TATA-Binding protein-TATA interaction is a key determinant of differential transcription of silkworm constitutive and silk gland-specific tRNA(Ala) genes

The choreography of chromatin in RNA polymerase III regulation

Regulation of eukaryotic gene expression involves a dynamic interplay between the core transcriptional machinery, transcription factors, and chromatin organization and modification. While this applies to transcription by all RNA polymerase complexes, RNA polymerase III (RNAPIII) seems to be atypical with respect to its mechanisms of regulation. One distinctive feature of most RNAPIII transcribed genes is that they are devoid of nucleosomes, which relates to the high levels of transcription. Moreover, most of the regulatory sequences are not outside but within the transcribed open chromatin regions. Yet, several lines of evidence suggest that chromatin factors affect RNAPIII dynamics and activity and that gene sequence alone does not explain the observed regulation of RNAPIII. Here we discuss the role of chromatin modification and organization of RNAPIII transcribed genes and how they interact with the core transcriptional RNAPIII machinery and regulatory DNA elements in and around the transcribed genes.

BmTBP upregulates the transcription of BmSuc1 in silkworm (Bombyx mori) by binding to BmTfΙΙA-S

The BmSuc1 gene, which encodes a novel animal-type β-fructofuranosidase (EC 3.2.1.26), was first cloned and identified in silkworm (Bombyx mori). As an essential sucrase, the activity of BmSUC1 is unaffected by alkaloidal sugar mimics in mulberry leaves. This enzyme may also directly regulate the degree of sucrose hydrolysis in the silkworm midgut. In addition, BmSUC1 is involved in the synthesis of sericin 1 in the silk gland tissue. However, the mechanism underlying the regulation of BmSuc1 transcription remains unclear. In this study, we analyzed the BmSuc1 promoter activity using a dual-luciferase reporter assay and identified 4 regions that are critical for transcriptional activation. The gene encoding a predicted transcription factor (TATA-box-binding protein; BmTBP) capable of binding to the core promoter regions was cloned. A quantitative real-time polymerase chain reaction analysis indicated the gene was highly expressed in the midgut. Downregulating BmTBP expression via RNA interference decreased the expression of BmSuc1 at the transcript and protein levels. An electrophoretic mobility shift analysis and chromatin immunoprecipitation indicated that BmTBP can bind to the TATA-box cis-regulatory element in the BmSuc1 promoter. Furthermore, a bioinformatics-based analysis and a far-western blot revealed the interaction between BmTBP and another transcription factor (BmTfIIA-S). The luciferase reporter gene assay results confirmed that the BmTBP-BmTfIIA-S complex increases the BmSuc1 promoter activity. Considered together, these findings suggest that BmTBP regulates BmSuc1 expression through its interaction with BmTfIIA-S.

Effect of mRNA/tRNA mutations on translation speed: Implications for human diseases

Recent discoveries establish tRNAs as central regulators of mRNA translation dynamics, and therefore cotranslational folding and function of the encoded protein. The tRNA pool, whose composition and abundance change in a cell- and tissue-dependent manner, is the main factor which determines mRNA translation velocity. In this review, we discuss a group of pathogenic mutations, in the coding sequences of either protein-coding genes or in tRNA genes, that alter mRNA translation dynamics. We also summarize advances in tRNA biology that have uncovered how variations in tRNA levels on account of genetic mutations affect protein folding and function, and thereby contribute to phenotypic diversity in clinical manifestations.

Insights from a chum salmon (Oncorhynchus keta) genome assembly regarding whole-genome duplication and nucleotide variation influencing gene function

Chum salmon are ecologically important to Pacific Ocean ecosystems and commercially important to fisheries. To improve the genetic resources available for this species, we sequenced and assembled the genome of a male chum salmon using Oxford Nanopore read technology and the Flye genome assembly software (contig N50: ∼2 Mbp, complete BUSCOs: ∼98.1%). We also resequenced the genomes of 59 chum salmon from hatchery sources to better characterize the genome assembly and the diversity of nucleotide variants impacting phenotype variation. With genomic sequences from a doubled haploid individual, we were able to identify regions of the genome assembly that have been collapsed due to high sequence similarity between homeologous (duplicated) chromosomes. The homeologous chromosomes are relics of an ancient salmonid-specific genome duplication. These regions were enriched with genes whose functions are related to the immune system and responses to toxins. From analyzing nucleotide variant annotations of the resequenced genomes, we were also able to identify genes that have increased levels of variants thought to moderately impact gene function. Genes related to the immune system and the detection of chemical stimuli (olfaction) had increased levels of these variants based on a gene ontology enrichment analysis. The tandem organization of many of the enriched genes raises the question of why they have this organization.

