Synthesis-Mediated Release of a Small RNA Inhibitor of RNA Polymerase

Wassarman, Karen M.; Saecker, Ruth M.

doi:10.1126/science.1134830

Cited by 160 publications

(271 citation statements)

References 25 publications

Supporting

Mentioning

258

Contrasting

Order By: Relevance

“…Such a network of contacts was not present during the assembly of the artificial elongation complexes (18). Interestingly, Escherichia coli 6S RNA has been shown to block bacterial RNA polymerase from binding promoter DNA (19). Here, we found that binding of an inhibitory ncRNA to Pol II also prevented interaction with promoter DNA; however, in the eukaryotic system the interactions between Pol II and the GTFs allowed complexes that contained promoter DNA to form.…”

Section: Discussionmentioning

confidence: 62%

“…Here, we found that binding of an inhibitory ncRNA to Pol II also prevented interaction with promoter DNA; however, in the eukaryotic system the interactions between Pol II and the GTFs allowed complexes that contained promoter DNA to form. The single-stranded region of 6S RNA can engage the active site of bacterial RNA polymerase and serve as a template for synthesis of short RNA transcripts, which functions to derepress transcription (19). Future studies will likely reveal whether an analogous regulatory mechanism can occur with B2 and Alu RNAs.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes

Yakovchuk

Goodrich

Kugel

2009

Proc. Natl. Acad. Sci. U.S.A.

145

135

View full text Add to dashboard Cite

Noncoding RNAs (ncRNAs) are now recognized as transregulators of eukaryotic transcription, a role once attributed exclusively to protein factors. Two ncRNAs in mammalian cells have been shown to repress general mRNA transcription by RNA polymerase II (Pol II) in response to heat shock: mouse B2 RNA and human Alu RNA. B2 and Alu RNAs bind directly and tightly to Pol II and co-occupy the promoters of repressed genes along with the polymerase. Here, we identified the molecular mechanism by which mouse B2 RNA and human Alu RNA repress Pol II transcription. Biochemical assays to probe the network of protein-DNA interactions at the promoter revealed that B2 and Alu RNAs prevent Pol II from establishing contacts with the promoter both upstream and downstream of the TATA box during closed complex formation. Disruption of these contacts correlates with transcriptional repression. We conclude that B2 and Alu RNA prevent Pol II from properly engaging the DNA during closed complex formation, resulting in complexes with an altered conformation that are transcriptionally inert. In the absence of its normal contacts with the promoter, Pol II is likely held in these inactive complexes on DNA through interactions with promoter-bound TATA box-binding protein and transcription factor IIB.T ranscription is an intricate biological process in which DNA is copied into RNA; it is the critical first step in gene expression. In eukaryotes, the enzyme RNA polymerase II (Pol II) transcribes protein-encoding genes into mRNA with assistance of general transcription factors (GTFs; specifically TFIIA, TFIID, TFIIB, TFIIF, TFIIE, and TFIIH) that are thought to function at most promoters (1). Transcriptional regulation of specific genes occurs through the remarkably balanced interplay of auxiliary factors such as promoter-specific activators and repressors, coregulators, and chromatin-modifying complexes (1). Traditionally, it was thought that all of these factors were proteins, but now it is becoming clear that noncoding RNAs (ncRNAs) also play important roles in regulating transcription. Indeed, diverse ncRNAs have been identified as regulators of nearly every step in the process of mRNA transcription from controlling chromatin structure through regulating transcript elongation (2).Our laboratory reported that 2 ncRNAs, mouse B2 RNA and human Alu RNA, repress mRNA transcription by binding to Pol II during the cellular heat shock response (3, 4). B2 and Alu RNAs are transcribed by RNA polymerase III from short interspersed elements (SINEs) (5). Upon heat shock, the levels of B2 RNA and Alu RNA increase (6, 7) and they function as general repressors of mRNA transcription (3, 4). Biochemical experiments showed that B2 and Alu RNAs bind directly to core Pol II with low nM affinity (4, 8). Other SINE RNAs have been identified in mammalian cells, including mouse B1 RNA and human scAlu RNA (5), the latter of which is likely derived from cleavage of full-length Alu RNA (9). The biological functions for B1 and scAlu RNAs are not known. In vitro both of...

show abstract

Section: Discussionmentioning

confidence: 62%

Section: Discussionmentioning

confidence: 99%

B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes

Yakovchuk

Goodrich

Kugel

2009

Proc. Natl. Acad. Sci. U.S.A.

