Unusual enhancer function in yeast rRNA transcription

The rRNA genes in most eucaryotic organisms are present in a tandem array. There is substantial evidence that transcription of one of these genes may not be independent of transcription of others. In particular, in the yeast Saccharomyces cerevisiae, the enhancer of rRNA transcription that lies 2.2 kilobases 5' of the transcription initiation site is at least partly within the upstream transcription unit. To ask more directly about the relationship of the tandemness of these genes to their transcription, we have constructed a minirepeat containing two identifiable test genes, with or without enhancer(s). On integration into the URA3 locus, these genes were transcribed by RNA polymerase I. A single enhancer effectively stimulated transcription of both genes by 10- to 30-fold, even when it was located upstream of both or downstream of both. Two enhancers had roughly additive effects. These results suggest a model of enhancer function in tandemly repeated genes.

Download Full-text

The rRNA enhancer regulates rRNA transcription in Saccharomyces cerevisiae

Molecular and Cellular Biology ◽

10.1128/mcb.13.2.1283-1289.1993 ◽

1993 ◽

Vol 13 (2) ◽

pp. 1283-1289

Author(s):

B E Morrow ◽

S P Johnson ◽

J R Warner

Keyword(s):

Saccharomyces Cerevisiae ◽

Carbon Source ◽

Binding Sites ◽

Major Element ◽

Transcription Unit ◽

Rrna Genes ◽

Nutritional Regulation ◽

Rrna Transcription ◽

Enhancer Function

In Saccharomyces cerevisiae, the rRNA genes are organized as a tandem array of head-to-tail repeats. An enhancer of rRNA transcription is present just at the end of each transcription unit, 2 kb away from the next one. This enhancer is unusual for S. cerevisiae in that it acts both upstream and downstream of, and even across, genes. The role of the enhancer in the nutritional regulation of rRNA transcription was studied by introducing a centromere plasmid carrying two rRNA minigenes in tandem, flanking a single enhancer, into cells. Analysis of the transcripts from the two minigenes showed that the enhancer was absolutely required for the stimulation of transcription of rRNA that occurs when cells are shifted from a poor carbon source to a good carbon source. While full enhancer function is provided by a 45-bp region at the 3' end of the 190-bp enhancer, some activity was also conferred by other elements, including both a T-rich stretch and a region containing the binding sites for the proteins Reb1p and Abf1p. We conclude that the enhancer is composed of redundant elements and that it is a major element in the regulation of rRNA transcription.

Download Full-text

The rRNA enhancer regulates rRNA transcription in Saccharomyces cerevisiae.

Molecular and Cellular Biology ◽

10.1128/mcb.13.2.1283 ◽

1993 ◽

Vol 13 (2) ◽

pp. 1283-1289 ◽

Cited By ~ 20

Author(s):

B E Morrow ◽

S P Johnson ◽

J R Warner

Keyword(s):

Saccharomyces Cerevisiae ◽

Carbon Source ◽

Binding Sites ◽

Major Element ◽

Transcription Unit ◽

Rrna Genes ◽

Nutritional Regulation ◽

Rrna Transcription ◽

Enhancer Function

In Saccharomyces cerevisiae, the rRNA genes are organized as a tandem array of head-to-tail repeats. An enhancer of rRNA transcription is present just at the end of each transcription unit, 2 kb away from the next one. This enhancer is unusual for S. cerevisiae in that it acts both upstream and downstream of, and even across, genes. The role of the enhancer in the nutritional regulation of rRNA transcription was studied by introducing a centromere plasmid carrying two rRNA minigenes in tandem, flanking a single enhancer, into cells. Analysis of the transcripts from the two minigenes showed that the enhancer was absolutely required for the stimulation of transcription of rRNA that occurs when cells are shifted from a poor carbon source to a good carbon source. While full enhancer function is provided by a 45-bp region at the 3' end of the 190-bp enhancer, some activity was also conferred by other elements, including both a T-rich stretch and a region containing the binding sites for the proteins Reb1p and Abf1p. We conclude that the enhancer is composed of redundant elements and that it is a major element in the regulation of rRNA transcription.

