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Agrawal S, Ganley ARD. The conservation landscape of the human ribosomal RNA gene repeats. PLoS One 2018; 13:e0207531. [PMID: 30517151 PMCID: PMC6281188 DOI: 10.1371/journal.pone.0207531] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 11/01/2018] [Indexed: 01/27/2023] Open
Abstract
Ribosomal RNA gene repeats (rDNA) encode ribosomal RNA, a major component of ribosomes. Ribosome biogenesis is central to cellular metabolic regulation, and several diseases are associated with rDNA dysfunction, notably cancer, However, its highly repetitive nature has severely limited characterization of the elements responsible for rDNA function. Here we make use of phylogenetic footprinting to provide a comprehensive list of novel, potentially functional elements in the human rDNA. Complete rDNA sequences for six non-human primate species were constructed using de novo whole genome assemblies. These new sequences were used to determine the conservation profile of the human rDNA, revealing 49 conserved regions in the rDNA intergenic spacer (IGS). To provide insights into the potential roles of these conserved regions, the conservation profile was integrated with functional genomics datasets. We find two major zones that contain conserved elements characterised by enrichment of transcription-associated chromatin factors, and transcription. Conservation of some IGS transcripts in the apes underpins the potential functional significance of these transcripts and the elements controlling their expression. Our results characterize the conservation landscape of the human IGS and suggest that noncoding transcription and chromatin elements are conserved and important features of this unique genomic region.
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Affiliation(s)
- Saumya Agrawal
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Austen R. D. Ganley
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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Mars JC, Sabourin-Felix M, Tremblay MG, Moss T. A Deconvolution Protocol for ChIP-Seq Reveals Analogous Enhancer Structures on the Mouse and Human Ribosomal RNA Genes. G3 (BETHESDA, MD.) 2018; 8:303-314. [PMID: 29158335 PMCID: PMC5765358 DOI: 10.1534/g3.117.300225] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/15/2017] [Indexed: 02/07/2023]
Abstract
The combination of Chromatin Immunoprecipitation and Massively Parallel Sequencing, or ChIP-Seq, has greatly advanced our genome-wide understanding of chromatin and enhancer structures. However, its resolution at any given genetic locus is limited by several factors. In applying ChIP-Seq to the study of the ribosomal RNA genes, we found that a major limitation to resolution was imposed by the underlying variability in sequence coverage that very often dominates the protein-DNA interaction profiles. Here, we describe a simple numerical deconvolution approach that, in large part, corrects for this variability, and significantly improves both the resolution and quantitation of protein-DNA interaction maps deduced from ChIP-Seq data. This approach has allowed us to determine the in vivo organization of the RNA polymerase I preinitiation complexes that form at the promoters and enhancers of the mouse (Mus musculus) and human (Homo sapiens) ribosomal RNA genes, and to reveal a phased binding of the HMG-box factor UBF across the rDNA. The data identify and map a "Spacer Promoter" and associated stalled polymerase in the intergenic spacer of the human ribosomal RNA genes, and reveal a very similar enhancer structure to that found in rodents and lower vertebrates.
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Affiliation(s)
- Jean-Clement Mars
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Québec, Canada
| | - Marianne Sabourin-Felix
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Québec, Canada
| | - Michel G Tremblay
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, G1R 3S3, Canada
| | - Tom Moss
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Québec, Canada
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Agrawal S, Ganley ARD. Complete Sequence Construction of the Highly Repetitive Ribosomal RNA Gene Repeats in Eukaryotes Using Whole Genome Sequence Data. Methods Mol Biol 2016; 1455:161-181. [PMID: 27576718 DOI: 10.1007/978-1-4939-3792-9_13] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The ribosomal RNA genes (rDNA) encode the major rRNA species of the ribosome, and thus are essential across life. These genes are highly repetitive in most eukaryotes, forming blocks of tandem repeats that form the core of nucleoli. The primary role of the rDNA in encoding rRNA has been long understood, but more recently the rDNA has been implicated in a number of other important biological phenomena, including genome stability, cell cycle, and epigenetic silencing. Noncoding elements, primarily located in the intergenic spacer region, appear to mediate many of these phenomena. Although sequence information is available for the genomes of many organisms, in almost all cases rDNA repeat sequences are lacking, primarily due to problems in assembling these intriguing regions during whole genome assemblies. Here, we present a method to obtain complete rDNA repeat unit sequences from whole genome assemblies. Limitations of next generation sequencing (NGS) data make them unsuitable for assembling complete rDNA unit sequences; therefore, the method we present relies on the use of Sanger whole genome sequence data. Our method makes use of the Arachne assembler, which can assemble highly repetitive regions such as the rDNA in a memory-efficient way. We provide a detailed step-by-step protocol for generating rDNA sequences from whole genome Sanger sequence data using Arachne, for refining complete rDNA unit sequences, and for validating the sequences obtained. In principle, our method will work for any species where the rDNA is organized into tandem repeats. This will help researchers working on species without a complete rDNA sequence, those working on evolutionary aspects of the rDNA, and those interested in conducting phylogenetic footprinting studies with the rDNA.
