Multiple dispersed loci produce small cytoplasmic Alu RNA

lncRNA BC200 is processed into a stable Alu monomer

The noncoding RNA BC200 is elevated in human cancers and is implicated in translation regulation as well as cell survival and proliferation. Upon BC200 overexpression, we observed correlated expression of a second, smaller RNA species. This RNA is expressed endogenously and exhibits cell-type-dependent variability relative to BC200. Aptamer-tagged expression constructs confirmed that the RNA is a truncated form of BC200, and sequencing revealed a modal length of 120 nt; thus, we refer to the RNA fragment as BC120. We present a methodology for accurate and specific detection of BC120 and establish that BC120 is expressed in several normal human tissues and is also elevated in ovarian cancer. BC120 exhibits remarkable stability relative to BC200 and is resistant to knockdown strategies that target the 3' unique sequence of BC200. Combined knockdown of BC200 and BC120 exhibits greater phenotypic impacts than knockdown of BC200 alone, and overexpression of BC120 negatively impacts translation of a GFP reporter, providing insight into a potential translational regulatory role for this RNA. The presence of a novel, truncated, and stable form of BC200 adds complexity to the investigation of this noncoding RNA that must be considered in future studies of BC200 and other related Alu RNAs.

The role of SRP9/SRP14 in regulating Alu RNA

SRP9/SRP14 is a protein heterodimer that plays a critical role in the signal recognition particle through its interaction with the scaffolding signal recognition particle RNA (7SL). SRP9/SRP14 binding to 7SL is mediated through a conserved structural motif that is shared with the primate-specific Alu RNA. Alu RNA are transcription products of Alu elements, a retroelement that comprises ~10% of the human genome. Alu RNA are involved in myriad biological processes and are dysregulated in several human disease states. This review focuses on the roles SRP9/SRP14 has in regulating Alu RNA diversification, maturation, and function. The diverse mechanisms through which SRP9/SRP14 regulates Alu RNA exemplify the breadth of protein-mediated regulation of non-coding RNA.

A Mechanism Leading to Changes in Copy Number Variations Affected by Transcriptional Level Might Be Involved in Evolution, Embryonic Development, Senescence, and Oncogenesis Mediated by Retrotransposons

In recent years, more and more evidence has emerged showing that changes in copy number variations (CNVs) correlated with the transcriptional level can be found during evolution, embryonic development, and oncogenesis. However, the underlying mechanisms remain largely unknown. The success of the induced pluripotent stem cell suggests that genome changes could bring about transformations in protein expression and cell status; conversely, genome alterations generated during embryonic development and senescence might also be the result of genome changes. With rapid developments in science and technology, evidence of changes in the genome affected by transcriptional level has gradually been revealed, and a rational and concrete explanation is needed. Given the preference of the HIV-1 genome to insert into transposons of genes with high transcriptional levels, we propose a mechanism based on retrotransposons facilitated by specific pre-mRNA splicing style and homologous recombination (HR) to explain changes in CNVs in the genome. This mechanism is similar to that of the group II intron that originated much earlier. Under this proposed mechanism, CNVs on genome are dynamically and spontaneously extended in a manner that is positively correlated with transcriptional level or contract as the cell divides during evolution, embryonic development, senescence, and oncogenesis, propelling alterations in them. Besides, this mechanism explains several critical puzzles in these processes. From evidence collected to date, it can be deduced that the message contained in genome is not just three-dimensional but will become four-dimensional, carrying more genetic information.

The Sm-core mediates the retention of partially-assembled spliceosomal snRNPs in Cajal bodies until their full maturation

Cajal bodies (CBs) are nuclear non-membrane bound organelles where small nuclear ribonucleoprotein particles (snRNPs) undergo their final maturation and quality control before they are released to the nucleoplasm. However, the molecular mechanism how immature snRNPs are targeted and retained in CBs has yet to be described. Here, we microinjected and expressed various snRNA deletion mutants as well as chimeric 7SK, Alu or bacterial SRP non-coding RNAs and provide evidence that Sm and SMN binding sites are necessary and sufficient for CB localization of snRNAs. We further show that Sm proteins, and specifically their GR-rich domains, are important for accumulating snRNPs in CBs. Accordingly, core snRNPs containing the Sm proteins, but not naked snRNAs, restore the formation of CBs after their depletion. Finally, we show that immature but not fully assembled snRNPs are able to induce CB formation and that microinjection of an excess of U2 snRNP-specific proteins, which promotes U2 snRNP maturation, chases U2 snRNA from CBs. We propose that the accessibility of the Sm ring represents the molecular basis for the quality control of the final maturation of snRNPs and the sequestration of immature particles in CBs.

