NanoRNAs Prime Transcription Initiation In Vivo

Goldman, Seth R.; Sharp, Josh S.; Vvedenskaya, Irina O.; Livny, Jonathan; Dove, Simon L.; Nickels, Bryce E.

doi:10.1016/j.molcel.2011.06.005

Cited by 113 publications

(117 citation statements)

References 42 publications

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“…Identical initiation and processing sites were described for several transcripts in Arabidopsis thaliana mitochondria (Kü hn et al, 2005). Recently it was demonstrated that the RNA polymerase of the Gram-negative bacterium Pseudomonas aeruginosa may use nanoRNAs as primers for transcription initiation, thus generating primary transcripts with 59 ends similar to processed ones (Goldman et al, 2011). Even though there is no indication that such a process takes place in plastids, a potential similar function of PEP, the bacteria-type RNA polymerase, would explain why no enrichment after TEX treatment of some primary transcripts was observed only in green libraries.…”

Section: Discussionmentioning

confidence: 99%

The Primary Transcriptome of Barley Chloroplasts: Numerous Noncoding RNAs and the Dominating Role of the Plastid-Encoded RNA Polymerase

et al. 2012

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Gene expression in plastids of higher plants is dependent on two different transcription machineries, a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP), which recognize distinct types of promoters. The division of labor between PEP and NEP during plastid development and in mature chloroplasts is unclear due to a lack of comprehensive information on promoter usage. Here, we present a thorough investigation into the distribution of PEP and NEP promoters within the plastid genome of barley (Hordeum vulgare). Using a novel differential RNA sequencing approach, which discriminates between primary and processed transcripts, we obtained a genome-wide map of transcription start sites in plastids of mature first leaves. PEP-lacking plastids of the albostrians mutant allowed for the unambiguous identification of NEP promoters. We observed that the chloroplast genome contains many more promoters than genes. According to our data, most genes (including genes coding for photosynthesis proteins) have both PEP and NEP promoters. We also detected numerous transcription start sites within operons, indicating transcriptional uncoupling of genes in polycistronic gene clusters. Moreover, we mapped many transcription start sites in intergenic regions and opposite to annotated genes, demonstrating the existence of numerous noncoding RNA candidates.

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Section: Discussionmentioning

confidence: 99%

The Primary Transcriptome of Barley Chloroplasts: Numerous Noncoding RNAs and the Dominating Role of the Plastid-Encoded RNA Polymerase

et al. 2012

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“…3 and 5C were performed essentially as described in ref. 29. RNA products generated in these reactions were analyzed by primer extension as described in ref.…”

Section: Methodsmentioning

confidence: 99%

“…RNA products generated in these reactions were analyzed by primer extension as described in ref. 29.…”