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Affiliation(s)
- Saumya Agrawal
- Institute of Natural and Mathematical Sciences, Massey University, Private Bag 102-904, Auckland, 0632, New Zealand.
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - Austen R D Ganley
- Institute of Natural and Mathematical Sciences, Massey University, Private Bag 102-904, Auckland, 0632, New Zealand.
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
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Komarova NY, Grabe T, Huigen DJ, Hemleben V, Volkov RA. Organization, differential expression and methylation of rDNA in artificial Solanum allopolyploids. PLANT MOLECULAR BIOLOGY 2004; 56:439-63. [PMID: 15604755 DOI: 10.1007/s11103-004-4678-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Uniparental activity of ribosomal RNA genes (rDNA) in interspecific hybrids is known as nucleolar dominance (ND). To see if difference in rDNA intergenic spacers (IGS) might be correlated with ND, we have used artificial Solanum allopolyploids and back-crossed lines. Combining fluorescence in situ hybridization and quantification of the level of the rRNA precursor by real-time PCR, we demonstrated that an expression hierarchy exists: In leaves, roots, and petals of the respective allopolyploids, rDNA of S lycopersicum (tomato) dominates over rDNA of S. tuberosum (potato), whereas rDNA of S. tuberosum dominates over that of the wild species S. bulbocastanum . Also in a monosomic addition line carrying only one NOR-bearing chromosome of tomato in a potato background the dominance effect was maintained. These results demonstrate that there is possible correlation between transcriptional dominance and number of conservative elements downstream of the transcription start in the Solanum rDNA. In anthers and callus tissues under-dominant rDNA was slightly (S. lycopersicum/S. tuberosum) or strongly (S. tuberosum/S. bulbocastanum) expressed indicating developmental modulation of ND. In leaves and petals, repression of the respective parental rDNA correlated with cytosine methylation at certain sites conserved in the IGS, whereas activation of under-dominant rDNA in anthers and callus tissues was not accompanied by considerable changes of the methylation pattern.
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MESH Headings
- Base Sequence
- Crosses, Genetic
- DNA Methylation
- DNA, Plant/chemistry
- DNA, Plant/genetics
- DNA, Plant/isolation & purification
- DNA, Ribosomal/genetics
- DNA, Ribosomal/metabolism
- DNA, Ribosomal Spacer/genetics
- Gene Expression Profiling
- Gene Expression Regulation, Plant
- In Situ Hybridization, Fluorescence
- Molecular Sequence Data
- Polyploidy
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Solanum/genetics
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Affiliation(s)
- Nataliya Y Komarova
- Department of General Genetics, Center of Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 28, Tübingen, 72076, Germany
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Hemleben V, Volkov RA, Zentgraf U, Medina FJ. Molecular Cell Biology: Organization and Molecular Evolution of rDNA, Nucleolar Dominance, and Nucleolus Structure. PROGRESS IN BOTANY 2004. [DOI: 10.1007/978-3-642-18819-0_5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Pikaard CS. Transcription and tyranny in the nucleolus: the organization, activation, dominance and repression of ribosomal RNA genes. THE ARABIDOPSIS BOOK 2002; 1:e0083. [PMID: 22303219 PMCID: PMC3243331 DOI: 10.1199/tab.0083] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Affiliation(s)
- Craig S Pikaard
- Biology Department, Washington University, Campus box 1137, 1 Brookings Drive, St. Louis, Missouri, 63130, USA ; FAX: 314-935-4432;
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Pikaard CS. Nucleolar dominance: uniparental gene silencing on a multi-megabase scale in genetic hybrids. PLANT MOLECULAR BIOLOGY 2000; 43:163-77. [PMID: 10999402 DOI: 10.1023/a:1006471009225] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Nucleolar dominance is a phenomenon in hybrids or allopolyploids in which nucleoli form on chromosomes inherited from only one of the two parents. The molecular basis for nucleolar dominance is the transcription by RNA polymerase I of only one parental set of ribosomal RNA genes (rRNA genes). These rRNA genes are clustered by the hundreds, or thousands, of copies, often spanning tens of millions of basepairs of chromosomal DNA at loci known as nucleolus organizer regions (NORs). Enforcement of nucleolar dominance appears to be accomplished by selectively silencing one set of rRNA genes via chemical modifications of chromatin. However, the mechanisms responsible for initially discriminating among the parental sets of rRNA genes and establishing nucleolar dominance remain unclear. Possibilities include mechanisms that act on each rRNA gene or mechanisms that affect whole NORs or even larger chromosomal domains. This review provides a historical perspective of nucleolar dominance research, explores the most popular hypotheses and their shortcomings, and offers some speculations concerning alternative hypotheses to be considered.
