Polyproline, β-turn helices. Novel secondary structures proposed for the tandem repeats within rhodopsin, synaptophysin, synexin, gliadin, RNA polymerase II, hordein, and gluten

Pervasive transcription is widespread in eukaryotes, generating large families of non-coding RNAs. Such pervasive transcription is a key player in the regulatory pathways controlling chromatin state and gene expression. Here, we describe long non-coding RNAs generated from the ribosomal RNA gene promoter called UPStream-initiating transcripts (UPS). In yeast, rDNA genes are organized in tandem repeats in at least two different chromatin states, either transcribed and largely depleted of nucleosomes (open) or assembled in regular arrays of nucleosomes (closed). The production of UPS transcripts by RNA Polymerase II from endogenous rDNA genes was initially documented in mutants defective for rRNA production by RNA polymerase I. We show here that UPS are produced in wild-type cells from closed rDNA genes but are hidden within the enormous production of rRNA. UPS levels are increased when rDNA chromatin states are modified at high temperatures or entering/leaving quiescence. We discuss their role in the regulation of rDNA chromatin states and rRNA production.

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Characterization and expression of a spliced leader RNA in the parasitic nematode Ascaris lumbricoides var. suum

Molecular and Cellular Biology ◽

10.1128/mcb.9.8.3543-3547.1989 ◽

1989 ◽

Vol 9 (8) ◽

pp. 3543-3547

Author(s):

T W Nilsen ◽

J Shambaugh ◽

J Denker ◽

G Chubb ◽

C Faser ◽

...

Keyword(s):

Caenorhabditis Elegans ◽

Secondary Structure ◽

Rna Polymerase ◽

Binding Site ◽

Rna Polymerase Ii ◽

Ascaris Lumbricoides ◽

Parasitic Nematode ◽

Secondary Structures ◽

Spliced Leader ◽

C Elegans

The parasitic nematode Ascaris spp. contains a 22-nucleotide spliced-leader (SL) sequence identical to the trans-SL previously described in Caenorhabditis elegans and other nematodes. The SL comprises the first 22 nucleotides of a approximately 110-base RNA and is transcribed by RNA polymerase II. The SL RNA contains a trimethylguanosine cap and a consensus Sm binding site. Furthermore, the Ascaris SL RNA has the potential to adopt a secondary structure which is nearly identical to potential secondary structures of similar SL RNAs in C. elegans and Brugia malayi.

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Tyrosine phosphorylation of mammalian RNA polymerase II carboxyl-terminal domain

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.90.23.11167 ◽

1993 ◽

Vol 90 (23) ◽

pp. 11167-11171 ◽

Cited By ~ 142

Author(s):

R Baskaran ◽

M E Dahmus ◽

J Y Wang

Keyword(s):

Tyrosine Kinase ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Tandem Repeats ◽

Consensus Sequence ◽

Src Tyrosine Kinase ◽

Terminal Domain ◽

Carboxyl Terminal Domain ◽

Carboxyl Terminal

The carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II is composed of tandem repeats of the consensus sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser. Phosphorylation of the CTD occurs during formation of the initiation complex and is correlated with the transition from complex assembly to elongation. Previously, serine and threonine residues within the CTD have been shown to be modified by the addition of phosphate and by the addition of O-linked GlcNAc. Our results establish that the CTD is also modified in vivo by phosphorylation on tyrosine. Furthermore, a nuclear tyrosine kinase encoded by the c-abl protooncogene phosphorylates the CTD to a high stoichiometry in vitro. Under conditions of maximum phosphorylation, approximately 30 mol of phosphate are incorporated per mol of CTD. The observation that the CTD is not phosphorylated by c-Src tyrosine kinase under identical conditions indicates that the CTD is not a substrate of all tyrosine kinases. Phosphorylation of tyrosine residues within the CTD may modulate the interaction of RNA polymerase II with the preinitiation complex and, hence, may be important in regulating gene expression.

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Characterization and expression of a spliced leader RNA in the parasitic nematode Ascaris lumbricoides var. suum.

Molecular and Cellular Biology ◽

10.1128/mcb.9.8.3543 ◽

1989 ◽

Vol 9 (8) ◽

pp. 3543-3547 ◽

Cited By ~ 47

Author(s):

T W Nilsen ◽

J Shambaugh ◽

J Denker ◽

G Chubb ◽

C Faser ◽

...

Keyword(s):

Caenorhabditis Elegans ◽

Secondary Structure ◽

Rna Polymerase ◽

Binding Site ◽

Rna Polymerase Ii ◽

Ascaris Lumbricoides ◽

Parasitic Nematode ◽

Secondary Structures ◽

Spliced Leader ◽

C Elegans

The parasitic nematode Ascaris spp. contains a 22-nucleotide spliced-leader (SL) sequence identical to the trans-SL previously described in Caenorhabditis elegans and other nematodes. The SL comprises the first 22 nucleotides of a approximately 110-base RNA and is transcribed by RNA polymerase II. The SL RNA contains a trimethylguanosine cap and a consensus Sm binding site. Furthermore, the Ascaris SL RNA has the potential to adopt a secondary structure which is nearly identical to potential secondary structures of similar SL RNAs in C. elegans and Brugia malayi.