Section: Methodsmentioning

confidence: 99%

Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection

Vvedenskaya

Vahedian-Movahed

Zhang

et al. 2016

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

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During transcription initiation, RNA polymerase (RNAP) holoenzyme unwinds ∼13 bp of promoter DNA, forming an RNAP-promoter open complex (RPo) containing a single-stranded transcription bubble, and selects a template-strand nucleotide to serve as the transcription start site (TSS). In RPo, RNAP core enzyme makes sequence-specific protein-DNA interactions with the downstream part of the nontemplate strand of the transcription bubble ("core recognition element," CRE). Here, we investigated whether sequence-specific RNAP-CRE interactions affect TSS selection. To do this, we used two next-generation sequencing-based approaches to compare the TSS profile of WT RNAP to that of an RNAP derivative defective in sequence-specific RNAP-CRE interactions. First, using massively systematic transcript end readout, MASTER, we assessed effects of RNAP-CRE interactions on TSS selection in vitro and in vivo for a library of 4 7 (∼16,000) consensus promoters containing different TSS region sequences, and we observed that the TSS profile of the RNAP derivative defective in RNAP-CRE interactions differed from that of WT RNAP, in a manner that correlated with the presence of consensus CRE sequences in the TSS region. Second, using 5′ merodiploid nativeelongating-transcript sequencing, 5′ mNET-seq, we assessed effects of RNAP-CRE interactions at natural promoters in Escherichia coli, and we identified 39 promoters at which RNAP-CRE interactions determine TSS selection. Our findings establish RNAP-CRE interactions are a functional determinant of TSS selection. We propose that RNAP-CRE interactions modulate the position of the downstream end of the transcription bubble in RPo, and thereby modulate TSS selection, which involves transcription bubble expansion or transcription bubble contraction (scrunching or antiscrunching).RNA polymerase | transcription start site selection | promoter | transcription bubble | transcription initiation T ranscription initiation consists of a number of biochemical steps leading to formation of a phosphodiester bond between a nucleoside triphosphate (NTP) bound in the RNA polymerase (RNAP) active-center initiating NTP binding site (i site) and an NTP bound in the RNAP active-center extending NTP binding site (i+1 site) (1-3). For bacterial RNAP, promoter-specific initiation requires the RNAP core enzyme (subunit composition α 2 ββ'ω) to associate with a σ factor forming the RNAP holoenzyme (subunit composition α 2 ββ'ωσ). The σ factor contains determinants for sequence-specific protein-DNA interactions with four core promoter elements: the −35 element, the extended −10 element, the −10 element, and the discriminator element (4).During transcription initiation, RNAP holoenzyme unwinds promoter DNA to form an RNAP-promoter open complex (RPo) containing an unwound, single-stranded "transcription bubble." The process of promoter unwinding begins within the promoter −10 element and propagates downstream, enabling single-stranded nucleotides at the downstream end of the transcription bubble template strand to occup...

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“…pGpG belongs to the class of "nanoRNA" molecules, which are 2 to 5 nucleotides long. NanoRNAs control gene expression, as they can serve as templates in the promoter-specific initiation of RNA synthesis by DNA-dependent RNA polymerases in vitro and in vivo (388). Thus, the possibility exists that pGpG may have a role in gene expression, presumably under conditions of high c-di-GMP concentrations.…”

Section: Open Questions In C-di-gmp Signalingmentioning

confidence: 99%

Cyclic di-GMP: the First 25 Years of a Universal Bacterial Second Messenger

Römling

Galperin

Gomelsky

2013

Microbiol Mol Biol Rev

1,500

1,698

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SUMMARY Twenty-five years have passed since the discovery of cyclic dimeric (3′→5′) GMP (cyclic di-GMP or c-di-GMP). From the relative obscurity of an allosteric activator of a bacterial cellulose synthase, c-di-GMP has emerged as one of the most common and important bacterial second messengers. Cyclic di-GMP has been shown to regulate biofilm formation, motility, virulence, the cell cycle, differentiation, and other processes. Most c-di-GMP-dependent signaling pathways control the ability of bacteria to interact with abiotic surfaces or with other bacterial and eukaryotic cells. Cyclic di-GMP plays key roles in lifestyle changes of many bacteria, including transition from the motile to the sessile state, which aids in the establishment of multicellular biofilm communities, and from the virulent state in acute infections to the less virulent but more resilient state characteristic of chronic infectious diseases. From a practical standpoint, modulating c-di-GMP signaling pathways in bacteria could represent a new way of controlling formation and dispersal of biofilms in medical and industrial settings. Cyclic di-GMP participates in interkingdom signaling. It is recognized by mammalian immune systems as a uniquely bacterial molecule and therefore is considered a promising vaccine adjuvant. The purpose of this review is not to overview the whole body of data in the burgeoning field of c-di-GMP-dependent signaling. Instead, we provide a historic perspective on the development of the field, emphasize common trends, and illustrate them with the best available examples. We also identify unresolved questions and highlight new directions in c-di-GMP research that will give us a deeper understanding of this truly universal bacterial second messenger.

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NanoRNAs Prime Transcription Initiation In Vivo

Cited by 113 publications

References 42 publications

The Primary Transcriptome of Barley Chloroplasts: Numerous Noncoding RNAs and the Dominating Role of the Plastid-Encoded RNA Polymerase

The Primary Transcriptome of Barley Chloroplasts: Numerous Noncoding RNAs and the Dominating Role of the Plastid-Encoded RNA Polymerase

Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection

Cyclic di-GMP: the First 25 Years of a Universal Bacterial Second Messenger

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