Synthesis and processing of small B2 transcripts in mouse embryonal carcinoma cells

Non-Coding RNAs As Transcriptional Regulators In Eukaryotes

Non-coding RNAs up to 1,000 nucleotides in length are widespread in eukaryotes and fulfil various regulatory functions, in particular during chromatin remodeling and cell proliferation. These RNAs are not translated into proteins: thus, they are non-coding RNAs (ncRNAs). The present review describes the eukaryotic ncRNAs involved in transcription regulation, first and foremost, targeting RNA polymerase II (RNAP II) and/or its major proteinaceous transcription factors. The current state of knowledge concerning the regulatory functions of SRA and TAR RNA, 7SK and U1 snRNA, GAS5 and DHFR RNA is summarized herein. Special attention is given to murine B1 and B2 RNAs and human Alu RNA, due to their ability to bind the active site of RNAP II. Discovery of bacterial analogs of the eukaryotic small ncRNAs involved in transcription regulation, such as 6S RNAs, suggests that they possess a common evolutionary origin.

Polyadenylation of RNA transcribed from mammalian SINEs by RNA polymerase III: Complex requirements for nucleotide sequences

It is generally accepted that only transcripts synthesized by RNA polymerase II (e.g., mRNA) were subject to AAUAAA-dependent polyadenylation. However, we previously showed that RNA transcribed by RNA polymerase III (pol III) from mouse B2 SINE could be polyadenylated in an AAUAAA-dependent manner. Many species of mammalian SINEs end with the pol III transcriptional terminator (TTTTT) and contain hexamers AATAAA in their A-rich tail. Such SINEs were united into Class T(+), whereas SINEs lacking the terminator and AATAAA sequences were classified as T(-). Here we studied the structural features of SINE pol III transcripts that are necessary for their polyadenylation. Eight and six SINE families from classes T(+) and T(-), respectively, were analyzed. The replacement of AATAAA with AACAAA in T(+) SINEs abolished the RNA polyadenylation. Interestingly, insertion of the polyadenylation signal (AATAAA) and pol III transcription terminator in T(-) SINEs did not result in polyadenylation. The detailed analysis of three T(+) SINEs (B2, DIP, and VES) revealed areas important for the polyadenylation of their pol III transcripts: the polyadenylation signal and terminator in A-rich tail, β region positioned immediately downstream of the box B of pol III promoter, and τ region located upstream of the tail. In DIP and VES (but not in B2), the τ region is a polypyrimidine motif which is also characteristic of many other T(+) SINEs. Most likely, SINEs of different mammals acquired these structural features independently as a result of parallel evolution.

Transcripts synthesized by RNA polymerase III can be polyadenylated in an AAUAAA-dependent manner

It is well known that nearly all eukaryotic mRNAs contain a 3' poly(A) tail. A polyadenylation signal (AAUAAA) nearby the 3' end of pre-mRNA is required for poly(A) synthesis. The protein complex involved in the pre-mRNA polyadenylation is coupled with RNA polymerase II during the transcription of a gene. According to the commonly accepted view, only RNAs synthesized by RNA polymerase II can be polyadenylated in an AAUAAA-dependent manner. Here we report the polyadenylation of short interspersed elements (SINEs) B2 and VES transcripts generated by RNA polymerase III. HeLa cells were transfected with SINE constructs with or without polyadenylation signals. The analyses of the SINE transcripts showed that only the RNAs with the AAUAAA-signal contained poly(A) tails. Polyadenylated B2 RNA was found to be much more stable in cells than B2 RNA without a poly(A) tail.

Regulation of RNA polymerase III transcription during hypertrophic growth

The cell division-independent growth of terminally differentiated cardiomyocytes is commonly associated with cardiovascular disease. We demonstrate that it is accompanied by a substantial rise in transcription by RNA polymerase (pol) III, which produces essential components of the biosynthetic apparatus, including 5S rRNA and tRNAs. This increase in transcription is achieved by changes in both the activity and level of the essential pol III-specific transcription factor TFIIIB. Erk and c-Myc, which directly activate TFIIIB in proliferating fibroblasts, also induce pol III transcription in growing cardiomyocytes. Furthermore, hypertrophic stimulation increases expression of the essential TFIIIB subunit Brf1, an effect not seen when fibroblasts proliferate. Erk mediates this induction of Brf1 expression and therefore contributes in at least two ways to pol III transcriptional activation during hypertrophy. Increased production of tRNA and 5S rRNA will contribute to the enhanced translational capacity required to sustain hypertrophic growth.