Perlman syndrome nuclease DIS3L2 controls cytoplasmic non-coding RNAs and provides surveillance pathway for maturing snRNAs

The exosome-independent exoribonuclease DIS3L2 is mutated in Perlman syndrome. Here, we used extensive global transcriptomic and targeted biochemical analyses to identify novel DIS3L2 substrates in human cells. We show that DIS3L2 regulates pol II transcripts, comprising selected canonical and histone-coding mRNAs, and a novel FTL_short RNA from the ferritin mRNA 5' UTR. Importantly, DIS3L2 contributes to surveillance of maturing snRNAs during their cytoplasmic processing. Among pol III transcripts, DIS3L2 particularly targets vault and Y RNAs and an Alu-like element BC200 RNA, but not Alu repeats, which are removed by exosome-associated DIS3. Using 3' RACE-Seq, we demonstrate that all novel DIS3L2 substrates are uridylated in vivo by TUT4/TUT7 poly(U) polymerases. Uridylation-dependent DIS3L2-mediated decay can be recapitulated in vitro, thus reinforcing the tight cooperation between DIS3L2 and TUTases. Together these results indicate that catalytically inactive DIS3L2, characteristic of Perlman syndrome, can lead to deregulation of its target RNAs to disturb transcriptome homeostasis.

Long noncoding RNA as a regulator for transcription

Investigation of noncoding RNAs is in rapid progress, especially regarding translational repression by small (short) noncoding RNAs like microRNAs with 20-25 nucleotide-lengths, while long noncoding RNAs with nucleotide length of more than two hundred are also emerging. Indeed, our analysis has revealed that a long noncoding RNA transcribed from cyclin D1 promoter of 200 and 300 nucleotides exerts transcriptional repression through its binding protein TLS instead of translational repression. Translational repression is executed by short noncoding RNAs, while transcriptional repression is mainly done by long noncoding RNAs. These long noncoding RNAs are heterogeneous molecules and employ divergent molecular mechanisms to exert transcriptional repression. In this review, I overview recent publications regarding the transcription regulation by long noncoding RNAs and explore their biological significance. In addition, the relation between a random transcriptional activity of RNA polymerase II and the origin of long noncoding RNAs is discussed.

RNA-Seq Analysis to Measure the Expression of SINE Retroelements

The intrinsic features of retroelements, like their repetitive nature and disseminated presence in their host genomes, demand the use of advanced methodologies for their bioinformatic and functional study. The short length of SINE (short interspersed elements) retrotransposons makes such analyses even more complex. Next-generation sequencing (NGS) technologies are currently one of the most widely used tools to characterize the whole repertoire of gene expression in a specific tissue. In this chapter, we will review the molecular and computational methods needed to perform NGS analyses on SINE elements. We will also describe new methods of potential interest for researchers studying repetitive elements. We intend to outline the general ideas behind the computational analyses of NGS data obtained from SINE elements, and to stimulate other scientists to expand our current knowledge on SINE biology using RNA-seq and other NGS tools.

Alu RNA regulates the cellular pool of active ribosomes by targeted delivery of SRP9/14 to 40S subunits

The human genome contains about 1.5 million Alu elements, which are transcribed into Alu RNAs by RNA polymerase III. Their expression is upregulated following stress and viral infection, and they associate with the SRP9/14 protein dimer in the cytoplasm forming Alu RNPs. Using cell-free translation, we have previously shown that Alu RNPs inhibit polysome formation. Here, we describe the mechanism of Alu RNP-mediated inhibition of translation initiation and demonstrate its effect on translation of cellular and viral RNAs. Both cap-dependent and IRES-mediated initiation is inhibited. Inhibition involves direct binding of SRP9/14 to 40S ribosomal subunits and requires Alu RNA as an assembly factor but its continuous association with 40S subunits is not required for inhibition. Binding of SRP9/14 to 40S prevents 48S complex formation by interfering with the recruitment of mRNA to 40S subunits. In cells, overexpression of Alu RNA decreases translation of reporter mRNAs and this effect is alleviated with a mutation that reduces its affinity for SRP9/14. Alu RNPs also inhibit the translation of cellular mRNAs resuming translation after stress and of viral mRNAs suggesting a role of Alu RNPs in adapting the translational output in response to stress and viral infection.