TATA-Like Boxes in RNA Polymerase III Promoters: Requirements for Nucleotide Sequences

tRNA and some other non-coding RNA genes are transcribed by RNA polymerase III (pol III), due to the presence of intragenic promoter, consisting of boxes A and B spaced by 30–40 bp. Such pol III promoters, called type 2, are also intrinsic to Short Interspersed Elements (SINEs). The contribution of 5′-flanking sequences to the transcription efficiency of genes containing type 2 promoters is still studied insufficiently. Here, we studied this issue, focusing on the genes of two small non-coding RNAs (4.5SH and 4.5SI), as well as B1 and B2 SINEs from the mouse genome. We found that the regions from position −31 to −24 may significantly influence the transcription of genes and SINEs. We studied the influence of nucleotide substitutions in these sites, representing TATA-like boxes, on transcription of 4.5SH and 4.5SI RNA genes. As a rule, the substitutions of A and T to G or C reduced the transcription level, although the replacement of C with A also lowered it. In 4.5SH gene, five distal nucleotides of −31/−24 box (TTCAAGTA) appeared to be the most important, while in the box −31/−24 of 4.5SI gene (CTACATGA), all nucleotides, except for the first one, contributed significantly to the transcription efficiency. Random sequences occurring at positions −31/−24 upstream of SINE copies integrated into genome, promoted their transcription with different efficacy. In the 5′-flanking sequences of 4.5SH and 4.5SI RNA genes, the recognition sites of CREB, C/EBP, and Sp1 factors were found, and their deletion decreased the transcription.

Differential expression of human tRNA genes drives the abundance of tRNA-derived fragments

The human genome encodes hundreds of transfer RNA (tRNA) genes but their individual contribution to the tRNA pool is not fully understood. Deep sequencing of tRNA transcripts (tRNA-Seq) can estimate tRNA abundance at single gene resolution, but tRNA structures and posttranscriptional modifications impair these analyses. Here we present a bioinformatics strategy to investigate differential tRNA gene expression and use it to compare tRNA-Seq datasets from cultured human cells and human brain. We find that sequencing caveats affect quantitation of only a subset of human tRNA genes. Unexpectedly, we detect several cases where the differences in tRNA expression among samples do not involve variations at the level of isoacceptor tRNA sets (tRNAs charged with the same amino acid but using different anticodons), but rather among tRNA genes within the same isodecoder set (tRNAs having the same anticodon sequence). Because isodecoder tRNAs are functionally equal in terms of genetic translation, their differential expression may be related to noncanonical tRNA functions. We show that several instances of differential tRNA gene expression result in changes in the abundance of tRNA-derived fragments (tRFs) but not of mature tRNAs. Examples of differentially expressed tRFs include PIWI-associated RNAs, tRFs present in tissue samples but not in cells cultured in vitro, and somatic tissue-specific tRFs. Our data support that differential expression of tRNA genes regulate noncanonical tRNA functions performed by tRFs.

Molecular organization of the 5S rDNA gene type II in elasmobranchs

The 5S rDNA gene is a non-coding RNA that can be found in 2 copies (type I and type II) in bony and cartilaginous fish. Previous studies have pointed out that type II gene is a paralog derived from type I. We analyzed the molecular organization of 5S rDNA type II in elasmobranchs. Although the structure of the 5S rDNA is supposed to be highly conserved, our results show that the secondary structure in this group possesses some variability and is different than the consensus secondary structure. One of these differences in Selachii is an internal loop at nucleotides 7 and 112. These mutations observed in the transcribed region suggest an independent origin of the gene among Batoids and Selachii. All promoters were highly conserved with the exception of BoxA, possibly due to its affinity to polymerase III. This latter enzyme recognizes a dT4 sequence as stop signal, however in Rajiformes this signal was doubled in length to dT8. This could be an adaptation toward a higher efficiency in the termination process. Our results suggest that there is no TATA box in elasmobranchs in the NTS region. We also provide some evidence suggesting that the complexity of the microsatellites present in the NTS region play an important role in the 5S rRNA gene since it is significantly correlated with the length of the NTS.