Evolution of microRNAs located withinHox gene clusters

MicroRNAs (miRNAs) form an abundant class of non-coding RNA genes that have an important function in post-transcriptional gene regulation and in particular modulate the expression of developmentally important transcription factors including Hox genes. Two families of microRNAs are genomically located in intergenic regions in the Hox clusters of vertebrates. Here we describe their evolution in detail. We show that the micro RNAs closely follow the patterns of protein evolution in the Hox clusters, which is characterized by cluster duplications followed by differential gene loss.

Coordinated and conserved expression of alphoid repeat and alphoid repeat-tagged coding sequences

We have found an alpha-like simple-sequence DNA repeat that is differentially expressed during early embryogenesis in both chick and zebrafish. Before and during the primitive streak stage, transcripts of the alphoid repeat sequence were ubiquitously expressed throughout zebrafish and chick embryos. After headfold formation, expression was limited to the cardiac neural crest, the head, and the heart. Two types of alphoid repeat sequence transcripts were identified: alphoid repeat RNA and alphoid repeat-tagged mRNA (ESalphaT). Several of the ESalphaTs were identified by (1) searching expressed sequence tag databases, (2) arbitrary rapid amplification of cDNA ends (RACE), and (3) screening embryonic cDNA libraries. The alphoid element was located in the 3' untranslated region of one ESalphaT that was obtained by RACE. The ESalphaT sequences encoded a variety of different types of proteins, but all were expressed within tissues that were positive for the alphoid repeat RNA. The presence of two types of coordinately expressed alphoid-like repeat transcripts in maternal RNA with subsequent restriction to the head and heart, and the conservation of these features in disparate vertebrate embryos, suggest that the alphoid repeat sequence may serve as a control element in the gene regulation network.

Tumoral environment triggers transcript anomalies in established tumors: induction of altered gene expression and of aberrant, truncated and B2 repeat-containing gene transcripts

In addition to eugenetic changes, cancerous cells exhibit extensive modifications in the expression levels of a variety of genes. The phenotypic switch observed after inoculation of T lymphoma cells into syngenic mice illustrates the active participation of tumoral environment in the induction of an aberrant gene expression pattern. To further substantiate this contribution, we performed polymerase chain reaction (PCR)-based subtraction suppression hybridization (SSH) to identify genes that are differentially expressed in tumor-derived EL4/13.3 cells compared to the same cells isolated from cultures. Besides a number of unknown genes, the subtracted library contained several known genes that have been reported to be expressed at increased levels in tumors and/or to contribute to carcinogenesis. Apart from clones representing translated transcripts, the subtracted library also contained a high number of clones representing B2 repeat elements, viz. short interspersed repetitive elements that are transcribed by RNA polymerase III. Northern blotting confirmed the induction of B2 transcripts in tumor tissue and also revealed induction of chimeric, B2 repeat-containing mRNA. The appearance of chimeric transcripts was accompanied by aberrant, shorter-than-full-length transcripts, specifically from upregulated genes. Accordingly, in addition to altered gene expression, tumoral environmental triggers constitute a potent mechanism to create an epigenetic diversity in cancers by inducing extensive transcript anomalies.

Rat B(2) sequences are induced in the hippocampal CA1 region after transient global cerebral ischemia

Global brain ischemia causes cell death in the CA1 region of the hippocampus 3-5 days after reperfusion. The biological pathway leading to such delayed neuronal damage has not been established. By using differential display analysis, we examined expression levels of poly(A) RNAs isolated from hippocampal extracts prepared from rats exposed to global ischemia and found an up-regulated transcript, clone 17a. Northern blot analysis of clone 17a showed an approximately 35-fold increase in the ischemic brain at 24 h after four-vessel occlusion. Rapid amplification of cDNA ends of clone 17a revealed a family of genes (160-540 base pairs) that had the characteristics of rodent B(2) sequences. In situ hybridization demonstrated that the elevated expression of this gene was localized predominantly in the CA1 pyramidal neurons. The level of expression in the CA1 region decreased dramatically between 24 and 72 h after ischemia. The elevated expression of clone 17a was not observed in four-vessel occlusion rats treated with the compound LY231617, an antioxidant known to exert neuroprotection in rats subjected to global ischemia. Since delayed neuronal death has the characteristics of apoptosis, we speculate that clone 17a may be involved in apoptosis. We examined the expression level of clone 17a in in vitro models of apoptosis using cerebellar granule neurons that were subjected to potassium removal, glutamate toxicity, or 6-hydroxydopamine treatment and found that clone 17a transcripts were induced in cerebellar granule neurons by glutamate or 6-hydroxydopamine stimulation but not potassium withdrawal.

