Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation

Sun, Mai; Schwalb, Björn; Schulz, Daniel; Pirkl, Nicole; Etzold, Stefanie; Larivière, L.; Maier, Kerstin; Seizl, Martin; Tresch, Achim; Cramer, Patrick

doi:10.1101/gr.130161.111

Cited by 271 publications

(404 citation statements)

References 48 publications

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“…As expected, new transcription was necessary to obtain 4TU-labeled RNA: preincubation with the general transcription inhibitor thiolutin, which has been shown to decrease transcription in N. crassa (Hoyt et al 2000;Lee et al 2009), severely reduced 4TU incorporation, as did chilling cells on ice ( Figure S3, C and D). Incorporation of 4TU into RNA rapidly diminished when excess uracil was added to cultures ( Figure S3E) and 4TU itself had minimal impact on N. crassa growth under the experimental conditions used (,30 min incubation) or during growth for extended periods ( Figure S3F), similar to its minimal effects on growth in S. cerevisiae (Munchel et al 2011) and S. pombe (Sun et al 2012). Furthermore, purified 4TU RNA, unlabeled total RNA and unlabeled poly(A) mRNA programmed the synthesis of [ 35 S]Met-labeled polypeptides with similar distributions of masses in N. crassa cell-free translation extracts ( Figure S3G).…”

Section: N Crassa Nmd Mutations Increase the Levels And Stability Ofmentioning

confidence: 59%

Control of mRNA Stability in Fungi by NMD, EJC and CBC Factors Through 3′UTR Introns

Zhang¹,

Sachs

2015

Genetics

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In higher eukaryotes the accelerated degradation of mRNAs harboring premature termination codons is controlled by nonsense-mediated mRNA decay (NMD), exon junction complex (EJC), and nuclear cap-binding complex (CBC) factors, but the mechanistic basis for this quality-control system and the specific roles of the individual factors remain unclear. Using Neurospora crassa as a model system, we analyzed the mechanisms by which NMD is induced by spliced 39-UTR introns or upstream open reading frames and observed that the former requires NMD, EJC, and CBC factors whereas the latter requires only the NMD factors. The transcripts for EJC components eIF4A3 and Y14, and translation termination factor eRF1, contain spliced 39-UTR introns and each was stabilized in NMD, EJC, and CBC mutants. Reporter mRNAs containing spliced 39-UTR introns, but not matched intronless controls, were stabilized in these mutants and were enriched in mRNPs immunopurified from wild-type cells with antibody directed against human Y14, demonstrating a direct role for spliced 39-UTR introns in triggering EJC-mediated NMD. These results demonstrate conclusively that NMD, EJC, and CBC factors have essential roles in controlling mRNA stability and that, based on differential requirements for these factors, there are branched mechanisms for NMD. They demonstrate for the first time autoregulatory control of expression at the level of mRNA stability through the EJC/CBC branch of NMD for EJC core components, eIF4A3 and Y14, and for eRF1, which recognizes termination codons. Finally, these results show that EJC-mediated NMD occurs in fungi and thus is an evolutionarily conserved quality-control mechanism.KEYWORDS nonsense-mediated mRNA decay (NMD); RNA stability; exon junction complex (EJC); cap-binding complex (CBC); spliced 39-UTR intron; post-transcriptional control; ribosome; translation; Neurospora crassa T HE nonsense-mediated mRNA decay (NMD) pathway targets mRNA for degradation through the recognition of translated termination codons determined to be premature (Nicholson et al. 2009;Kervestin and Jacobson 2012;Popp and Maquat 2013). The NMD pathway can degrade mRNAs that contain upstream open reading frames (uORFs) or long 39-UTRs. The termination-related processes that trigger uORFmediated or long 39-UTR-mediated NMD are considered to be similar (Amrani et al. 2004(Amrani et al. , 2006Nicholson et al. 2009) in that termination events occurring far from the context created by the mRNA poly(A) tail can result in mRNA degradation (the "faux-UTR" model). In higher eukaryotes, NMD can also act on mRNAs that contain an intron downstream of a termination codon, such as aberrantly spliced transcripts or 39-UTR introncontaining transcripts (Sauliere et al. 2010;Bicknell et al. 2012). When a spliced intron is positioned at least 50-55 nt downstream of a termination codon, the exon junction complex (EJC) positioned near the exon-exon junction is not displaced by translating ribosomes and its continued association with mRNA targets the mRNA for deg...