Stabilization of eukaryotic ribosomal termination complexes by deacylated tRNA

Stabilization of the ribosomal complexes plays an important role in translational control. Mechanisms of ribosome stabilization have been studied in detail for initiation and elongation of eukaryotic translation, but almost nothing is known about stabilization of eukaryotic termination ribosomal complexes. Here, we present one of the mechanisms of fine-tuning of the translation termination process in eukaryotes. We show that certain deacylated tRNAs, remaining in the E site of the ribosome at the end of the elongation cycle, increase the stability of the termination and posttermination complexes. Moreover, only the part of eRF1 recognizing the stop codon is stabilized in the A site of the ribosome, and the stabilization is not dependent on the hydrolysis of peptidyl-tRNA. The determinants, defining this property of the tRNA, reside in the acceptor stem. It was demonstrated by site-directed mutagenesis of tRNA^Val and construction of a mini-helix structure identical to the acceptor stem of tRNA. The mechanism of this stabilization is different from the fixation of the unrotated state of the ribosome by CCA end of tRNA or by cycloheximide in the E site. Our data allow to reveal the possible functions of the isodecoder tRNAs in eukaryotes.

Diversity of human tRNA genes from the 1000-genomes project

The sequence diversity of individual human genomes has been extensively analyzed for variations and phenotypic implications for mRNA, miRNA, and long non-coding RNA genes. TRNA (tRNA) also exhibits large sequence diversity in the human genome, but tRNA gene sequence variation and potential functional implications in individual human genomes have not been investigated. Here we capitalize on the sequencing data from the 1000-genomes project to examine the diversity of tRNA genes in the human population. Previous analysis of the reference human genome indicated an unexpected large number of diverse tRNA genes beyond the necessity of translation, suggesting that some tRNA transcripts may perform non-canonical functions. We found 24 new tRNA sequences in>1% and 76 new tRNA sequences in>0.2% of all individuals, indicating that tRNA genes are also subject to evolutionary changes in the human population. Unexpectedly, two abundant new tRNA genes contain base-pair mismatches in the anticodon stem. We experimentally determined that these two new tRNAs have altered structures in vitro; however, one new tRNA is not aminoacylated but extremely stable in HeLa cells, suggesting that this new tRNA can be used for non-canonical function. Our results show that at the scale of human population, tRNA genes are more diverse than conventionally understood, and some new tRNAs may perform non-canonical, extra-translational functions that may be linked to human health and disease.

Coadaptation of isoacceptor tRNA genes and codon usage bias for translation efficiency in Aedes aegypti and Anopheles gambiae

The transfer RNAs (tRNAs) are essential components of translational machinery. We determined that tRNA isoacceptors (tRNAs with different anticodons but incorporating the same amino acid in protein synthesis) show differential copy number abundance, genomic distribution patterns and sequence evolution between Aedes aegypti and Anopheles gambiae mosquitoes. The tRNA-Ala genes are present in unusually high copy number in the Ae. aegypti genome but not in An. gambiae. Many of the tRNA-Ala genes of Ae. aegypti are flanked by a highly conserved sequence that is not observed in An. gambiae. The relative abundance of tRNA isoacceptor genes is correlated with preferred (or optimal) and nonpreferred (or rare) codons for ∼2-4% of the predicted protein coding genes in both species. The majority (∼74-85%) of these genes are related to pathways involved with translation, energy metabolism and carbohydrate metabolism. Our results suggest that these genes and the related pathways may be under translational selection in these mosquitoes.