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Suppression Analysis Reveals a Functional Difference Between the Serines in Positions Two and Five in the Consensus Sequence of the C-Terminal Domain of Yeast RNA Polymerase II

Genetics ◽

10.1093/genetics/143.2.661 ◽

1996 ◽

Vol 143 (2) ◽

pp. 661-671 ◽

Cited By ~ 6

Author(s):

Anton Yuryev ◽

Jeffry L Corden

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Tandem Repeats ◽

Consensus Sequence ◽

Functional Difference ◽

Terminal Domain ◽

Truncation Mutation ◽

Cold Sensitive ◽

Substitution Mutations ◽

Multiple Substitution

Abstract The largest subunit of RNA polymerase II contains a repetitive C-terminal domain (CTD) consisting of tandem repeats of the consensus sequence TyrlSer2Pro3Thr4Ser5Pro6Ser7. Substitution of nonphosphe rylatable amino acids at positions two or five of the Saccharomyces cerevisiae CTD is lethal. We developed a selection ssytem for isolating suppressors of this lethal phenotype and cloned a gene, SCA1 (suppressor of CTD alanine), which complements recessive suppressors of lethal multiple-substitution mutations. A partial deletion of SCA1 (sca1Δ::hisG) suppresses alanine or glutamate substitutions at position two of the consensus CTD sequence, and a lethal CTD truncation mutation, but SCA1 deletion does not suppress alanine or glutamate substitutions at position five. SCA1 is identical to SRB9, a suppressor of a cold-sensitive CTD truncation mutation. Strains carrying dominant SRB mutations have the same suppression properties as a sca1Δ::hisG strain. These results reveal a functional difference between positions two and five of the consensus CTD heptapeptide repeat. The ability of SCA1 and SRB mutant alleles to suppress CTD truncation mutations suggest that substitutions at position two, but not at position five, cause a defect in RNA polymerase II function similar to that introduced by CTD truncation.

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Transcription Factor UAF, Expansion and Contraction of Ribosomal DNA (rDNA) Repeats, and RNA Polymerase Switch in Transcription of Yeast rDNA

Molecular and Cellular Biology ◽

10.1128/mcb.19.12.8559 ◽

1999 ◽

Vol 19 (12) ◽

pp. 8559-8569 ◽

Cited By ~ 54

Author(s):

Melanie Oakes ◽

Imran Siddiqi ◽

Loan Vu ◽

John Aris ◽

Masayasu Nomura

Keyword(s):

Transcription Factor ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Ribosomal Dna ◽

Tandem Repeats ◽

Single Mutation ◽

Rdna Transcription ◽

Pol Ii ◽

Pol I

ABSTRACT Strains of the yeast Saccharomyces cerevisiae defective in transcription factor UAF give rise to variants able to grow by transcribing endogenous ribosomal DNA (rDNA) by RNA polymerase II (Pol II). We have demonstrated that the switch to growth using the Pol II system consists of two steps: a mutational alteration in UAF and an expansion of chromosomal rDNA repeats. The first step, a single mutation in UAF, is sufficient to allow Pol II transcription of rDNA. In contrast to UAF mutations, mutations in Pol I or other Pol I transcription factors can not independently lead to Pol II transcription of rDNA, suggesting a specific role of UAF in preventing polymerase switch. The second step, expansion of chromosomal rDNA repeats to levels severalfold higher than the wild type, is required for efficient cell growth. Mutations in genes that affect recombination within the rDNA repeats, fob1 and sir2, decrease and increase, respectively, the frequency of switching to growth using Pol II, indicating that increased rDNA copy number is a cause rather than a consequence of the switch. Finally, we show that the switch to the Pol II system is accompanied by a striking alteration in the localization and morphology of the nucleolus. The altered state that uses Pol II for rDNA transcription is semistable and heritable through mitosis and meiosis. We discuss the significance of these observations in relation to the plasticity of rDNA tandem repeats and nucleolar structures as well as evolution of the Pol I machinery.

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Nutrient-regulated gene expression in eukaryotes

Biochemical Society Symposium ◽

10.1042/bss0730085 ◽

2006 ◽

Vol 73 ◽

pp. 85-96 ◽

Cited By ~ 8

Author(s):

Richard J. Reece ◽

Laila Beynon ◽

Stacey Holden ◽

Amanda D. Hughes ◽

Karine Rébora ◽

...

Keyword(s):

Gene Expression ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Transcriptional Control ◽

Direct Interaction ◽

Signalling Pathways ◽

A Cell ◽

One Step ◽

Higher Eukaryotes ◽

Regulated Gene Expression

The recognition of changes in environmental conditions, and the ability to adapt to these changes, is essential for the viability of cells. There are numerous well characterized systems by which the presence or absence of an individual metabolite may be recognized by a cell. However, the recognition of a metabolite is just one step in a process that often results in changes in the expression of whole sets of genes required to respond to that metabolite. In higher eukaryotes, the signalling pathway between metabolite recognition and transcriptional control can be complex. Recent evidence from the relatively simple eukaryote yeast suggests that complex signalling pathways may be circumvented through the direct interaction between individual metabolites and regulators of RNA polymerase II-mediated transcription. Biochemical and structural analyses are beginning to unravel these elegant genetic control elements.

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