Identification of RNA polymerase III-transcribed Alu loci by computational screening of RNA-Seq data

Of the ∼1.3 million Alu elements in the human genome, only a tiny number are estimated to be active in transcription by RNA polymerase (Pol) III. Tracing the individual loci from which Alu transcripts originate is complicated by their highly repetitive nature. By exploiting RNA-Seq data sets and unique Alu DNA sequences, we devised a bioinformatic pipeline allowing us to identify Pol III-dependent transcripts of individual Alu elements. When applied to ENCODE transcriptomes of seven human cell lines, this search strategy identified ∼1300 Alu loci corresponding to detectable transcripts, with ∼120 of them expressed in at least three cell lines. In vitro transcription of selected Alus did not reflect their in vivo expression properties, and required the native 5′-flanking region in addition to internal promoter. We also identified a cluster of expressed AluYa5-derived transcription units, juxtaposed to snaR genes on chromosome 19, formed by a promoter-containing left monomer fused to an Alu-unrelated downstream moiety. Autonomous Pol III transcription was also revealed for Alus nested within Pol II-transcribed genes. The ability to investigate Alu transcriptomes at single-locus resolution will facilitate both the identification of novel biologically relevant Alu RNAs and the assessment of Alu expression alteration under pathological conditions.

Alu- and 7SL RNA Analogues Suppress MCF-7 Cell Viability through Modulating the Transcription of Endoplasmic Reticulum Stress Response Genes

11% of the human genome is composed of Alu-retrotransposons, whose transcription by RNA polymerase III (Pol III) leads to the accumulation of several hundreds to thousands of Alu-RNA copies in the cytoplasm. Expression of Alu-RNA Pol III is significantly increased at various levels of stress, and the increase in the Alu-RNA level is accompanied by a suppression of proliferation, a decrease in viability, and induction of apoptotic processes in human cells. However, the question about the biological functions of Pol III Alu-transcripts, as well as their mechanism of action, remains open. In this work, analogues of Alu-RNA and its evolutionary ancestor, 7SL RNA, were synthesized. Transfection of human breast adenocarcinoma MCF-7 cells with the Alu-RNA and 7SL RNA analogues is accompanied by a decrease in viability and by induction of proapoptotic changes in these cells. The analysis of the combined action of these analogues and actinomycin D or tamoxifen revealed that the decreased viability of MCF-7 cells transfected with Alu-RNA and 7SL RNA was due to the modulation of transcription. A whole transcriptome analysis of gene expression revealed that increased gene expression of the transcription regulator NUPR1 (p8), as well as the transcription factor DDIT3 (CHOP), occurs under the action of both the Alu- and 7SL RNA analogues on MCF-7 cells. It has been concluded that induction of proapoptotic changes in human cells under the influence of the Alu-RNA and 7SL RNA analogues is related to the transcriptional activation of the genes of cellular stress factors, including the endoplasmic reticulum stress response factors.

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.

Noncoding RNA in development

Non-protein-coding sequences increasingly dominate the genomes of multicellular organisms as their complexity increases, in contrast to protein-coding genes, which remain relatively static. Most of the mammalian genome and indeed that of all eukaryotes is expressed in a cell- and tissue-specific manner, and there is mounting evidence that much of this transcription is involved in the regulation of differentiation and development. Different classes of small and large noncoding RNAs (ncRNAs) have been shown to regulate almost every level of gene expression, including the activation and repression of homeotic genes and the targeting of chromatin-remodeling complexes. ncRNAs are involved in developmental processes in both simple and complex eukaryotes, and we illustrate this in the latter by focusing on the animal germline, brain, and eye. While most have yet to be systematically studied, the emerging evidence suggests that there is a vast hidden layer of regulatory ncRNAs that constitutes the majority of the genomic programming of multicellular organisms and plays a major role in controlling the epigenetic trajectories that underlie their ontogeny.

Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock

Noncoding RNAs (ncRNAs) have recently been discovered to regulate mRNA transcription in trans, a role traditionally reserved for proteins. The breadth of ncRNAs as transacting transcriptional regulators and the diversity of signals to which they respond are only now becoming recognized. Here we show that human Alu RNA, transcribed from short interspersed elements (SINEs), is a transacting transcriptional repressor during the cellular heat shock response. Alu RNA blocks transcription by binding RNA polymerase II (Pol II) and entering complexes at promoters in vitro and in human cells. Transcriptional repression by Alu RNA involves two loosely structured domains that are modular, a property reminiscent of classical protein transcriptional regulators. Two other SINE RNAs, human scAlu RNA and mouse B1 RNA, also bind Pol II but do not repress transcription in vitro. These studies provide an explanation for why mouse cells harbor two major classes of SINEs, whereas human cells contain only one.

