a sequence related to the Alu family of interspersed repeated DNA. A previous study identified a tandem array of 4.2-kb repeating units that contain the 4.5 S RNA coding sequence as well as many short repetitive sequences. To understand the genomic organization of this gene family, we have isolated and characterized 4.5 S RNA sequences that are part of the tandem array as well as identified members that are not part of the array. One variant 4.5 S RNA gene family member exhibits length polymorphisms in its minisatellite sites relative to the single previously reported gene. The 4.5 S RNA sequences that are not part of the tandem array possess many of the features of processed pseudogenes and are found adjacent to other interspersed repeated elements. These findings suggest that the mouse 4.5 S RNA can behave as a retroposon, resulting in the accumulation of 4.5 S RNA-like elements at many sites in the genome.

Repetitive sequence transcripts and U1 RNA in mouse oocytes and eggs

Others have reported that about two-thirds of the polyadenylated RNA of sea urchin or frog eggs contains short interspersed repetitive sequence transcripts, a much larger proportion than that found in mRNA of somatic cells. Thus, it appears that incompletely processed transcripts accumulate in these oocytes. Also, in what may be a related phenomenon, the nuclear concentration of U1 RNA (involved in processing hnRNA) decreases during growth of frog oocytes. To pursue this question in mammals, Northern blots of RNA from mouse oocytes and eggs collected before and after meiotic maturation were probed with genomic clones containing rodent Alu-equivalent sequences. The Alu sequence is the predominant short interspersed repetitive element in the genome and is abundant in hnRNA. When compared on the basis of mRNA content, the oocyte and egg RNA contained less short repetitive sequence transcripts than liver or brain cytoplasmic RNA. Using a U1 RNA-specific probe, the concentration of U1 RNA in mouse oocyte nuclei was found to be quite similar to that in somatic cells, and U1 RNA was stable during meiotic maturation. These results suggest that processing of transcripts in mouse oocytes does not possess the unusual features observed in lower animals.

Biosynthesis and cytoplasmic distribution of small poly(A)-containing B2 RNA

Previously, we described a small polyadenylated RNA predominantly located in cytoplasm and hybridizing with the ubiquitous B2 sequence of the mouse genome (Kramerov, D.A., Lekakh, I.V., Samarina, O.P. and Ryskov, A.P. (1982) Nucleic Acids Res. 10, 7477-7491). This 180-300 nucleotide long RNA was designated B2 RNA. Here, we demonstrate that B2 RNA is complementary to just one of the strands of cloned B2 sequence. The synthesis of B2 is rather resistant to ultraviolet irradiation of Ehrlich ascites carcinoma cells. The treatment of the cells with alpha-amanitin at a concentration completely blocking the formation of small nuclear RNAs U1, U2 and U3 does not interfere with the B2 RNA synthesis. These results suggest that B2 RNA formation is directly transcribed with the aid of RNA polymerase III, rather than being formed in the course of the processing of large RNA molecules which are known to contain a lot of B2 sequences. We also surprisingly found that the synthesis of up to 50% of long poly(A) +RNA in Ehrlich carcinoma cells is rather resistant to alpha-amanitin. The possible role of genetic elements including B2 sequences able to promote large RNA-polymerase III transcripts is discussed. B2 RNA in the cytoplasm is incorporated into the ribonucleoprotein particles, both small (12-18 S) and heavy. The latter probably correspond to informosomes. After deproteinization of heavy particles, a major part of B2 RNA still cosediments with mRNA and is split from it only after denaturation. We suggest that the B2 RNA of heavy ribonucleoproteins is associated with mRNA by short complementary stretches. About half of the B2 RNA is recovered in the cytoskeletal fraction. The possible role of B2 RNA in mRNA transport or in translation regulation is discussed.

The cytoplasmic 4S translation inhibitory RNA species of chick embryonic muscle: fractionation of biologically active subspecies by high performance liquid chromatography

A 4S RNA species (iRNA) isolated from chick embryonic muscle which is a potent inhibitor of mRNA translation in vitro shows heterogeneity in the 70-100 nucleotide size range (Sarkar, S., Mukherjee, A.K., and Guha, C. (1981) J. Biol. Chem., 256, 5077-5086). The iRNA was fractionated by HPLC on different size exclusion columns using a variety of elution conditions. Chromatography of iRNA on a TSK 4000 SW column and elution with a low ionic strength buffer gave three components, one of which contained a pure subspecies of about 90-100 nucleotides size, as shown by a single band on PAGE analysis in 99% formamide. The biological activity of this purified subspecies showed that this is a more potent inhibitor of globin mRNA translation than unfractionated iRNA (Sarkar, S., Mukherjee, A.K., and Guha, C., (1981) J. Biol. Chem. 256, 5077-5086). Partial resolution of three additional low molecular weight iRNA subspecies in the 70-80 nucleotide size range in biologically active form was obtained on chromatography of unfractionated iRNA on TSK 4000 SW column in the presence of 0.5 M NaCl or on TSK 3000 SW column in the presence of low salt. The fractionation of iRNA by HPLC appears to be primarily based on size. These results strongly suggest that HPLC may also be useful for the fractionation of a variety of low molecular weight eukaryotic nuclear and cytoplasmic RNAs with retention of biological activity.

Organization and expression of non-Alu family interspersed repetitive DNA sequences in the mouse genome

The mouse genome is complex with regard to DNA sequence organization and transcriptional activity. To more fully understand the role of interspersed repetitive DNA sequences we have isolated and characterized five different mouse non-Alu DNA sequence families. We have found that: (1) the distribution of repetitive sequences is non-random in the genome; (2) two of the five families (Bam5 and R) were previously described by Fanning (1982) and Gebhard et al. (1982), respectively. We found that these two families are linked to each other and are found adjacent to seven of seven studied structural genes but in randomly selected DNA fragments showed much less significant linkage. (3) The position of the Bam5 and R family repeat units relative to beta-globin and relative to a housekeeping gene has been evolutionarily conserved in mice and humans. (4) Three previously undescribed families representing from 200 to 40,000 copies per genome have been characterized and shown to have equivalent human sequences. (5) All five families studied are represented in RNA polymerase II transcripts. Little RNA polymerase III transcription homologous to these three families could be detected. The structural and functional features of these five families defined in this paper provide a basis for studies on the functional role of interspersed repetitive DNA in the mouse.