Different sequence signatures in the upstream regions of plant and animal tRNA genes shape distinct modes of regulation

In eukaryotes, the transcription of tRNA genes is initiated by the concerted action of transcription factors IIIC (TFIIIC) and IIIB (TFIIIB) which direct the recruitment of polymerase III. While TFIIIC recognizes highly conserved, intragenic promoter elements, TFIIIB binds to the non-coding 5'-upstream regions of the tRNA genes. Using a systematic bioinformatic analysis of 11 multicellular eukaryotic genomes we identified a highly conserved TATA motif followed by a CAA-motif in the tRNA upstream regions of all plant genomes. Strikingly, the 5'-flanking tRNA regions of the animal genomes are highly heterogeneous and lack a common conserved sequence signature. Interestingly, in the animal genomes the tRNA species that read the same codon share conserved motifs in their upstream regions. Deep-sequencing analysis of 16 human tissues revealed multiple splicing variants of two of the TFIIIB subunits, Bdp1 and Brf1, with tissue-specific expression patterns. These multiple forms most likely modulate the TFIIIB-DNA interactions and explain the lack of a uniform signature motif in the tRNA upstream regions of animal genomes. The anticodon-dependent 5'-flanking motifs provide a possible mechanism for independent regulation of the tRNA transcription in various human tissues.

Silent mutations in sight: co-variations in tRNA abundance as a key to unravel consequences of silent mutations

Mutations that alter the amino acid sequence are known to potentially exert deleterious effects on protein function, whereas substitutions of nucleotides without amino acid change are assumed to be neutral for the protein's functionality. However, cumulative evidence suggests that synonymous substitutions might also induce phenotypic variability by affecting splicing accuracy, translation fidelity, and conformation and function of proteins. tRNA isoacceptors mediate the translation of codons to amino acids, and asymmetric tRNA abundance causes variations in the rate of translation of each single triplet. Consequently, the effect of a silent point mutation in the coding region could be significant due to differential abundances of the cognate tRNA(s), emphasizing the importance of precise assessment of tRNA composition. Here, we provide an overview of the methods used to quantitatively determine the concentrations of tRNA species and discuss synonymous mutations in the context of tRNA composition of the cell, thus providing a new twist on the detrimental impact of the silent mutations.

Diversity of tRNA genes in eukaryotes

We compare the diversity of chromosomal-encoded transfer RNA (tRNA) genes from 11 eukaryotes as identified by tRNAScan-SE of their respective genomes. They include the budding and fission yeast, worm, fruit fly, fugu, chicken, dog, rat, mouse, chimp and human. The number of tRNA genes are between 170 and 570 and the number of tRNA isoacceptors range from 41 to 55. Unexpectedly, the number of tRNA genes having the same anticodon but different sequences elsewhere in the tRNA body (defined here as tRNA isodecoder genes) varies significantly (10-246). tRNA isodecoder genes allow up to 274 different tRNA species to be produced from 446 genes in humans, but only up to 51 from 275 genes in the budding yeast. The fraction of tRNA isodecoder genes among all tRNA genes increases across the phylogenetic spectrum. A large number of sequence differences in human tRNA isodecoder genes occurs in the internal promoter regions for RNA polymerase III. We also describe a systematic, ligation-based method to detect and quantify tRNA isodecoder molecules in human samples, and show differential expression of three tRNA isodecoders in six human tissues. The large number of tRNA isodecoder genes in eukaryotes suggests that tRNA function may be more diverse than previously appreciated.

Modulation of differential transcription of tRNA genes through chromatin organization

In higher eukaryotes, tRNA multigene families comprise several copies encoding the same tRNA isoacceptor species. Of the 11 copies of a tRNA1Gly family from the mulberry silkworm Bombyx mori, individual members are differentially transcribed in vivo in the B. mori-derived BmN cell lines and in vitro in silk gland nuclear extracts. These genes have identical coding regions and hence harbour identical internal control sequences (the A and B boxes), but differ significantly in their 5' and 3' flanking regions. In the present study, we demonstrate the role of chromatin structure in the down-regulation of the poorly expressed copy, tRNA1Gly-6,7. Distinct footprints in the 5'-upstream region of the poorly transcribed gene in vitro as well as in vivo suggested the presence of nucleosomes. A theoretical analysis of the immediate upstream sequence of this gene copy also revealed a high propensity of nucleosome formation. The low transcription of tRNA1Gly-6,7 DNA was further impaired on assembly into chromatin and this inhibition was relieved by externally supplemented TFIIIC with an associated histone acetyltransferase activity. The inhibition due to nucleosome assembly was absent when the 5'-upstream region beyond -53 nt was deleted or entirely swapped with the 5'-upstream region of the highly transcribed gene copy, which does not position a nucleosome. Footprinting of the in vitro assembled tRNA1Gly-6,7 chromatin confirmed the presence of a nucleosome in the immediate upstream region potentially masking TFIIIB binding. Addition of TFIIIC unmasked the footprints present on account of the nucleosome. Our studies provide the first evidence for nucleosomal repression leading to differential expression of individual members from within a tRNA multigene family.