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Affiliation(s)
- C S Pikaard
- Biology Department, Washington University, St. Louis, MO 63130, USA.
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Arts GJ, Englmeier L, Mattaj IW. Energy- and temperature-dependent in vitro export of RNA from synthetic nuclei. Biol Chem 1997; 378:641-9. [PMID: 9278143 DOI: 10.1515/bchm.1997.378.7.641] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We describe a novel assay for the study of RNA export from the nucleus in vitro. Nuclei are assembled in Xenopus egg extract on paramagnetic beads coated with DNA containing a specific template for transcription. T7 RNA polymerase, to which a nuclear localisation signal is attached, is added to the nuclei, and after its import into the assembled nuclei, transcription is allowed to proceed. The use of radioactive NTPs coupled with the possibility to purify the nuclei on a magnet and thus rapidly change the extract in which the nuclei are incubated allows pulse-chase labelling experiments. Using these protocols we show that U1 snRNA-derived templates are transcribed inside the synthetic nuclei, and that the transcripts leave the intact nuclei in a time-, temperature- and energy-dependent way. This offers the possibility of a biochemical approach to the dissection of RNA export.
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Affiliation(s)
- G J Arts
- Gene Expression Programme, European Molecular Biology Laboratory, Heidelberg, Germany
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Mougey EB, Pape LK, Sollner-Webb B. Virtually the entire Xenopus laevis rDNA multikilobase intergenic spacer serves to stimulate polymerase I transcription. J Biol Chem 1996; 271:27138-45. [PMID: 8900206 DOI: 10.1074/jbc.271.43.27138] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The promoter-distal half of the spacer separating the tandem Xenopus laevis rRNA genes consists of "0" and "1" repetitive elements that have been considered unimportant in polymerase I transcriptional activation. Utilizing oocyte microinjection, we now demonstrate that the 0/1 region, as well as its component 0 and 1 repeats, substantially stimulate transcription from a ribosomal promoter in cis and inhibit transcription when located in trans. Both the cis and trans responses increase linearly with increasing numbers of 0 or 1 repeats until saturation is approached. The 0/1 block and its component elements stimulate transcription in both orientations, over distances, and when placed downstream of the initiation site, properties for which the 60/81-base pair (bp) repeats have been defined as polymerase I enhancers. In their natural promoter-distal rDNA location, the 0/1 repeats can stimulate transcription from the rRNA gene promoter, above the level afforded by the intervening 60/81-bp repeats and spacer promoter. In addition, as with the 60/81-bp repeats, the 0/1 repeats bind a factor in common with the rDNA promoter. Thus, the entire X. laevis rDNA intergenic spacer (the 0 repeats, 1 repeats, spacer promoter repeats, and 60/81-bp repeats) acts together to enhance ribosomal transcription.