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Section: N Crassa Nmd Mutations Increase the Levels And Stability Ofmentioning

confidence: 59%

Control of mRNA Stability in Fungi by NMD, EJC and CBC Factors Through 3′UTR Introns

Zhang¹,

Sachs

2015

Genetics

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“…Genome-wide expression studies in yeast have shown that mRNA synthesis and decay are mechanistically and functionally coordinated, thus supporting the existence of common molecular effectors [6][7][8][9] . In particular, the CCR4-NOT deadenylation complex was first described as a transcriptional regulator and has been implicated in initiation and elongation by RNA polymerase II 10,11 .…”

mentioning

confidence: 94%

The transcription factor ERG recruits CCR4–NOT to control mRNA decay and mitotic progression

Rambout

Detiffe

Bruyr

et al. 2016

Nat Struct Mol Biol

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nature structural & molecular biology advance online publication a r t i c l e sAlthough undisputable evidence has clearly demonstrated that the nuclear steps of mRNA processing are mechanistically linked to transcription, a conceptual evolution in gene regulation has come with the realization that transcription might also be functionally connected to more remote processes occurring in the cytoplasm, such as mRNA decay 1,2 . Cytoplasmic mRNA decay is initiated by deadenylation, a rate-limiting event during which the poly(A) tail of the transcript is trimmed off by the CCR4-NOT complex, the main deadenylation machinery in eukaryotes 3 . The degradation of specific mRNAs, a key process in the regulation of eukaryotic gene expression, is achieved through the recruitment of the CCR4-NOT complex by sequence-specific RNA-binding proteins (RBPs) or by the microRNA machinery 3,4 . Poly(A)-shortened mRNAs, along with factors involved in the deadenylation, decapping and mRNA-degradation machineries, accumulate in microscopic mRNA-protein complex (mRNP) aggregates called processing bodies (PBs) 5 .The idea of coupling between mRNA synthesis and degradation has recently emerged. Genome-wide expression studies in yeast have shown that mRNA synthesis and decay are mechanistically and functionally coordinated, thus supporting the existence of common molecular effectors [6][7][8][9] . In particular, the CCR4-NOT deadenylation complex was first described as a transcriptional regulator and has been implicated in initiation and elongation by RNA polymerase II 10,11 . More surprisingly, it has also been shown that degradation of yeast mRNAs is determined by cis-acting sequence elements in promoters 12,13 . These findings have led to the concept of mRNA imprinting, in which sequence-specific DNA-binding factors might orchestrate mRNA synthesis and decay. This decay would occur via loading of factors regulating cytoplasmic mRNA degradation onto the transcribing mRNA 14 . However, the identity of these DNA-binding mRNA coordinators is still obscure, and it remains to be tested whether such coupling between transcription and decay also exists in higher eukaryotes. E26 (Ets) proteins, a family of 28 helix-loop-helix transcription factors (TFs) in metazoans, are characterized by a highly conserved DNA-binding ETS domain 15 . Through this domain, Ets factors bind specific gene promoters and act as key regulators in many biological processes including cellular proliferation, apoptosis, differentiation and survival 16 . ERG, FLI1 and the more structurally divergent FEV compose the Erg subfamily of Ets factors and have been identified as driving factors in prostate cancer, Ewing's tumors and leukemias 15,17 . Using ERG as a paradigm, we sought to investigate the possibility that eukaryotic transcription factors might be directly involved in cytoplasmic mRNA decay. We demonstrate that ERG triggers degradation of mRNAs connected to Aurora signaling by recruiting RBPs and the CCR4-NOT deadenylation complex and that this activity is important fo...

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“…Recent research suggests that RNA turnover is tightly connected to transcription and that mRNA degradation factors influence the rate of transcription and vice versa (Sun et al 2012(Sun et al , 2013Haimovich et al 2013;Braun and Young 2014). Particularly, Xrn1p appears to play an important role in "buffering" mRNA levels by decreasing the transcription rate, for example, when mRNA degradation rates are slowed (Sun et al 2013;Medina et al 2014).…”

Section: Introductionmentioning

confidence: 99%

The Rtr1p CTD phosphatase autoregulates its mRNA through a degradation pathway involving the REX exonucleases

Hodko

Ward

Chanfreau

2016

RNA

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Rtr1p is a phosphatase that impacts gene expression by modulating the phosphorylation status of the C-terminal domain of the large subunit of RNA polymerase II. Here, we show that Rtr1p is a component of a novel mRNA degradation pathway that promotes its autoregulation through turnover of its own mRNA. We show that the 3 ′ UTR of the RTR1 mRNA contains a cis element that destabilizes this mRNA. RTR1 mRNA turnover is achieved through binding of Rtr1p to the RTR1 mRNP in a manner that is dependent on this cis element. Genetic evidence shows that Rtr1p-mediated decay of the RTR1 mRNA involves the 5 ′ -3 ′ DExD/H-box RNA helicase Dhh1p and the 3 ′ -5 ′ exonucleases Rex2p and Rex3p. Rtr1p and Rex3p are found associated with Dhh1p, suggesting a model for recruiting the REX exonucleases to the RTR1 mRNA for degradation. Rtr1p-mediated decay potentially impacts additional transcripts, including the unspliced BMH2 pre-mRNA. We propose that Rtr1p may imprint its RNA targets cotranscriptionally and determine their downstream degradation mechanism by directing these transcripts to a novel turnover pathway that involves Rtr1p, Dhh1p, and the REX family of exonucleases.

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Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation

Cited by 271 publications

References 48 publications

Control of mRNA Stability in Fungi by NMD, EJC and CBC Factors Through 3′UTR Introns

Control of mRNA Stability in Fungi by NMD, EJC and CBC Factors Through 3′UTR Introns

The transcription factor ERG recruits CCR4–NOT to control mRNA decay and mitotic progression

The Rtr1p CTD phosphatase autoregulates its mRNA through a degradation pathway involving the REX exonucleases

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