Transcription of individual tRNAGly1 genes from within a multigene family is regulated by transcription factor TFIIIB

Members of a multigene family from the silkworm Bombyx mori have been classified based on their transcriptions in homologous nuclear extracts, into three groups of highly, moderately and poorly transcribed genes. Because all these gene copies have identical coding sequences and consequently identical promoter elements (the A and B boxes), the flanking sequences modulate their expression levels. Here we demonstrate the interaction of transcription factor TFIIIB with these genes and its role in regulating differential transcriptions. The binding of TFIIIB to the poorly transcribed gene -6,7 was less stable compared with binding of TFIIIB to the highly expressed copy, -1. The presence of a 5' upstream TATA sequence closer to the coding region in -6,7 suggested that the initial binding of TFIIIC to the A and B boxes sterically hindered anchoring of TFIIIB via direct interactions, leading to lower stability of TFIIIC-B-DNA complexes. Also, the multiple TATATAA sequences present in the flanking regions of this poorly transcribed gene successfully competed for TFIIIB reducing transcription. The transcription level could be enhanced to some extent by supplementation of TFIIIB but not by TATA box binding protein. The poor transcription of -6,7 was thus attributed both to the formation of a less stable transcription complex and the sequestration of TFIIIB. Availability of the transcription factor TFIIIB in excess could serve as a general mechanism to initiate transcription from all the individual members of the gene family as per the developmental needs within the tissue.

Differential expression and interaction of transcription co-activator MBF1 with TATA-binding protein (TBP) in the apicomplexan Cryptosporidium parvum

All gene-specific transcriptional activators initiate gene transcriptions by binding to promoter sequences and recruiting general transcription factors including TATA-binding protein (TBP) to upstream of targeted genes. Some of them require multiprotein bridging factors (MBFs); for example, the type 1 MBF (MBF1) which interconnects the gene activator with TBP. In this study, the properties of a previously cloned type 1 multiprotein bridging factor (CpMBF1) and a newly identified TBP (CpTBP1) from the apicomplexan Cryptosporidium parvum were investigated. Genes encoding both proteins were differentially expressed as determined by semi-quantitative RT-PCRs during the parasite life cycle, but in different patterns. The highest level of expression of CpMBF1 was in the well-developed intracellular parasites, whereas that of CpTBP1 was found in intact oocysts and late intracellular stages, possibly correlated with the formation of oocysts. Both CpMBF1 and CpTBP1 were expressed as maltose-binding protein fusion proteins. The function of CpTBP1 was confirmed by its ability to bind a biotinylated DNA oligonucleotide containing TATA consensus sequence. The interaction between CpMBF1 and CpTBP1 was also observed by an electrophoretic mobility shift assay. Since little is known about the regulation and control of gene activity in C. parvum, this study may point to a new direction for the study of gene activation associated with the development of the complex life cycle of this parasite.

A composite upstream sequence motif potentiates tRNA gene transcription in yeast

Transcription of eukaryotic tRNA genes relies on the TFIIIC-dependent recruitment of TFIIIB on a approximately 50 bp region upstream of the transcription start site (TSS). TFIIIC specifically interacts with highly conserved, intragenic promoter elements, while the contacts between TFIIIB and the upstream DNA have long been considered as largely non-specific. Through a computer search procedure designed to detect shared, yet degenerate sequence features, we have identified a conserved sequence pattern upstream of Saccharomyces cerevisiae tDNAs. This pattern consists of four regions in which particular sequences are over-represented. The most downstream of these regions surrounds the TSS, while the other three districts of sequence conservation (appearing as a centrally located TATA-like sequence flanked by T-rich elements on both sides) are located across the DNA region known to interact with TFIIIB. Upstream regions whose sequence conforms to this pattern were found to potentiate tRNA gene transcription, both in vitro and in vivo, by enhancing TFIIIB binding. A conserved pattern of DNA bendability was also revealed, with peaks of bending propensity centered on the TATA-like and the TSS regions. Sequence analysis of other eukaryotic genomes further revealed the widespread occurrence of conserved sequence patterns upstream of tDNAs, with striking lineage-specific differences in the number and sequence of conserved motifs. Our data strongly support the notion that tRNA gene transcription in eukaryotes is modulated by composite TFIIIB binding sites that may confer responsiveness to variation in TFIIIB activity and/or concentration.