PCR-based detection of Pol III-transcribed transposons and its application to the rodent model of ultraviolet response

Cellular levels of RNAs containing transposable elements increase in response to various stresses. Polymerase III (Pol III)-dependent transcripts of transposons are different from transposon-containing RNAs generated by read-through Pol II-dependent transcription. Until now, Pol III transcripts were detected by primer extension followed by time-consuming gel electrophoresis. In this paper, we describe a more sensitive PCR-based method for the selective detection of Pol III-transcribed RNAs. The method is based on the difference in sequences at the 5' ends of the Pol II- and Pol III-dependent transcripts. We employed this method to quantify Pol III transcripts of transposon B1 in rodent cells and revealed that their levels are affected by UV irradiation. We therefore conclude that the abundance of the Pol III-transcribed fraction of cellular RNA may serve as marker of stress response and can be conveniently quantified by the method described.

Evidence of Alu and B1 expression in dbEST

Alus and B1s are short interspersed repeat elements (SINEs) derived from the 7SL RNA gene. Alus and B1s exist in the cytoplasm as non-coding RNA indicating that they are actively transcribed, but their function, if any, is unknown. Transcription of individual SINEs is a prerequisite for retroposition, but it is also possible that individual Alu and B1 elements have some cellular functions. Previous studies suggest that transcription of Alu elements depends on the presence of an RNA polymerase-III bipartite promoter and the poly-A tail. Sequencing of small RNAs has demonstrated that the members of the Y and S subfamily are expressed. We analyzed almost one million Alu sequences longer than 200 nucleotides for the presence of RNA polymerase-III bipartite promoter sequences. More than half contained a promoter indicating some potential for expression. We searched 7.7 million human EST sequences in dbEST for the presence of Alu non-coding RNAs and found evidence for the expression of 452. Analysis of mouse spermatogenic dbEST libraries revealed an apparent relationship between the level of differentiation and the level of B1-related sequences in the EST library.

An Unusual Primate Locus that Attracted Two Independent Alu Insertions and Facilitates their Transcription

BC200 RNA, a neuronal, small non-messenger RNA that originated from a monomeric Alu element is specific to anthropoid primates. Tarsiers lack an insert at the orthologous genomic position, whereas strepsirrhines (Lemuriformes and Lorisiformes) acquired a dimeric Alu element, independently from anthropoids. In Galago moholi, the CpG dinucleotides are conspicuously conserved, while in Eulemur coronatus a large proportion is changed, indicating that the G.moholi Alu is under purifying selection and might be transcribed. Indeed, Northern blot analysis of total brain RNA from G.moholi with a specific probe revealed a prominent signal. In contrast, a corresponding signal was absent from brain RNA from E.coronatus. Isolation and sequence analysis of additional strepsirrhine loci confirmed the differential sequence conservation including CpG patterns of the orthologous dimeric Alu elements in Lorisiformes and Lemuriformes. Interestingly, all examined Alu elements from Lorisiformes were transcribed, while all from Lemuriformes were silent when transiently transfected into HeLa cells. Upstream sequences, especially those between the transcriptional start site and -22 upstream, were important for basal transcriptional activity. Thus, the BC200 RNA gene locus attracted two independent Alu insertions during its evolutionary history and provided upstream promoter elements required for their transcription.

Differential stress induction of individual Alu loci: implications for transcription and retrotransposition

While human Alu repeats can be considered to be members of an extremely large, globally regulated, multigene family, each member of this family resides within a different sequence context that might uniquely modulate its transcription. Unique 3' flanking sequences for several transcriptionally active human Alu elements were identified by cDNA cloning and used for primer extension analysis to compare the basal and stress-induced expression of the corresponding Alu loci. Each of six Alu loci investigated exhibits a unique pattern of expression in three different human cell lines and in response to stress induction. The sequence context surrounding each Alu member uniquely determines its transcriptional regulation. In many cases, the individual Alu loci and total Alu RNA exhibit opposing patterns of expression implying that local rather than global regulation ultimately determines the expression of individual members. Some of the stresses, which induce Alu transcription, increase co-expression of LINE1 RNA, another requirement for Alu retrotransposition.