Download Full-text

A Novel RNA Polymerase I Transcription Initiation Factor, TIF-IE, Commits rRNA Genes by Interaction with TIF-IB, Not by DNA Binding

Molecular and Cellular Biology ◽

10.1128/mcb.22.3.750-761.2002 ◽

2002 ◽

Vol 22 (3) ◽

pp. 750-761 ◽

Cited By ~ 4

Author(s):

Anna Maria Al-Khouri ◽

Marvin R. Paule

Keyword(s):

Dna Binding ◽

Rna Polymerase ◽

Transcription Initiation ◽

Rna Polymerase I ◽

Initiation Factor ◽

Rrna Genes ◽

Rrna Transcription ◽

Transcription Initiation Factor ◽

Binding Factor ◽

Polymerase I

ABSTRACT In the small, free-living amoeba Acanthamoeba castellanii, rRNA transcription requires, in addition to RNA polymerase I, a single DNA-binding factor, transcription initiation factor IB (TIF-IB). TIF-IB is a multimeric protein that contains TATA-binding protein (TBP) and four TBP-associated factors that are specific for polymerase I transcription. TIF-IB is required for accurate and promoter-specific initiation of rRNA transcription, recruiting and positioning the polymerase on the start site by protein-protein interaction. In A. castellanii, partially purified TIF-IB can form a persistent complex with the ribosomal DNA (rDNA) promoter while homogeneous TIF-IB cannot. An additional factor, TIF-IE, is required along with homogeneous TIF-IB for the formation of a stable complex on the rDNA core promoter. We show that TIF-IE by itself, however, does not bind to the rDNA promoter and thus differs in its mechanism from the upstream binding factor and upstream activating factor, which carry out similar complex-stabilizing functions in vertebrates and yeast, respectively. In addition to its presence in impure TIF-IB, TIF-IE is found in highly purified fractions of polymerase I, with which it associates. Renaturation of polypeptides excised from sodium dodecyl sulfate-polyacrylamide gels showed that a 141-kDa polypeptide possesses all the known activities of TIF-IE.

Download Full-text

The Chloroplast Phylogenomics and Systematics of Zoysia (Poaceae)

Plants ◽

10.3390/plants10081517 ◽

2021 ◽

Vol 10 (8) ◽

pp. 1517

Author(s):

Se-Hwan Cheon ◽

Min-Ah Woo ◽

Sangjin Jo ◽

Young-Kee Kim ◽

Ki-Joong Kim

Keyword(s):

Northeast Asia ◽

Single Copy ◽

Rrna Genes ◽

Bootstrap Support ◽

Trna Genes ◽

Protein Coding ◽

Tropical Regions ◽

Relationship Of ◽

The Relationship ◽

Simple Sequence

The genus Zoysia Willd. (Chloridoideae) is widely distributed from the temperate regions of Northeast Asia—including China, Japan, and Korea—to the tropical regions of Southeast Asia. Among these, four species—Zoysia japonica Steud., Zoysia sinica Hance, Zoysia tenuifolia Thiele, and Zoysia macrostachya Franch. & Sav.—are naturally distributed in the Korean Peninsula. In this study, we report the complete plastome sequences of these Korean Zoysia species (NCBI acc. nos. MF953592, MF967579~MF967581). The length of Zoysia plastomes ranges from 135,854 to 135,904 bp, and the plastomes have a typical quadripartite structure, which consists of a pair of inverted repeat regions (20,962~20,966 bp) separated by a large (81,348~81,392 bp) and a small (12,582~12,586 bp) single-copy region. In terms of gene order and structure, Zoysia plastomes are similar to the typical plastomes of Poaceae. The plastomes encode 110 genes, of which 76 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Fourteen genes contain single introns and one gene has two introns. Three evolutionary hotspot spacer regions—atpB~rbcL, rps16~rps3, and rpl32~trnL-UAG—were recognized among six analyzed Zoysia species. The high divergences in the atpB~rbcL spacer and rpl16~rpl3 region are primarily due to the differences in base substitutions and indels. In contrast, the high divergence between rpl32~trnL-UAG spacers is due to a small inversion with a pair of 22 bp stem and an 11 bp loop. Simple sequence repeats (SSRs) were identified in 59 different locations in Z. japonica, 63 in Z. sinica, 62 in Z. macrostachya, and 63 in Z. tenuifolia plastomes. Phylogenetic analysis showed that the Zoysia (Zoysiinae) forms a monophyletic group, which is sister to Sporobolus (Sporobolinae), with 100% bootstrap support. Within the Zoysia clade, the relationship of (Z. sinica, Z japonica), (Z. tenuifolia, Z. matrella), (Z. macrostachya, Z. macrantha) was suggested.

