The Mitochondrial RNA Landscape of Saccharomyces cerevisiae

Turk, Edward M.; Das, Vaijayanti; Seibert, Ryan D.; Andrulis, Erik D.

doi:10.1371/journal.pone.0078105

Cited by 69 publications

(134 citation statements)

References 110 publications

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“…Of hybrids associated with ORFs, 42% occurred in the 10% most highly expressed genes. Hybrids also occurred in the polymerase II-driven sn/snoRNAs, ncRNAs, and Ty1 elements; polymerase I-driven rDNA; polymerase III-driven tRNA and other genes; and, as previously noted by El Hage et al (2014), the mitochondrial genome-all of which are highly expressed (Curcio et al 1990;French et al 2003;Pelechano et al 2010;Turk et al 2013;Jordán-Pla et al 2015). High expression alone is sufficient for R-loop formation regardless of genomic context, as both the transposition of highly expressed genes to an artificial chromosome and overexpression of low transcribed ORFs caused R loops.…”

Section: Discussionsupporting

confidence: 72%

S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation

et al. 2016

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R loops form when transcripts hybridize to homologous DNA on chromosomes, yielding a DNA:RNA hybrid and a displaced DNA single strand. R loops impact the genome of many organisms, regulating chromosome stability, gene expression, and DNA repair. Understanding the parameters dictating R-loop formation in vivo has been hampered by the limited quantitative and spatial resolution of current genomic strategies for mapping R loops. We report a novel whole-genome method, S1-DRIP-seq (S1 nuclease DNA:RNA immunoprecipitation with deep sequencing), for mapping hybrid-prone regions in budding yeast Saccharomyces cerevisiae. Using this methodology, we identified ∼800 hybrid-prone regions covering 8% of the genome. Given the pervasive transcription of the yeast genome, this result suggests that R-loop formation is dictated by characteristics of the DNA, RNA, and/or chromatin. We successfully identified two features highly predictive of hybrid formation: high transcription and long homopolymeric dA:dT tracts. These accounted for >60% of the hybrid regions found in the genome. We demonstrated that these two factors play a causal role in hybrid formation by genetic manipulation. Thus, the hybrid map generated by S1-DRIP-seq led to the identification of the first global genomic features causal for R-loop formation in yeast.

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Section: Discussionsupporting

confidence: 72%

S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation

et al. 2016

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“…This correlation is consistent with NAD + being added to 5′ ends cotranscriptionally. Moreover, transcription initiation in mitochondria begins with an adenosine residue at all promoters (20). Surprisingly, we saw no enrichment of the COX1 mRNA, which is at the 5′ end of a transcription unit in the mitochondrial genome and is not known to undergo 5′ end processing (20).…”

Section: Significancementioning

confidence: 64%

“…Moreover, transcription initiation in mitochondria begins with an adenosine residue at all promoters (20). Surprisingly, we saw no enrichment of the COX1 mRNA, which is at the 5′ end of a transcription unit in the mitochondrial genome and is not known to undergo 5′ end processing (20). However, closer inspection of the RNA-Seq reads for COX1 revealed that the reads do not extend to the transcriptional start site (Fig.…”

Section: Significancementioning

confidence: 80%

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Identification of NAD ⁺ capped mRNAs in Saccharomyces cerevisiae

Walters

Matheny

Mizoue

et al. 2016

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

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RNAs besides tRNA and rRNA contain chemical modifications, including the recently described 5′ nicotinamide-adenine dinucleotide (NAD + ) RNA in bacteria. Whether 5′ NAD-RNA exists in eukaryotes remains unknown. We demonstrate that 5′ NAD-RNA is found on subsets of nuclear and mitochondrial encoded mRNAs in Saccharomyces cerevisiae. NAD-mRNA appears to be produced cotranscriptionally because NAD-RNA is also found on pre-mRNAs, and only on mitochondrial transcripts that are not 5′ end processed. These results define an additional 5′ RNA cap structure in eukaryotes and raise the possibility that this 5′ NAD + cap could modulate RNA stability and translation on specific subclasses of mRNAs.T he number and prevalence of known chemical modifications on mRNAs have dramatically increased in the past several years (1). Quantification of these modification events suggests they occur in many RNAs (2, 3). Importantly, several of these modifications have functional consequences (4-6). For example, the presence of a single N 6 -methyladenosine within the 5′ UTR of an mRNA increases translation initiation (4). In addition, the methylation status of cytosine residues within the 3′ UTR of the p16(INK4) human mRNA affects mRNA stability (6). Due to the increasing sensitivity of RNA sequencing (RNA-Seq) and small-molecule mass spectrometry, it is reasonable to hypothesize that many novel chemical modifications within mRNAs remain to be discovered.One modification recently identified in bacteria is 5′ nicotinamide-adenine dinucleotide (NAD + )-linked RNA (7, 8). Because canonical bacterial RNAs contain a 5′ triphosphate terminus, addition of NAD + to the 5′ end of RNAs represents a rudimentary "capping" mechanism, perhaps designed to impart specific properties for these RNAs by granting them a more structurally complex 5′ end. Consistent with this idea, NAD + addition to RNAs appears to occur during transcription initiation (9), as opposed to the more complex eukaryote 5′ capping, which occurs after transcription has commenced (10). Because the NAD + modification defines the 5′ end of NAD-RNAs, this modification can affect RNA stability in Escherichia coli (7, 9).For decades, 5′ end classification and study of eukaryotic mRNAs have been restricted to canonical 7-methylguanosine (m 7 G) "caps" and their methylated variants (11). The m 7 G cap modulates numerous facets of mRNA metabolism, including stability (12, 13), translation (14, 15), and export (16). The importance of this modification is underscored by the substantial cellular machinery dedicated to its addition and removal (17,18). Thus, mRNAs containing noncanonical 5′ termini may have distinct properties and be subject to alternative metabolic events.Described herein is the identification of NAD-RNAs in the eukaryote Saccharomyces cerevisiae. Examples of NAD-RNAs in S. cerevisiae include nuclear encoded mRNAs for ribosomal proteins, as well as some mitochondrial encoded transcripts. Our data suggest that the NAD + moiety is added during initiation in both nuclear and mitoc...