Analysis of the SINE S1 Pol III promoter from Brassica; impact of methylation and influence of external sequences

Transcription is an important control point in the transposable element mobilization process. To better understand the regulation of the plant SINE (Short Interspersed Elements) S1, its promoter sequence was studied using an in vitro pol III transcription system derived from tobacco cells. We show that the internal S1 promoter can be functional although upstream external sequences were found to enhance this basal level of transcription. For one putative 'master' locus (na7), three CAA triplets (in positions -12, -7 and -2) and two overlapping TATA motifs (in positions -54 to -43) were important to stimulate transcription. For this locus, two transcription initiation regions were characterized, one centered on position + 1 (first nucleotide of the S1 element) and one centered on position - 19 independently of the internal motifs. The CAA triplets only influence transcription in + 1 and work in association with the internal motifs. We show that methylation can inhibit transcription at the na7 locus. We also observe that S1 RNA is cleaved in a smaller Poly (A) minus product by a process analogous to the maturation of mammalian SINEs.

An RNA polymerase III transcription unit located in the upstream control regions of the human proliferating-cell nucleolar protein p120 gene is transcribed in vitro and in vivo

An RNA polymerase III (Pol III) transcription unit containing homology to highly repeated Alu sequences was identified in the upstream flanking sequences of the gene for the human proliferating-cell nucleolar antigen p120. When transcribed in vitro, this Pol III unit produced three RNA transcripts, designated by nucleotide length as T150, T385 and T635; RNA transcript T635 was the most abundant accounting for over 90%. The transcription initiates at nucleotide -729 of the human p120 promoter and proceeds in the opposite orientation to the p120 gene transcription. Northern blot analysis and cDNA cloning followed by sequencing showed the presence of the T635 RNA in HeLa cells, indicating that this Pol III transcription unit is functional and transcribed in vivo. Disruption of this Pol III transcription unit by deletion of the Box A residues (-733 to -744) resulted in a sixfold reduction of the p120 gene transcription. A possible role for this Pol III transcription unit in p120 gene transcription is discussed.

A novel human DNA-binding protein with sequence similarity to a subfamily of redox proteins which is able to repress RNA-polymerase-III-driven transcription of the Alu-family retroposons in vitro

In this study we identified a novel protein which may contribute to the transcriptional inactivity of Alu retroposons in vivo. A human cDNA clone encoding this protein (ACR1) was isolated from a human expression library using South-western screening with an Alu subfragment, implicated in the regulation of Alu in vitro transcription and interacting with a HeLa nuclear protein down-regulated in adenovirus-infected cells. Bacterially expressed ACR1 is demonstrated to inhibit RNA polymerase III (Pol III)-dependent Alu transcription in vitro but showed no repression of transcription of a tRNA gene or of a reporter gene under control of a Pol II promoter. ACR1 mRNA is also found to be down-regulated in adenovirus-infected HeLa cells, consistent with a possible repressor function of the protein in vivo. ACR1 is mainly (but not exclusively) located in cytoplasm and appears to be a member of a weakly characterized redox protein family having a central, highly conserved sequence motif, PGAFTPXCXXXXLP. One member of the family identified earlier as peroxisomal membrane protein (PMP)20 is known to interact in a sequence-specific manner with a yeast homolog of mammalian cyclosporin-A-binding protein cyclophilin, and mammalian cyclophilin A (an abundant ubiquitously expressed protein) is known to interact with human transcriptional repressor YY1, which is a major sequence-specific Alu-binding protein in human cells. It appears, therefore, that transcriptional silencing of Alu in vivo is a result of complex interactions of many proteins which bind to its Pol III promoter.

Control of genes by mammalian retroposons

Available data on possible genetic impacts of mammalian retroposons are reviewed. Most important is the growing number of established examples showing the involvement of retroposons in modulation of expression of protein-coding genes transcribed by RNA polymerase II (Pol II). Retroposons contain conserved blocks of nucleotide sequence for binding of some important Pol II transcription factors as well as sequences involved in regulation of stability of mRNA. Moreover, these mobile genes provide short regions of sequence homology for illegitimate recombinations, leading to diverse genome rearrangements during evolution. Therefore, mammalian retroposons representing a significant fraction of noncoding DNA cannot be considered at present as junk DNA but as important genetic symbionts driving the evolution of regulatory networks controlling gene expression.