Download Full-text

Adenovirus 5 E2 transcription unit: an E1A-inducible promoter with an essential element that functions independently of position or orientation

Molecular and Cellular Biology ◽

10.1128/mcb.4.5.875-882.1984 ◽

1984 ◽

Vol 4 (5) ◽

pp. 875-882

Author(s):

M J Imperiale ◽

J R Nevins

Keyword(s):

Transcription Initiation ◽

Essential Element ◽

Inducible Promoter ◽

Initiation Site ◽

Transcription Unit ◽

Upstream Sequence ◽

Wild Type ◽

Promoter Sequences ◽

Adenovirus 5 ◽

Wild Type Promoter

Utilizing deletion mutants of a plasmid containing the adenovirus E2 gene, an E1A-inducible transcription unit, we determined the promoter sequences required for full expression in transient transfection assays. Wild-type expression was obtained from plasmids containing only 79 nucleotides of upstream sequence relative to the transcription initiation site. Removal of an additional nine nucleotides lowered expression 10-fold, and deletion to -59 resulted in near total loss of transcription. Wild-type levels of expression were restored to a -28 deletion mutant by insertion of the sequence from -21 to -262 from the wild-type promoter at the -28 position, in either orientation, even though when inserted in the opposite orientation the relevant sequences were ca. 270 nucleotides upstream from their normal position. Finally, this sequence could be placed at a distance of 4,000 nucleotides from the E2 cap site and still retain near total function. Thus, the E2 promoter element can function independent of orientation and position, properties characteristic of enhancer elements.

Download Full-text

Epigenetic Programming of the rRNA Promoter by MBD3

Molecular and Cellular Biology ◽

10.1128/mcb.01880-06 ◽

2007 ◽

Vol 27 (13) ◽

pp. 4938-4952 ◽

Cited By ~ 61

Author(s):

Shelley E. Brown ◽

Moshe Szyf

Keyword(s):

Small Interfering Rna ◽

Rna Polymerase I ◽

Rrna Genes ◽

Rrna Gene ◽

Rrna Transcription ◽

Epigenetic Programming ◽

Binding Factor ◽

Upstream Binding Factor ◽

Polymerase I ◽

Interfering Rna

ABSTRACT Within the human genome there are hundreds of copies of the rRNA gene, but only a fraction of these genes are active. Silencing through epigenetics has been extensively studied; however, it is essential to understand how active rRNA genes are maintained. Here, we propose a role for the methyl-CpG binding domain protein MBD3 in epigenetically maintaining active rRNA promoters. We show that MBD3 is localized to the nucleolus, colocalizes with upstream binding factor, and binds to unmethylated rRNA promoters. Knockdown of MBD3 by small interfering RNA results in increased methylation of the rRNA promoter coupled with a decrease in RNA polymerase I binding and pre-rRNA transcription. Conversely, overexpression of MBD3 results in decreased methylation of the rRNA promoter. Additionally, overexpression of MBD3 induces demethylation of nonreplicating plasmids containing the rRNA promoter. We demonstrate that this demethylation occurs following the overexpression of MBD3 and its increased interaction with the methylated rRNA promoter. This is the first demonstration that MBD3 is involved in inducing and maintaining the demethylated state of a specific promoter.