Cloning of a putative Bombyx mori TFIIB-related factor (BRF)

To identify the protein domains responsible for its conserved and specialized functions, putative TFIIB-Related Factor (BRF) from the silkworm (Bombyx mori) was compared with BRFs from other organisms. The Bombyx BRF coding region was assembled from three separate and overlapping cDNA fragments. Fragments encoding the middle portion and the 3' end were discovered in the Bombyx mori Genome Project "Silkbase" collection through sequence homology with human BRF1, and the fragment encoding the N-terminus was isolated in our laboratory using the 5' RACE method. Southern analysis showed that silkworm BRF is encoded by a single-copy gene. Bombyx BRF contains the following domains that have been noted in all other BRFs, and that are likely, therefore, to provide highly conserved functions: a zinc finger domain, an imperfect repeat, three "BRF Homology" domains, and an acidic domain at the C-terminus. As expected from the evolutionary relationships among insects and mammals, Bombyx BRF is more similar overall to Drosophila BRF (55% identical) than to human BRF1 (42% identical). Detailed examination of individual domains reveals a remarkable exception, however. Domain II of Bombyx BRF is more similar to its human counterpart than to Drosophila Domain II. This result indicates that Domain II has undergone unusual divergence in Drosophila, and suggests a structural basis for Drosophila BRF's unique pattern of interaction with other transcription factors.

The fission yeast TFIIB-related factor limits RNA polymerase III to a TATA-dependent pathway of TBP recruitment

The RNA polymerase (pol) III-transcribed (e.g. tRNA and 5S rRNA) genes of traditionally studied organisms rely on gene-internal promoters that precisely position the initiation factor, TFIIIB, on the upstream promoter-less DNA. This is accomplished by the ability of the TFIIIB subunit, TFIIB-related factor (Brf1), to make stable protein-protein interactions with TATA-binding protein (TBP) and place it on the promoter-less upstream DNA. Unlike traditional model organisms, Schizosaccharomyces pombe tRNA and 5S rRNA genes contain upstream TATA promoters that are required to program functional pol III initiation complexes. In this study we demonstrate that S.pombe (Sp)Brf does not form stable interactions with TBP in the absence of DNA using approaches that do reveal stable association of TBP and S.cerevisiae (Sc)Brf1. Gel mobility analyses demonstrate that a TBP-TATA DNA complex can recruit SpBrf to a Pol III promoter. Consistent with this, overproduction of SpBrf in S.pombe increases the expression of a TATA-dependent, but not a TATA-less, suppressor tRNA gene. Since previous whole genome analysis also revealed TATA elements upstream of tRNA genes in Arabidopsis, this pathway may be more widespread than appreciated previously.

A novel TATA-box-binding factor from the silk glands of the mulberry silkworm, Bombyx mori

The presence of one or more TATATAA motifs in the flanking sequences of individual members of a multi-gene tRNA(Gly)(1) family from the mulberry silkworm, Bombyx mori, negatively modulated the transcription of the gene copies. Characterization of proteins from posterior silk gland nuclear extracts, binding to the TATATAA motif, identified a novel 43 kD protein, designated here as P43 TATA-box-binding factor (TBF). The protein was purified to homogeneity. P43 TBF binding was highly sequence-specific and showed a 100-fold-higher affinity for binding than the TATA-box-binding protein (TBP). The protein also showed binding to the TATAAA sequence of the actin5C promoter. P43 TBF inhibited transcription of all the tRNA genes examined, as well as RNA polymerase II transcription from the actin5C promoter. The amino acid sequence of eleven peptides generated from P43 TBF did not share homology with proteins that bind the TATA box, such as TBP, TRF (TBP-related factor) or TLFs (TBP-like factors) reported from other sources. Inhibition of transcription of tRNA genes by P43 TBF could not be reversed by TBP. The inhibitory effect appeared to be exerted through sequestration of the associated transcription factors.

