Genome-Wide Mapping of Decay Factor–mRNA Interactions in Yeast Identifies Nutrient-Responsive Transcripts as Targets of the Deadenylase Ccr4

Miller, Jason E.; Zhang, Liye; Jiang, Haoyang; Li, Yunfei; Pugh, B. Franklin; Reese, Joseph C.

doi:10.1534/g3.117.300415

Cited by 33 publications

(36 citation statements)

References 104 publications

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“…Cells were grown in YPD at 30°C until an OD 600 of 0.8-1.0 and then treated with cyclohexidine and 4-NQO at concentrations of 100 µg/mL and 5 µg/mL, respectively. Cells were harvested, and cell extracts were prepared by the TCA method (Miller et al 2018). In the AA studies, cells were treated with 1 µg/mL rapamycin for 30 min prior to treatment with 4-NQO.…”

Section: Rpb1 Degradation Assay and Analysis Of Rpb1 Ubiquitylation Imentioning

confidence: 99%

Ccr4–Not maintains genomic integrity by controlling the ubiquitylation and degradation of arrested RNAPII

et al. 2019

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The Ccr4–Not complex regulates essentially every aspect of gene expression, from mRNA synthesis to protein destruction. The Not4 subunit of the complex contains an E3 RING domain and targets proteins for ubiquitin-dependent proteolysis. Ccr4–Not associates with elongating RNA polymerase II (RNAPII), which raises the possibility that it controls the degradation of elongation complex components. Here, we demonstrate that Ccr4–Not controls the ubiquitylation and turnover of Rpb1, the largest subunit of RNAPII, during transcription arrest. Deleting NOT4 or mutating its RING domain strongly reduced the DNA damage-dependent ubiquitylation and destruction of Rpb1. Surprisingly, in vitro ubiquitylation assays indicate that Ccr4–Not does not directly ubiquitylate Rpb1 but instead promotes Rpb1 ubiquitylation by the HECT domain-containing ligase Rsp5. Genetic analyses suggest that Ccr4–Not acts upstream of RSP5, where it acts to initiate the destruction process. Ccr4–Not binds Rsp5 and forms a ternary complex with it and the RNAPII elongation complex. Analysis of mutant Ccr4–Not lacking the RING domain of Not4 suggests that it both recruits Rsp5 and delivers the E2 Ubc4/5 to RNAPII. Our work reveals a previously unknown function of Ccr4–Not and identifies an essential new regulator of RNAPII turnover during genotoxic stress.

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Section: Rpb1 Degradation Assay and Analysis Of Rpb1 Ubiquitylation Imentioning

confidence: 99%

Ccr4–Not maintains genomic integrity by controlling the ubiquitylation and degradation of arrested RNAPII

et al. 2019

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“…The restriction on mobility of genetic elements in yeast has earlier been shown conserved in APOBEC(33). While genes such as CCR4 and DHH1 that physically interact with TMS-1 have been implicated in yeast retrotransposon activity (34,35) the mechanism that TMS-1 would manifest on retroelements remains to be investigated. TMS-1 in fly may still be required to regulate the mobility of gypsy retroelements as the gypsy envelope has been shown to pseudotype MoMLV-based vector to efficiently infect fly cells (36,37).…”

Section: Discussionmentioning

confidence: 99%

Coevolution of retroviruses withSERINCs following whole-genome duplication divergence

Ramdas

Bhardwaj

Singh

et al. 2020

Preprint

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9The SERINC gene family comprises of five paralogs in humans of which SERINC3 and 10 SERINC5 inhibit HIV-1 infectivity and are counteracted by Nef. The origin of this anti-retroviral 11 activity, its prevalence among the remaining human paralogs, and its ability to target 12 retroviruses remain largely unknown. Here we show that despite their early divergence, the 13 anti-retroviral activity is functionally conserved among four human SERINC paralogs with 14 SERINC2 being an exception. The lack of activity in human SERINC2 is associated with its 15 post-whole genome duplication (WGD) divergence, as evidenced by the ability of pre-WGD 16 orthologs from yeast, fly, and a post-WGD-proximate SERINC2 from coelacanth to inhibit nef-17 defective HIV-1. Intriguingly, potent retroviral factors from HIV-1 and MLV are not able to relieve 18 the SERINC2-mediated particle infectivity inhibition, indicating that such activity was directed 19 towards other retroviruses that are found in coelacanth (like foamy viruses). However, foamy-20 derived vectors are intrinsically resistant to the action of SERINC2, and we show that a foamy 21 virus envelope confers this resistance. Despite the presence of weak arms-race signatures, the 22 functional reciprocal adaptation among SERINC2 and SERINC5 and, in response, the 23 emergence of antagonizing ability in foamy virus appears to have resulted from a long-term 24 conflict with the host. 25 26 27 28 Introduction 29Viruses have been exploiting the host machinery for their persistence, and, in response, the 30 host has continued to evolve increasingly intricate antiviral defense strategies. As part of this 31 ongoing arms-race, while viruses have relied on acquisition and fusion of diverse genes (1), 32 the host-defense mechanism has been made possible by the functional divergence of gene 33 copies following duplication of genes as well as whole-genomes (2-7). Restriction factors being 34 at the forefront of this long-term conflict (8-10), show clear molecular signatures of arms-race 35 (11,12). In fact, the presence of these signatures has been proposed to be a hallmark of 36 restriction factors (8,13), and has been used as a screening strategy to identify potential 37 candidates (2,14). In contrast, the recently identified anti-retroviral host inhibitors SERINC5 and 38 SERINC3 display an uneventful evolutionary history (15). This is counterintuitive, because 39 distant retroviruses, with wide host-range, encode anti-SERINC5 virulent factors (16)(17)(18). We, 40Ramdas et al.therefore, sought to trace the origins of this antiretroviral activity and its relevance for retroviral 41 inhibition. Our analysis to comprehend the evolutionary origins of the antiretroviral activity in 42 SERINCs, identifies an active SERINC2 with a hitherto unknown interaction with a foamy virus. 44 Results 45Antiretroviral activity among human SERINC paralogs 46 Analysis of sequence similarity and gene structure conservation reveals that SERINC5 and 47 SERINC4 share a recent ancestry (Fig-S1). Similarly, SERINC3 and...