Alu sequences

Alu sequences are frequently encountered during study of human genomic nucleic acid and form a major component of repetitive DNA. This review describes the origin of Alu sequences and their subsequent amplification and evolution into distinct subfamilies. In recent years a number of different functional roles for Alu sequences have been described. The multiple influences of Alu sequences on RNA polymerase II-mediated gene expression and the presence of Alu sequences in RNA polymerase III-generated transcripts are discussed.

A human 28S ribosomal RNA retropseudogene

A human genomic clone designated LhrRAX3 isolated from an X chromosome-specific library was found to have a 28S ribosomal RNA retropseudogene symbolized as RNRP2 within a 12.5-kb human DNA insert. The sequence of the rRNA retropseudogene has an identity of 96% with about 300 nucleotides at the 3'-terminus of the human 28S rRNA gene. RNRP2 is flanked by a pair of perfect direct repeats of 16 nucleotides, the hallmark characteristic of a processed pseudogene having been integrated into the genome. The structural element has a long A-rich tract at its 3'-end, apparently the result of an aberrant polyadenylation event of a RNA polymerase I transcript, prior to its subsequent reverse transcription and retroposition into the genome. An Alu repeat sequence truncated by 80 nucleotides at the 5'-region occurs about 800 base pairs downstream and is of opposite orientation to RNRP2. The Alu element is bounded by 16-nucleotide direct repeats and is a member of the Alu Y subfamily.

cDNAs derived from primary and small cytoplasmic Alu (scAlu) transcripts

We have isolated and sequenced twenty-six cDNAs derived from primary Alu transcripts. Most cDNAs (22/26) sequenced end in multiple T residues, known to be at the termination for RNA polymerase III-directed transcripts. We conclude that these cDNAs were derived from authentic, RNA polymerase III-directed primary Alu transcripts. Sequence alignment of the cDNAs with Alu consensus sequences show that the cDNAs belong to different, previously described Alu subfamilies. The sequence variation observed in the 3' non-Alu regions of each of the cDNAs led us to conclude that they were derived from different genomic loci, thus demonstrating that multiple Alu loci are transcriptionally active. The subfamily distribution of the cDNAs suggests that transcriptional activity is biased towards evolutionarily younger Alu subfamilies, with a strong selection for the consensus sequence in the first 42 bases and the promoter B box. Sequence data from seven cDNAs derived from small cytoplasmic Alu (scAlu) transcripts, a processed form of Alu transcripts, also have a similar bias towards younger Alu subfamilies. About half of these cDNAs are due to processing or degradation, but the other half appear to be due to the formation of a cryptic RNA polymerase III termination signal in multiple loci. Using our sequence data, we have isolated a transcriptionally active genomic Alu element belonging to the Ya5 subfamily. In vitro transcription studies of this element suggest that its flanking sequences contribute to its transcriptional activity. The role of flanking sequences and other factors involved in transcriptional activity of Alu elements are discussed.

BC1 RNA, the transcript from a master gene for ID element amplification, is able to prime its own reverse transcription

ID elements are short interspersed elements (SINEs) found in high copy number in many rodent genomes. BC1 RNA, an ID-related transcript, is derived from the single copy BC1 RNA gene. The BC1 RNA gene has been shown to be a master gene for ID element amplification in rodent genomes. ID elements are dispersed through a process termed retroposition. The retroposition process involves a number of potential regulatory steps. These regulatory steps may include transcription in the appropriate tissue, transcript stability, priming of the RNA transcript for reverse transcription and integration. This study focuses on priming of the RNA transcript for reverse transcription. BC1 RNA gene transcripts are shown to be able to prime their own reverse transcription in an efficient intramolecular and site-specific fashion. This self-priming ability is a consequence of the secondary structure of the 3'-unique region. The observation that a gene actively amplified throughout rodent evolution makes a RNA capable of efficient self-primed reverse transcription strongly suggests that self-priming is at least one feature establishing the BC1 RNA gene as a master gene for amplification of ID elements.