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“…This suggests that the two proteins are functional analogs. The fact that the deficiency in human elongation factor results in a more severe phenotype than inactivation of Mss116p in yeast may be due to the organization of the human mt genome, which has just two promoters from which much longer transcripts are synthesized, whereas in yeast mitochondrial transcription involves multiple promoters driving transcription over much shorter regions (68). On the other hand, yeast are exposed to more severe environmental stress than the cells of multicellular organisms, making the presence of an analogous elongation factor that would stabilize transcription complexes essential under certain stress conditions but perhaps not under all conditions.…”

Section: Discussionmentioning

confidence: 99%

Yeast DEAD Box Protein Mss116p Is a Transcription Elongation Factor That Modulates the Activity of Mitochondrial RNA Polymerase

Markov

Wojtas

Tessitore

et al. 2014

Molecular and Cellular Biology

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DEAD box proteins have been widely implicated in regulation of gene expression. Here, we show that the yeast Saccharomyces cerevisiae DEAD box protein Mss116p, previously known as a mitochondrial splicing factor, also acts as a transcription factor that modulates the activity of the single-subunit mitochondrial RNA polymerase encoded by RPO41. Binding of Mss116p stabilizes paused mitochondrial RNA polymerase elongation complexes in vitro and favors the posttranslocated state of the enzyme, resulting in a lower concentration of nucleotide substrate required to escape the pause; this mechanism of action is similar to that of elongation factors that enhance the processivity of multisubunit RNA polymerases. In a yeast strain in which the RNA splicing-related functions of Mss116p are dispensable, overexpression of RPO41 or MSS116 increases cell survival from colonies that were exposed to low temperature, suggesting a role for Mss116p in enhancing the efficiency of mitochondrial transcription under stress conditions. E nergy production in eukaryotic cells depends upon the function of mitochondria, double-membrane organelles that are thought to have evolved from an ancient bacterial endosymbiont (1, 2). While most proteins that are essential for mitochondrial (mt) function are encoded by nuclear genes and imported into the organelle, a subset of critical proteins, mostly components of the oxidative phosphorylation complex and mitochondrion-specific ribosomal and tRNAs, are encoded in the mt genome (3, 4). Therefore, expression of nuclear and mt genes must be coordinately regulated (5, 6). As a consequence, mitochondria have developed a highly active RNA surveillance/degradation system to ensure the integrity of mt transcripts and to regulate the availability of mt mRNA by balancing the rates of RNA synthesis and degradation (7,8,9).Little is known about how transcription is controlled in mitochondria and what proteins participate in adjusting the rates of mt RNA synthesis and degradation. In the yeast Saccharomyces cerevisiae, mt transcription is carried out by an RNA polymerase (RNAP) consisting of a single-subunit catalytic core (Rpo41p) that is related to T7 RNA polymerase (T7 RNAP) and an additional transcription factor (Mtf1p) for initiation (10,11,12). RNA degradation in turn depends upon a two-subunit mt degradosome that includes Suv3p, a processive helicase that unwinds double-stranded RNA (dsRNA), and Dss1p, a 3= to 5= exonuclease (13,14). Importantly, deletion of SUV3 is suppressed by mutations in RPO41 and MTF1, suggesting that alterations in these components of the transcription system help to restore the balance between RNA synthesis and degradation (8). The SUV3 deletion is also suppressed by overexpression of Mss116p, an mt DEAD box protein that is involved in RNA splicing, processing, and possibly translation (15,16). While this effect might be attributed to compensation for Suv3p deficiency by a protein that has RNA unwinding activity, we have recently found that Mss116p is associated with the mt trans...

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The Mitochondrial RNA Landscape of Saccharomyces cerevisiae

Cited by 69 publications

References 110 publications

S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation

S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation

Identification of NAD ⁺ capped mRNAs in Saccharomyces cerevisiae

Yeast DEAD Box Protein Mss116p Is a Transcription Elongation Factor That Modulates the Activity of Mitochondrial RNA Polymerase

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The Mitochondrial RNA Landscape of Saccharomyces cerevisiae

Cited by 69 publications

References 110 publications

S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation

S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation

Identification of NAD + capped mRNAs in Saccharomyces cerevisiae

Yeast DEAD Box Protein Mss116p Is a Transcription Elongation Factor That Modulates the Activity of Mitochondrial RNA Polymerase

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Identification of NAD ⁺ capped mRNAs in Saccharomyces cerevisiae