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Affiliation(s)
- E B Mougey
- Department of Biological Chemistry, Johns Hopkins University, School of Medicine, Baltimore, Maryland 21205, USA
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Kang JJ, Yokoi TJ, Holland MJ. Binding sites for abundant nuclear factors modulate RNA polymerase I-dependent enhancer function in Saccharomyces cerevisiae. J Biol Chem 1995; 270:28723-32. [PMID: 7499394 DOI: 10.1074/jbc.270.48.28723] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The 190-base pair (bp) rDNA enhancer within the intergenic spacer sequences of Saccharomyces cerevisiae rRNA cistrons activates synthesis of the 35S-rRNA precursor about 20-fold in vivo (Mestel,, R., Yip, M., Holland, J. P., Wang, E., Kang, J., and Holland, M. J. (1989) Mol. Cell. Biol. 9, 1243-1254). We now report identification and analysis of transcriptional activities mediated by three cis-acting sites within a 90-bp portion of the rDNA enhancer designated the modulator region. In vivo, these sequences mediated termination of transcription by RNA polymerase I and potentiated the activity of the rDNA enhancer element. Two trans-acting factors, REB1 and REB2, bind independently to sites within the modulator region (Morrow, B. E., Johnson, S. P., and Warner, J. R. (1989) J. Biol. Chem. 264, 9061-9068). We show that REB2 is identical to the ABF1 protien. Site-directed mutagenesis of REB1 and ABF1 binding sites demonstrated uncoupling of RNA polymerase I-dependent termination from transcriptional activation in vivo. We conclude that REB1 and ABF1 are required for RNA polymerase I-dependent termination and enhancer function, respectively, Since REB1 and ABF1 proteins also regulate expression of class II genes and other nuclear functions, our results suggest further similarities between RNA polymerase I and II regulatory mechanisms. Two rDNA enhancers flanking a rDNA minigene stimulated RNA polymerase I transcription in a "multiplicative" fashion. Deletion mapping analysis showed that similar cis-acting sequences were required for enhancer function when positioned upstream or downstream from a rDNA minigene.
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Affiliation(s)
- J J Kang
- Department of Biological Chemistry, School of Medicine, University of California, Davis 95616-8635, USA
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12
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Moss T, Stefanovsky VY. Promotion and regulation of ribosomal transcription in eukaryotes by RNA polymerase I. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1995; 50:25-66. [PMID: 7754036 DOI: 10.1016/s0079-6603(08)60810-7] [Citation(s) in RCA: 154] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- T Moss
- Cancer Research Centre, Laval University, Hôtel-Dieu de Québec, Canada
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13
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Abstract
We examine the RNA polymerase II-dependent transcription directed by several promoters in extracts prepared from distinct developmental stages of Xenopus laevis. RNA polymerase II accurately initiates transcription from the cytomegalovirus, herpes simplex virus thymidine kinase, and Xenopus heat-shock protein (hsp) 70 promoters. The efficiency of transcription of these different promoters is dependent on whether extracts from oocytes, eggs, or somatic cells are used and on the temperature of incubation. In contrast to the viral promoters, the hsp 70 promoter is more active at heat shock temperatures in oocyte and egg extracts (31 degrees-34 degrees C) than at physiological temperatures for Xenopus (20 degrees-25 degrees C). These in vitro transcription extracts should be useful in examining the molecular mechanisms responsible for differential gene expression during Xenopus development.
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Affiliation(s)
- T Toyoda
- Laboratory of Molecular Embryology, National Institutes of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
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Toyoda T, Wolffe AP. In vitro transcription by RNA polymerase II in extracts of Xenopus oocytes, eggs, and somatic cells. Anal Biochem 1992; 203:340-7. [PMID: 1416031 DOI: 10.1016/0003-2697(92)90322-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We describe procedures for preparing extracts of Xenopus oocytes, eggs, and somatic cells that will accurately transcribe class II genes. A variety of viral and Xenopus promoters direct the accurate initiation of transcription by RNA polymerase II in these extracts. Optimal ionic conditions (100-200 mM KCl, 12 mM MgCl2), template concentration (20-40 micrograms/ml), incubation time (30-60 min), and temperature (25 degrees C) for class II gene transcription are described.