A transcriptional analysis of the S1Bn (Brassica napus) family of SINE retroposons

S1Bn is a plant short interspersed element (SINE) whose amplification probably involves the reverse transcription of an RNA intermediate. In this report, we identified and characterized S1Bn transcripts from different Brassica napus tissues. Despite the presence of a consensus internal POL III promoter in a large number of genomic S1Bn elements, we observed that S1Bn transcripts are rare in B. napus cells. The use of two very sensitive methods (RT-PCR and RACE PCR) allowed the characterization of 102 independent S1Bn cDNA clones from three different tissues (shoot, root and callus). From this analysis, we conclude that the majority of S1Bn transcripts probably result from a small number of cotranscriptional events where an S1Bn element is transcribed due to its presence in a POL II transcriptional unit. Specific POL III RNA transcripts, initiating at the first 5' nucleotide of the DNA element, are also present in the tested tissues and possibly result from the transcriptional activity of as few as three genomic elements. Two of these transcripts could represent master transcripts responsible for the amplification of S1Bn subfamilies. We also observed that the population of specific POL III transcripts varies among the three tested tissues and that some transcripts appear completely tissue-specific.

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.

Sequences attaching loops of nuclear and mitochondrial DNA to underlying structures in human cells: the role of transcription units

DNA sequences attaching loops of nuclear and mitochondrial DNA to underlying structures in HeLa cells have been cloned and 106 representative clones sequenced; 10 clones containing random genomic fragments served as controls. As chromatin is prone to rearrangement, care was taken to isolate sequences using 'physiological' conditions that did not create additional attachments. Comparison (by Southern blotting) of the concentration of each cloned sequence in 'total' and 'attached' fractions of DNA showed that most clones did contain attached sequences, but even highly-attached sequences were not attached in all cells in the population. Results demonstrated that 28% of clones were derived from three specific parts of the mitochondrial genome and 22% from different parts of the alu repeat. In addition, 41% of clones contained unique nuclear sequences; these contained no more of the motifs found attached to nuclear scaffolds or matrices (ie SARs or MARs) than would be expected from their base composition. No other attachment motif(s) could be identified by sequence analysis. However, Northern blotting showed that all the mitochondrial clones and 76% of clones containing unique sequences were transcribed; the degree of attachment correlated with transcriptional activity. These results are consistent with transcription being responsible for ever-changing attachments in both nuclei and mitochondria.

Specific binding sites for a pol III transcriptional repressor and pol II transcription factor YY1 within the internucleosomal spacer region in primate Alu repetitive elements

Alu interspersed repetitive elements possess internal RNA polymerase III promoters that are transcribed in vitro and in transfected mouse cells but are nearly silent in human HeLa cells. Transcriptional repression of these elements is to some extent reversible, as pol III-dependent Alu expression can be induced with herpes simplex or adenovirus. To assess whether sequence-specific DNA binding proteins might contribute to Alu transcriptional silencing, we examined the internucleosomal spacer region surrounding the B box of the Alu pol III promoter in HeLa cell nuclei for evidence of proteins bound at specific sites in vivo. We identified a DNase I-hypersensitive site 5' to the B box and a DNase I-resistant region 3' to the B box in nuclei. An Alu-specific repressor binds to a 5-bp inverted repeat motif overlapping the 5' end of the TFIIIC binding site and may inhibit pol III transcription through competitive displacement. The level of Alu-specific pol III repressor activity is significantly reduced in adenovirus-infected HeLa cells, suggesting that the repressor may contribute to Alu transcriptional silencing in vivo. The 3' DNase I-resistant region coincided with a binding site for the pol II transcription factor YY1 in vitro. YY1 is one of the major proteins in HeLa cells having binding specificity for Alu elements. YY1 bound to tandem arrays of genomic Alu elements may play a role in chromatin organization and silencing.

Evidence for a regulatory protein complex on RNA polymerase III promoter of human retroposons of Alu family

Abundant human retroposons of the Alu family produce few RNA polymerase III (RPIII)-dependent transcripts in vivo. This suggests that either the bulk of the repeats has no proper promoter elements or that transcription of Alu by RPIII is repressed. In this study, we analyzed complexes formed by human nuclear proteins with the Alu B-box and with an adjacent downstream sequence (DB-sequence). Four complexes (C1-C4) were detected and two of them (C2 and C3) were found to be induced by different proteins. C3 formation was found to be sensitive to minor sequence variation within the Alu DB-sequence. The C2 complex is specifically repressed by the competing VA1 B-box oligonucleotide and was found to be very stable. In addition, it is downregulated in human cells transformed by adenovirus 5. This is consistent with a view that the C2 complex is formed by a protein (designated as ACR1) that is different from TFIIIC2. The ACR1 protein may be involved in the modulation of Alu transcription in vivo by interfering or cooperating with TFIIIC2. A similar complex is detected with the efficiently transcribed adenovirus VA1 RNA gene B-box. We compared the affinity of complexes formed by ACR1 with Alu and VA1 B-boxes. It was found that both B-boxes bind ACR1 with equal affinity with a dissociation constant of about 2 nM. However, DB-sequences in Alu and VA1 promoters are non-homologous, and C3/C4 complexes are found to be formed with Alu DB, but not formed with VA1 DB sequences. The Alu-specific protein forming C3 (named as ACR2) may cooperate with ACR1 in selective repression of RPIII-dependent Alu transcription in vivo.