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“…For example, Ccr4 has been shown to physically interact with TFIIS and to directly modulate backtracking in conjunction with TFIIS (Dutta et al 2015; Kruk et al 2011). Likewise, Dhh1, Pat1, and Lsm1 also interact with TFIIS both physically and genetically (Collins et al 2007; Costanzo et al 2010; Costanzo et al 2016; Dutta et al 2015; Kuzmin et al 2018; Miller et al 2018; Srivas et al 2016; Wilmes et al 2008). Recently, Xrn1 was shown to increase TFIIS recruitment to Pol II (Begley et al 2019), consistent with the role we assign to Xrn1 as a regulator of backtracking.…”

Section: Discussionmentioning

confidence: 99%

Cytoplasmic mRNA decay factors modulate RNA polymerase II processivity in 5’ and 3’ gene regions in yeast

Fischer

Song

Yosef

et al. 2019

Preprint

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19mRNA levels are determined by the balance between mRNA synthesis and decay. tors that mediate both processes, including the 5' to 3' exonuclease Xrn1, are responsible for 21 the cross talk between the two processes in a manner that buffers steady-state mRNA lev-22 els. However, these proteins' roles in transcription remain elusive and controversial. Applying 23 NET-seq to yeast cells, we show that Xrn1 functions mainly as a transcriptional activator 24 and that its disruption manifests via the reduction of RNA polymerase II (Pol II) occupancy 25 downstream of transcription start sites. We combine our data and novel mathematical mod-26 eling of transcription to suggest that transcription initiation and elongation of targeted genes 27 is modulated by Xrn1. Furthermore, Pol II occupancy markedly increases near cleavage and 28 polyadenylation sites in xrn1∆ cells while its activity decreases, a characteristic feature of 29 backtracked Pol II. We also provide indirect evidence that Xrn1 is involved in transcription 30 termination downstream of polyadenylation sites. Two additional decay factors, Dhh1 and 31 Lsm1, seem to function similarly to Xrn1 in transcription, perhaps as a complex, while the 32 decay factors Ccr4 and Rpb4 also perturb transcription in other ways. Interestingly, DFs are 33 capable of differentiating between SAGA-and TFIID-dominated promoters. These two classes 34 of genes respond differently to XRN 1 deletion in mRNA synthesis and differentially utilize 35 mRNA decay pathways, raising the possibility that one distinction between the two types of 36 genes lies in the mechanism(s) that balance these processes. 37 Introduction 38 Steady-state mRNA levels are determined by the balance between synthesis and decay rates. 39 Once thought to function separately, recent studies have discovered that these two processes 40 are linked. In previous work we showed that the major cytoplasmic yeast mRNA degradation 41 pathway, consisting of the decapping enzyme Dcp1/2, the decapping activator Pat1/Lsm1-7, the 42 helicase Dhh1, and the 5'-3' exonuclease Xrn1, shuttles between the cytoplasm and the nucleus 43 to participate in both processes. Notably, the elements of this pathway were found to degrade 44 most mRNAs in the cytoplasm while stimulating transcription in the nucleus. The proteins 45 Dcp2, Lsm1, and Xrn1 were further shown to bind chromatin, probably as a complex, and to 46 stimulate transcription initiation and elongation (Haimovich et al. 2013). We also uncovered 47 a connection between how Xrn1 functions in transcription and mRNA decay by revealing the 48 2 correlation between the effects of Xrn1 disruption on mRNA synthesis and decay in the nucleus and 49 cytoplasm, respectively (Haimovich et al. 2013; Medina et al. 2014). We subsequently ranked genes 50 according to their responsiveness to Xrn1 disruption in optimally proliferating yeast cells; the most 51 responsive were dubbed the "Xrn1 synthegradon" and consisted of genes whose transcription and 52 decay rates exhibited the highest...

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Genome-Wide Mapping of Decay Factor–mRNA Interactions in Yeast Identifies Nutrient-Responsive Transcripts as Targets of the Deadenylase Ccr4

Cited by 33 publications

References 104 publications

Ccr4–Not maintains genomic integrity by controlling the ubiquitylation and degradation of arrested RNAPII

Ccr4–Not maintains genomic integrity by controlling the ubiquitylation and degradation of arrested RNAPII

Coevolution of retroviruses withSERINCs following whole-genome duplication divergence

Cytoplasmic mRNA decay factors modulate RNA polymerase II processivity in 5’ and 3’ gene regions in yeast

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