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Affiliation(s)
- T Toyoda
- Laboratory of Molecular Embryology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
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15
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Gruendler P, Unfried I, Pascher K, Schweizer D. rDNA intergenic region from Arabidopsis thaliana. Structural analysis, intraspecific variation and functional implications. J Mol Biol 1991; 221:1209-22. [PMID: 1682499 DOI: 10.1016/0022-2836(91)90929-z] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The ribosomal gene intergenic region from Arabidopsis thaliana contains four clusters of mutually unrelated repeated sequences. By comparison with the respective regions in two other Brassicaceae, Raphanus and Sinapis, the putative promoter sequence for RNA polymerase I was located. The homologies suggest that the RNA polymerase I promoter in Brassicaceae ranges further upstream than in animals. Upstream duplications of at least a part of the promoter region were found to be located between individual blocks of the largest internal repeat family ("A" repeats), which is made up of multiple repeats of two closely related sequences 21 or 20 bp in length. Overall structural similarities of the A. thaliana rDNA intergenic region with those from wheat and from Xenopus laevis are discussed. We also present data on the range of intraspecific length heterogeneities found in the central EcoRI fragment of the intergenic region and on the frequencies with which specific length variants occur in the genome. To determine the nature of the length heterogeneities, we sequenced the central EcoRI fragments from four independently isolated genomic clones. Three levels of rearrangements were detected. Length variation can be caused by duplication of a whole A repeat block, or, most frequently, by insertion and/or deletion of one or a few A repeat units. Surprisingly, single base mutations are extremely rare, which hints at some mechanism of homogenization which might be acting on the intergenic region. A possible function of the described sequences in transcriptional regulation is discussed and will be the aim of further investigations.
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Affiliation(s)
- P Gruendler
- University of Vienna, Department of Cytology and Genetics, Austria
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Butlin M, Quincey R. The yeast rRNA gene enhancer does not function by recycling RNA polymerase I and cannot act as a UAS. Curr Genet 1991; 20:9-16. [PMID: 1934122 DOI: 10.1007/bf00312759] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The mechanism of action of the yeast rRNA gene enhancer was investigated by measuring transcription of an rRNA minigene, cloned into a multicopy plasmid, in transformed yeast. Expression of the minigene was increased when the enhancer was cloned either upstream of or downstream from the minigene. When an enhancer was present both upstream and downstream of the minigene, the upstream element was functionally dominant. The upstream enhancer was active in this construct in the absence of detectable read-through by any RNA polymerase. In a construct containing tandem rRNA minigenes, an enhancer element located between the two promoters activated transcription from both independently. Therefore, the enhancer does not appear to activate transcription by recycling RNA polymerase I molecules to the promoter. The enhancer also failed to activate transcription from the intact promoter of the yeast CYC1 gene, and was unable to functionally substitute for the natural upstream activation sequences (UASs) of this gene. Therefore, the enhancer functions differently to UASs of RNA polymerase II genes, and is probably polymerase-specific.
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Affiliation(s)
- M Butlin
- School of Biochemistry, University of Birmingham, UK
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Kermekchiev M, Pettersson M, Matthias P, Schaffner W. Every enhancer works with every promoter for all the combinations tested: could new regulatory pathways evolve by enhancer shuffling? Gene Expr 1991; 1:71-81. [PMID: 1668145 PMCID: PMC5952201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/1990] [Accepted: 01/15/1991] [Indexed: 12/28/2022]
Abstract
The promoters and enhancers of cell type-specific genes are often conserved in evolution, and hence one might expect that a given enhancer has evolved to work best with its own promoter. While this expectation may be realized in some cases, we have not found evidence for it. A total of 27 combinations of different promoters and enhancers were tested by transfection into cultured cells. We found that the relative efficiency of the enhancers is approximately the same, irrespective of the type of promoter used, i.e., there was no strong preference for any given enhancer/promoter combination. Notably, we do not see particularly strong transcription when the immunoglobulin kappa enhancer (or the immunoglobulin heavy chain enhancer) is used to activate a kappa gene promoter. We propose that a generally permissive enhancer/promoter interaction is of evolutionary benefit for higher eukaryotes: by enhancer shuffling, genes could be easily brought under a new type of inducibility/cell type specificity.
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Affiliation(s)
- M Kermekchiev
- Institute for Molecular Biology II, University of Zurich, Switzerland
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Abstract
Although the typical, actively growing eukaryotic cell contains over 10,000 different transcripts, half of its RNA synthetic capacity is devoted to the production of a single kind of RNA. This is the pre-ribosomal RNA, which is synthesized in a special compartment of the nucleus, the nucleolus, and is the exclusive product of transcription by RNA polymerase I. In vivo and in vitro approaches have revealed the major features of rRNA gene transcription and of the subsequent processing of the primary transcript.
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Affiliation(s)
- B Sollner-Webb
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
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19
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Lue NF, Kornberg RD. Accurately initiated, enhancer-dependent transcription by RNA polymerase I in yeast extracts. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(17)44720-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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