Flanking sequences of an Alu source stimulate transcription in vitro by interacting with sequence-specific transcription factors

An Alu source gene, called the EPL Alu, was previously isolated by a phylogenetic strategy. Sequences flanking the EPL Alu family member stimulate its RNA polymerase III (Pol III) template activity in vitro. One cis-acting element maps within a 40-nucleotide region immediately upstream to the EPL Alu. This same region contains an Ap1 site which, when mutated, abolishes the transcriptional stimulation provided by this region. The flanking sequence, as assayed by gel mobility shift, forms sequence-specific complexes with several nuclear factors including Ap1. These results demonstrate that an an ancestral Alu source sequence fortuitously acquired positive transcriptional control elements by insertion into the EPL locus, thereby providing biochemical evidence for a model which explains the selective amplification of Alu subfamilies.

Human signal recognition particle (SRP) Alu-associated protein also binds Alu interspersed repeat sequence RNAs. Characterization of human SRP9

Nearly 1 million interspersed Alu elements reside in the human genome. Alu retrotransposition is presumably mediated by full-length Alu transcripts synthesized by RNA polymerase III, while some polymerase III-synthesized Alu transcripts undergo 3'-processing and accumulate as small cytoplasmic (sc) RNAs of unknown function. Interspersed Alu sequences also reside in the untranslated regions of some mRNAs. The Alu sequence is related to a portion of the 7SL RNA component of signal recognition particle (SRP). This region of 7SL RNA together with 9- and 14-kDa polypeptides (SRP9/14) regulates translational elongation of ribosomes engaged by SRP. Here we characterize human (h) SRP9 and show that it, together with hSRP14 (SRP9/14), forms the activity previously identified as Alu RNA-binding protein (RBP). The primate-specific C-terminal tail of hSRP14 does not appreciably affect binding to scAlu RNA. Kd values for three Alu-homologous scRNAs were determined using Alu RBP (SRP9/14) purified from HeLa cells. The Alu region of 7SL, scAlu, and scB1 RNAs exhibited Kd values of 203 pM, 318 pM, and 1.8 nM, respectively. Finally, Alu RBP can bind with high affinity to synthetic mRNAs that contain interspersed Alus in their untranslated regions.

Evolution of secondary structure in the family of 7SL-like RNAs

Primate and rodent genomes are populated with hundreds of thousands copies of Alu and B1 elements dispersed by retroposition, i.e., by genomic reintegration of their reverse transcribed RNAs. These, as well as primate BC200 and rodent 4.5S RNAs, are ancestrally related to the terminal portions of 7SL RNA sequence. The secondary structure of 7SL RNA (an integral component of the signal recognition particle) is conserved from prokaryotes to distant eukaryotic species. Yet only in primates and rodents did this molecule give rise to retroposing Alu and B1 RNAs and to apparently functional BC200 and 4.5S RNAs. To understand this transition and the underlying molecular events, we examined, by comparative analysis, the evolution of RNA structure in this family of molecules derived from 7SL RNA. RNA sequences of different simian (mostly human) and prosimian Alu subfamilies as well as rodent B1 repeats were derived from their genomic consensus sequences taken from the literature and our unpublished results (prosimian and New World Monkey). RNA secondary structures were determined by enzymatic studies (new data on 4.5S RNA are presented) and/or energy minimization analyses followed by phylogenetic comparison. Although, with the exception of 4.5S RNA, all 7SL-derived RNA species maintain the cruciform structure of their progenitor, the details of 7SL RNA folding domains are modified to a different extent in various RNA groups. Novel motifs found in retropositionally active RNAs are conserved among Alu and B1 subfamilies in different genomes. In RNAs that do not proliferate by retroposition these motifs are modified further. This indicates structural adaptation of 7SL-like RNA molecules to novel functions, presumably mediated by specific interactions with proteins; these functions were either useful for the host or served the selfish propagation of RNA templates within the host genome.