Use of a repetitive mouse B2 element to identify transplanted mouse cells in mouse-chick chimeras

Monitoring the migrations of cells during embryonic development requires a system in which cells can be identified in situ during locomotion. One promising system involves the generation of chimeras by transplanting mouse cells into chick embryos in ovo to exploit the wealth of mouse genetic variants. The success of this technique relies on the ability to detect individual mouse cells in a chick environment with high specificity. The murine B2 family of short interspersed elements is present in the mouse genome at copy numbers in excess of 10(5), whereas this sequence is absent in the chick genome based on hybridization techniques. This differential of five orders of magnitude produces signals in mouse cells that are easily identified, even in an environment that is predominantly chick. Thus, the B2 repeat probe is highly effective for the purpose of identifying mouse cells in mouse-chick chimeras.

Evolution of B2 repeats: the muroid explosion

B2 repeats are a group of short interspersed elements (SINEs) specific for rodent genomes. Copy numbers were determined for different rodent genera. All the Muroid (rat, mouse, deer mouse, hamster, gerbil) rodent genomes analyzed exhibited 80,000-100,000 copies per haploid genome, whereas the squirrel genome contains only 2,500 copies, and fewer than 100 (if any) copies were observed for the Hystricognath rodents (guinea pig and nutria). These findings demonstrate that there was an 'explosion' of amplification of B2 elements within muroid rodents. The similar copy number of B2 elements within the different muroid species could be explained by formation of a high proportion of the B2 elements prior to the divergence of the different muroid species. However, the 3'-end of the B2 sequence is unique between murid and cricetid rodents suggesting that the majority of elements amplified after the divergence of these species. Also consistent with recent amplification of these elements in parallel within the muroid genomes is the finding that within mouse and rat there are distinct subfamilies of B2 repeats. The pattern of consistent parallel amplification of B2 elements in muroid species contrasts with the sporadic nature of ID repeat amplification in the same genomes. The consensus of the young mouse subfamily of elements corresponds to the B2 RNA that is preferentially transcribed in embryonic, tumor, and normal liver cells. The subfamily is young based on both its low divergence from the subfamily consensus sequence and the finding that the most recent B2 element insertions in the mouse genome are members of this subfamily.

The gene encoding the MOK-2 zinc-finger protein: characterization of its promoter and negative regulation by mouse Alu type-2 repetitive elements

The mouse gene MOK-2 encodes a protein with seven highly similar zinc fingers. The MOK-2 transcripts are preferentially detected in transformed cell lines, brain and testis tissues. The characterized 5'-flanking sequence differs from those of tissue-specific genes previously described. DNA sequence analysis shows that the promoter region lacks TATA and CCAAT boxes. Two short interspersed mouse genomic repeats (B2 sequences) found in this region exert a negative cis-acting effect on MOK-2 promoter activity.

Transcribed repetitive DNA sequences in telomeric regions of rice (Oryza sativa)

We have isolated and characterized from rice three repetitive DNA sequences, Os48, Osc-567, and OsG3-430. Our results indicate that these repetitive sequences are highly transcribed, and transcripts complementary to both strands of the Os48 family of sequences account for up to 3% of the total cellular RNA. Pulsed-field gel electrophoresis, restriction mapping, and DNA sequence analyses have revealed a complex pattern of structural organization of the three families of repetitive sequences. Os48 and Osc-567 are organized in long tandem arrays, whereas copies of the OsG3-340 sequence are interspersed with other sequences including arrays of the Os48 and Osc567 families. Interestingly, the three families of repetitive sequences are closely linked not only to each other, but also to telomeric sequences of rice, suggesting that transcription of these repetitive sequences may occur in regions very close to telomeres in rice.