Intragenic promoter adaptation and facilitated RNA polymerase III recycling in the transcription of SCR1, the 7SL RNA gene of Saccharomyces cerevisiae

The SCR1 gene, coding for the 7SL RNA of the signal recognition particle, is the last known class III gene of Saccharomyces cerevisiae that remains to be characterized with respect to its mode of transcription and promoter organization. We show here that SCR1 represents a unique case of a non-tRNA class III gene in which intragenic promoter elements (the TFIIIC-binding A- and B-blocks), corresponding to the D and TpsiC arms of mature tRNAs, have been adapted to a structurally different small RNA without losing their transcriptional function. In fact, despite the presence of an upstream canonical TATA box, SCR1 transcription strictly depends on the presence of functional, albeit quite unusual, A- and B-blocks and requires all the basal components of the RNA polymerase III transcription apparatus, including TFIIIC. Accordingly, TFIIIC was found to protect from DNase I digestion an 80-bp region comprising the A- and B-blocks. B-block inactivation completely compromised TFIIIC binding and transcription capacity in vitro and in vivo. An inactivating mutation in the A-block selectively affected TFIIIC binding to this promoter element but resulted in much more dramatic impairment of in vivo than in vitro transcription. Transcriptional competition and nucleosome disruption experiments showed that this stronger in vivo defect is due to a reduced ability of A-block-mutated SCR1 to compete with other genes for TFIIIC binding and to counteract the assembly of repressive chromatin structures through TFIIIC recruitment. A kinetic analysis further revealed that facilitated RNA polymerase III recycling, far from being restricted to typical small sized class III templates, also takes place on the 522-bp-long SCR1 gene, the longest known class III transcriptional unit.

Differential expression of individual gene copies from within a tRNA multigene family in the mulberry silkworm Bombyx mori

In mulberry silkworm Bombyx mori, tRNA1(Gly) constitutes a multigene family from which the individual members are transcribed at different levels in vitro in homologous nuclear extracts. We report here the quantification of functional transcripts of these gene copies in vivo in B. mori-derived BmN cells based on a suppression assay. The gene copies were converted to encode suppressor tRNAs and co-transfected into cell lines with reporter gene(s) harbouring one or more nonsense mutations and the reporter gene activity was quantified. Individual members of the gene family were transcribed to very high-, medium- and very low-levels, following the same pattern as in vitro. All these gene copies were maximally expressed in Bm cells as compared to other insect cell lines.

Widespread use of TATA elements in the core promoters for RNA polymerases III, II, and I in fission yeast

In addition to directing transcription initiation, core promoters integrate input from distal regulatory elements. Except for rare exceptions, it has been generally found that eukaryotic tRNA and rRNA genes do not contain TATA promoter elements and instead use protein-protein interactions to bring the TATA-binding protein (TBP), to the core promoter. Genomewide analysis revealed TATA elements in the core promoters of tRNA and 5S rRNA (Pol III), U1 to U5 snRNA (Pol II), and 37S rRNA (Pol I) genes in Schizosaccharomyces pombe. Using tRNA-dependent suppression and other in vivo assays, as well as in vitro transcription, we demonstrated an obligatory requirement for upstream TATA elements for tRNA and 5S rRNA expression in S. pombe. The Pol III initiation factor Brf is found in complexes with TFIIIC and Pol III in S. pombe, while TBP is not, consistent with independent recruitment of TBP by TATA. Template commitment assays are consistent with this and confirm that the mechanisms of transcription complex assembly and initiation by Pol III in S. pombe differ substantially from those in other model organisms. The results were extended to large-rRNA synthesis, as mutation of the TATA element in the Pol I promoter also abolishes rRNA expression in fission yeast. A survey of other organisms' genomes reveals that a substantial number of eukaryotes may use widespread TATAs for transcription. These results indicate the presence of TATA-unified transcription systems in contemporary eukaryotes and provide insight into the residual need for TBP by all three Pols in other eukaryotes despite a lack of TATA elements in their promoters.