145

135

View full text Add to dashboard Cite

show abstract

“…The nTSS for the RNase P RNA (rnpB), 4.5S RNA (ffs), 6S RNA, and tmRNA (ssrA) matched the published experimental data (15,16) or genome annotation. We also detected the very short 6S RNA-associated product RNA (pRNA) (17) starting at position c1686546, which corresponds to the bulge-internal adenosine position of Escherichia coli 6S RNA (17). Although the cyanobacterial pRNAs are slightly longer (19-30 nt) than their counterparts in E. coli (14-20 nt), their detection in a phylogenetically distant cyanobacterium suggests that 6S RNA-mediated regulation of RNA polymerase activity is very widely conserved.…”

Section: Resultsmentioning

confidence: 94%

An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803

Mitschke

Georg

Scholz

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

349

459

View full text Add to dashboard Cite

There has been an increasing interest in cyanobacteria because these photosynthetic organisms convert solar energy into biomass and because of their potential for the production of biofuels. However, the exploitation of cyanobacteria for bioengineering requires knowledge of their transcriptional organization. Using differential RNA sequencing, we have established a genome-wide map of 3,527 transcriptional start sites (TSS) of the model organism Synechocystis sp. PCC6803. One-third of all TSS were located upstream of an annotated gene; another third were on the reverse complementary strand of 866 genes, suggesting massive antisense transcription. Orphan TSS located in intergenic regions led us to predict 314 noncoding RNAs (ncRNAs). Complementary microarray-based RNA profiling verified a high number of noncoding transcripts and identified strong ncRNA regulations. Thus, ∼64% of all TSS give rise to antisense or ncRNAs in a genome that is to 87% protein coding. Our data enhance the information on promoters by a factor of 40, suggest the existence of additional small peptide-encoding mRNAs, and provide corrected 5′ annotations for many genes of this cyanobacterium. The global TSS map will facilitate the use of Synechocystis sp. PCC6803 as a model organism for further research on photosynthesis and energy research.gene expression regulation | promoter prediction | RNA polymerase

show abstract

“…Indeed, though VirP1 appears to be important for PSTVd infection, there is no evidence for its involvement in replication (Kalantidis et al, 2007); instead, hypotheses center around its possible involvement in systemic spread of PSTVd (Maniataki et al, 2003) or in RNA-mediated DNA methylation (Kalantidis et al, 2007). d 70 , the "housekeeping" sigma factor involved in the transcription of most genes in growing bacterial cells (Gruber and Gross, 2003), is necessary for 6S RNA template transcription in E. coli (Wassarman and Saecker, 2006). Thus, this protein aids transcription of both DNA and RNA templates by a DdRP, though the mechanism by which it accomplishes a switch in substrate specificity remains unclear.…”

Section: Discussionmentioning

confidence: 99%

“…In response to nutrient availability, the DdRP transcribes a short RNA from the 6S RNA template that leads to desequestration of DdRP. This step in turn enables binding to DNA promoters and synthesis of protein-coding mRNAs (Wassarman and Saecker, 2006). Mammalian Pol II can bind to a hairpin formed by the noncoding B2 RNA and use the longer strand of the hairpin sequence as a template to extend the short strand by transcription.…”

Section: Introductionmentioning

confidence: 99%

A Land Plant-Specific Transcription Factor Directly Enhances Transcription of a Pathogenic Noncoding RNA Template by DNA-Dependent RNA Polymerase II

Wang

et al. 2015

The Plant Cell

106

View full text Add to dashboard Cite

Some DNA-dependent RNA polymerases (DdRPs) possess RNA-dependent RNA polymerase activity, as was first discovered in the replication of Potato spindle tuber viroid (PSTVd) RNA genome in tomato (Solanum lycopersicum). Recent studies revealed that this activity in bacteria and mammals is important for transcriptional and posttranscriptional regulatory mechanisms. Here, we used PSTVd as a model to uncover auxiliary factors essential for RNA-templated transcription by DdRP. PSTVd replication in the nucleoplasm generates (2)-PSTVd intermediates and (+)-PSTVd copies. We found that the Nicotiana benthamiana canonical 9-zinc finger (ZF) Transcription Factor IIIA (TFIIIA-9ZF) as well as its variant TFIIIA-7ZF interacted with (+)-PSTVd, but only TFIIIA-7ZF interacted with (2)-PSTVd. Suppression of TFIIIA-7ZF reduced PSTVd replication, and overexpression of TFIIIA-7ZF enhanced PSTVd replication in planta. Consistent with the locale of PSTVd replication, TFIIIA-7ZF was found in the nucleoplasm and nucleolus, in contrast to the strictly nucleolar localization of TFIIIA-9ZF. Footprinting assays revealed that only TFIIIA-7ZF bound to a region of PSTVd critical for initiating transcription. Furthermore, TFIIIA-7ZF strongly enhanced the in vitro transcription of circular (+)-PSTVd by partially purified Pol II. Together, our results identify TFIIIA-7ZF as a dedicated cellular transcription factor that acts in DdRP-catalyzed RNA-templated transcription, highlighting both the extraordinary evolutionary adaptation of viroids and the potential of DdRPs for a broader role in cellular processes.

show abstract

Synthesis-Mediated Release of a Small RNA Inhibitor of RNA Polymerase

Cited by 160 publications

References 25 publications

B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes

B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes

An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803

A Land Plant-Specific Transcription Factor Directly Enhances Transcription of a Pathogenic Noncoding RNA Template by DNA-Dependent RNA Polymerase II

Contact Info

Product

Resources

About