Capping signals correspond to the 5' end in four eukaryotic small RNAs containing gamma-monomethylphosphate cap structure

In eukaryotic cells, the gamma-monomethylphosphate cap structure has been identified in four small RNAs, namely, U6, 7SK, B2, and plant U3 RNAs. In this study, we show that in the case of 7SK and B2, as well as in plant U3 RNAs, the 5' stem-loop followed by a short single-stranded region serves as the capping signal. We previously showed that the nucleotides 1-25 of mouse U6 snRNA, also comprised of a stem-loop followed by a short single-stranded region, function as the capping signal. These data show that capping signals in all four RNAs have common features. The length of the stem-loop among these capped RNAs varied from 20 to 108 nucleotides, with no significant variation in the capping efficiency. In addition to the capping signal, we also observed a minimum RNA length requirement of about 15-25 nucleotides following the stem-loop for efficient capping in vitro. The capping signal in plant U3 snRNA corresponds to the additional 5' stem-loop found in U3 RNAs from plants and lower eukaryotes but absent in U3 RNA from higher animals. Consistent with this observation, the human U3 RNA that lacks the additional 5' stem-loop was not a suitable substrate for capping when compared to U6 snRNA.

Molecular structure and transcriptional function of the rat vascular AT1a angiotensin receptor gene

Rat vascular angiotensin receptors (AT1a receptors) are encoded by two mRNA transcripts sharing an identical receptor coding sequence but differing in their 5' and 3' untranslated sequences. We screened male Sprague-Dawley rat genomic libraries to clone the vascular AT1a receptor gene. Two sets of overlapping clones were isolated that encode over 90 kb of genomic sequence around the AT1a receptor gene. Four overlapping clones were identified from the 5' flanking portion of the gene. These contain the promoter region and two exons, 141 bp and 89 bp in size, respectively, encoding the alternatively spliced 5' untranslated mRNA sequence. Six additional clones overlap each other but do not overlap the set of clones from the 5' flanking region of the gene. These contain a single 1977-bp exon that encodes 900 bp of the 5' and 3' untranslated sequences in addition to a 1077-bp open reading frame identical to that found in vascular smooth muscle cell AT1a receptor cDNAs. Primer extension and RNase protection studies indicate that the transcription start site for this gene begins 9 bp upstream from the most 5' sequence found within the AT1a receptor cDNAs. Our mapping studies of the cloned gene, which so far includes an uncloned gap within the second intron, indicate that the transcription start site is no less than 67 kb upstream from the receptor coding exon. Promoter-reporter assays were performed by transfection of vascular smooth muscle cells with deletions of a 3.2-kb promoter region fused to a luciferase cDNA reporter plasmid. Relatively strong basal transcriptional activity is observed from the 5'-most 2 kb of the promoter and diminishes markedly with deletions within 1 kb of the early promoter region, suggesting strong promoter elements in the more upstream regions of the gene. Deletion of a 53-bp early promoter region containing the transcription start site and a putative TATA box completely abolishes the ability of upstream elements to drive transcription of the luciferase cDNA. These results indicate that we have isolated the AT1a receptor gene and its functional promoter.

Identification of differentiation-dependent DNase I-hypersensitive sites in the mouse EndoA gene

DNase I hypersensitive (DH) sites in a 12-kb genomic fragment carrying the mouse EndoA gene were examined to obtain information on the changes in chromatin structure associated with activation of this gene encoding extra-endodermal cytoskeletal protein A (EndoA) during early mouse embryogenesis. Seven DH sites were found in this locus in parietal yolk-sac-like cells, PYS-2, which produce EndoA constitutively. In differentiated mouse teratocarcinoma F9 cells that produce EndoA inductively, this locus has three DH sites. In both cell lines, these sites were mapped to the upstream region of the promoter, the promoter and the 3' enhancer region. The DNA of PYS-2 cells has one more DH site within the first exon and three additional DH sites within the first intron. These DH sites are not present in DNA from BALB/c 3T3 cells and undifferentiated F9 cells that do not produce EndoA. Thus, the formation of these differentiation-dependent DH sites is required for the differentiation-specific expression of the mouse EndoA. In addition, another strong DH site, which may be associated with the B2 element expression, was detected in the third intron of the gene in undifferentiated F9 cells.