Download Full-text

Identification of the transcription initiation site of the asexually expressed rRNA genes of the malaria parasite Plasmodium berghei

Molecular and Biochemical Parasitology ◽

10.1016/s0166-6851(99)00016-x ◽

1999 ◽

Vol 99 (2) ◽

pp. 193-205 ◽

Cited By ~ 4

Author(s):

Rosalina M.L. van Spaendonk ◽

Glenn A. McConkey ◽

Jai Ramesar ◽

Andrei Gabrielian ◽

Thomas F. McCutchan ◽

...

Keyword(s):

Plasmodium Berghei ◽

Transcription Initiation ◽

Malaria Parasite ◽

Initiation Site ◽

Transcription Initiation Site ◽

Rrna Genes ◽

Parasite Plasmodium

Download Full-text

An unusual Y chromosome of Drosophila simulans carrying amplified rDNA spacer without rRNA genes.

Genetics ◽

10.1093/genetics/125.2.399 ◽

1990 ◽

Vol 125 (2) ◽

pp. 399-406

Author(s):

A R Lohe ◽

P A Roberts

Keyword(s):

Y Chromosome ◽

Initiation Site ◽

Drosophila Simulans ◽

Rrna Genes ◽

Rdna Transcription ◽

Nontranscribed Spacer ◽

Protein Factor ◽

Y Chromosomes ◽

Full Complement ◽

Polymerase I

Abstract The X and Y chromosomes of Drosophila melanogaster each contain a cluster of several hundred ribosomal RNA genes (rDNA). A nontranscribed spacer region separates adjacent rRNA genes and contains tandem copies of 240 bp repeats that include the initiation site for RNA polymerase I transcription. We show here that Drosophila simulans, a sibling species of D. melanogaster, contains few, if any, rRNA genes on its Y chromosome but carries instead a large block (3,000 kb or 12,500 copies) of 240 bp nontranscribed spacer repeats. The repeats are located at the tip of the long arm of the simulans Y chromosome, in contrast to their location among rRNA genes on the short arm of the Y chromosome of D. melanogaster. The bobbed mutation in homozygous females of D. melanogaster shortens and thins the bristles, owing to a partial deletion of rRNA genes on the X chromosome. The bristles of bobbed/Y males are normal owing to the presence of a full complement of rRNA genes on the Y chromosome. Peculiarly, in bobbed/Y males of D. simulans the short bristle phenotype does not return to normal but is enhanced by the presence of the Y chromosome. We propose that the 12,500 nontranscribed spacer repeats on the Y chromosome are responsible for this biological effect by competition for a protein factor(s) essential for normal levels of rDNA transcription at the X-linked locus.

Download Full-text

Events during eucaryotic rRNA transcription initiation and elongation: conversion from the closed to the open promoter complex requires nucleotide substrates

Molecular and Cellular Biology ◽

10.1128/mcb.8.5.1940-1946.1988 ◽

1988 ◽

Vol 8 (5) ◽

pp. 1940-1946

Author(s):

E Bateman ◽

M R Paule

Keyword(s):

Rna Polymerase ◽

Transcription Initiation ◽

Topological Analysis ◽

Acanthamoeba Castellanii ◽

Rna Polymerase I ◽

Initiation Factor ◽

Rrna Transcription ◽

Promoter Complex ◽

Polymerase I

Chemical footprinting and topological analysis were carried out on the Acanthamoeba castellanii rRNA transcription initiation factor (TIF) and RNA polymerase I complexes with DNA during transcription initiation and elongation. The results show that the binding of TIF and polymerase to the promoter does not alter the supercoiling of the DNA template and the template does not become sensitive to modification by diethylpyrocarbonate, which can identify melted DNA regions. Thus, in contrast to bacterial RNA polymerase, the eucaryotic RNA polymerase I-promoter complex is in a closed configuration preceding addition of nucleotides in vitro. Initiation and 3'-O-methyl CTP-limited translocation by RNA polymerase I results in separation of the polymerase-TIF footprints, leaving the TIF footprint unaltered. In contrast, initiation and translocation result in a significant change in the conformation of the polymerase-DNA complex, culminating in an unwound DNA region of at least 10 base pairs.

Download Full-text