Differential gene expression in wild-type and X-ray-sensitive mutants of Chinese hamster ovary cell lines

Complementary DNA cloning, differential screening and Northern hybridization techniques were used to study differential gene expression in the wild-type Chinese hamster ovary (CHO) K1 cell line and its two X-ray sensitive mutants, xrs-5 and xrs-6. 11 species of mRNAs were found underexpressed in the two independently isolated mutants. The steady-state levels of those mRNAs are 3-26-fold less in the two mutants, depending on the particular species. 6 of the underexpressed mRNAs have been identified by comparing the sequences of the cloned cDNAs to the known sequences in GenBank. 4 of them code for the structural proteins of ferritin heavy chain, nonmuscle myosin light chain 3nm, ribosomal protein S17 and L7, respectively. The other two have strong homology with mouse B2 or retroviral sequences. The remaining 5 mRNAs did not show significant homology with any of the known sequences and apparently represent newly isolated species. The effect of 137Cs gamma-rays on the expression of the 11 mRNAs has been studied. Radiation inhibited the expression of the B2-like gene in the mutants but not in the wild-type CHO cells. The levels of the other 10 mRNAs were not affected by radiation. The underexpression of this group of genes in both xrs-5 and xrs-6 mutants seems to be related to their radiation-sensitive phenotype, although the specific gene responsible has not been identified. Two models are proposed to explain the mechanism of underexpression. It is suggested that a cellular factor or/and chromosome structural changes are involved.

Alu RNA transcripts in human embryonal carcinoma cells. Model of post-transcriptional selection of master sequences

Alu master sequences colonized the human genome using RNA as amplification intermediate. To understand this phenomenon better we isolated and analyzed Alu RNA from NTera2D1 pluripotential cells. Northern hybridization, primer extension, cDNA cloning and sequencing data are congruent and demonstrate a low level of Alu specific transcription. These bona fide RNA Polymerase III Alu transcripts, although enriched in the cytoplasm, are not dominated by a single master species but rather originate from a variety of loci. However, when compared with the genomic average, or to repeats from RNA Polymerase II co-transcripts, they belong to the youngest group of Alu subfamilies (p less than 0.001) and have a higher content of intact CpG-dinucleotides. This suggests that Alu transcription is influenced both by mutations and the genomic context, and points to a possible role of DNA methylation in silencing the bulk of genomic repeats. Because of the heterogeneity of Alu transcripts a post-transcriptional selection mechanism recruiting Alu master sequences for retroposition is required. We propose that Alu RNA masters could have evolved as selfish satellites to a more complex retroposition system equipped with a reverse transcriptase activity and that their structure was conserved through "phenotypic" selection of the RNA level.

Modulation of B2 containing small RNAs during induced differentiation of murine erythroleukemia cells

We identified a B2 repetitive element approximately 1.9kb down stream from mouse p53 coding gene. This element was then used as a probe to investigate the expression of B2 containing RNA during the induced differentiation of murine erythroleukemia (MEL) cells. This probe revealed two nuclear and one cytoplasmic RNA species. Nuclear small RNAs had a biphasic variation: a decrease followed by a reaccumulation. The cytoplasmic species was essentially non polysomal, and disappeared after the induced differentiation. The presented results suggest that the regulation of these RNAs is associated to cell proliferation and differentiation respectively.

The rodent B2 sequence can affect expression when present in the transcribed region of a reporter gene

The mouse B2 element is a moderately repetitive nt sequence of 180 bp transcribed by RNA polymerase III (Pol III) at high levels in embryonic and transformed cells. The B2 sequence is present in either orientation within the noncoding regions of a number of genes transcribed by RNA polymerase II (Pol II). We sought to determine if the small B2 transcripts generated by Pol III are natural antisense RNA molecules which might hybridize to complementary sequences present within Pol II transcripts. Chimaeric reporter genes encoding Escherichia coli gpt were constructed containing a B2 repeat in either orientation within the 5'- or 3'-untranslated regions. These constructs were transfected into embryonal carcinoma (EC) cells and expression of the reporter gene was analysed in EC cells and retinoic acid-treated EC cells, which contain high and low levels of small B2 RNAs, respectively. Although the B2 sequences affected expression of the reporter gene, these effects did not appear to be due to hybridization of the small B2 RNA to the reporter transcripts. The presence of B2 sequences near a Pol II-transcribed gene can alter expression of that gene in a position- and orientation-dependent manner, suggesting these repetitive elements may be cis-acting regulators of gene expression.