DDX17 Specifically, and Independently of DDX5, Controls Use of the HIV A4/5 Splice Acceptor Cluster and Is Essential for Efficient Replication of HIV

Sithole, Nyaradzai; Williams, Claire; Vaughan, Aisling; Kenyon, Julia C.; Lever, Andrew

doi:10.1016/j.jmb.2018.06.052

Cited by 12 publications

(11 citation statements)

References 72 publications

(93 reference statements)

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“…6), as previously reported 33 . Indeed, the RNA helicase activities of DDX5 and DDX17 have been implicated in resolving RNA structures, facilitating the recognition of the 5′ splice site (which can be embedded in secondary structures), and exposing RNA-binding motifs to additional splicing regulators 33,42,[48][49][50] . However, even though some RNA-binding specificity has been reported for DDX17 51,52 , these RNA helicases are devoid of a proper RNA-binding domain, and their activity in splicing likely depends on additional factors that are able to provide target specificity.…”

Section: Discussionmentioning

confidence: 99%

Intragenic recruitment of NF-κB drives splicing modifications upon activation by the oncogene Tax of HTLV-1

et al. 2020

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Chronic NF-κB activation in inflammation and cancer has long been linked to persistent activation of NF-κB-responsive gene promoters. However, NF-κB factors also massively bind to gene bodies. Here, we demonstrate that recruitment of the NF-κB factor RELA to intragenic regions regulates alternative splicing upon NF-κB activation by the viral oncogene Tax of HTLV-1. Integrative analyses of RNA splicing and chromatin occupancy, combined with chromatin tethering assays, demonstrate that DNA-bound RELA interacts with and recruits the splicing regulator DDX17, in an NF-κB activation-dependent manner. This leads to alternative splicing of target exons due to the RNA helicase activity of DDX17. Similar results were obtained upon Tax-independent NF-κB activation, indicating that Tax likely exacerbates a physiological process where RELA provides splice target specificity. Collectively, our results demonstrate a physical and direct involvement of NF-κB in alternative splicing regulation, which significantly revisits our knowledge of HTLV-1 pathogenesis and other NF-κB-related diseases.

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Section: Discussionmentioning

confidence: 99%

Intragenic recruitment of NF-κB drives splicing modifications upon activation by the oncogene Tax of HTLV-1

et al. 2020

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“…IBV [81] dsRNA sensing (with DDX21 and DHX36) [21] Transmissible gastroenteritis virus [18] NF-κB signaling [19] DDX3X Arenavirus [38] JEV [47] HIV [74,84] IFN-β induction (with TBK1) [26] Innate immune signaling [27,28] HBV [36,93] Myxoma virus [88] VACV K7 [34] HBV polymerase [35] HCV 3 UTR [37] DDX5 JEV [47] HIV [84] Myxoma virus [88] DDX6 Negative regulation of ISG induction [66] RVFV, LACV [40] IVB [65] Flaviviruses: sequestered by sfRNA [67,68] DDX10 HIV [89] DDX17 HIV [84,94] RVFV [41] Cofactor for ZAP [43] Tombusviruses [45] DDX18…”

Section: Ddx1mentioning

confidence: 99%

DEAD-Box Helicases: Sensors, Regulators, and Effectors for Antiviral Defense

Taschuk

Cherry

2020

Viruses

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DEAD-box helicases are a large family of conserved RNA-binding proteins that belong to the broader group of cellular DExD/H helicases. Members of the DEAD-box helicase family have roles throughout cellular RNA metabolism from biogenesis to decay. Moreover, there is emerging evidence that cellular RNA helicases, including DEAD-box helicases, play roles in the recognition of foreign nucleic acids and the modulation of viral infection. As intracellular parasites, viruses must evade detection by innate immune sensing mechanisms and degradation by cellular machinery while also manipulating host cell processes to facilitate replication. The ability of DEAD-box helicases to recognize RNA in a sequence-independent manner, as well as the breadth of cellular functions carried out by members of this family, lead them to influence innate recognition and viral infections in multiple ways. Indeed, DEAD-box helicases have been shown to contribute to intracellular immune sensing, act as antiviral effectors, and even to be coopted by viruses to promote their replication. However, our understanding of the mechanisms underlying these interactions, as well as the cellular roles of DEAD-box helicases themselves, is limited in many cases. We will discuss the diverse roles that members of the DEAD-box helicase family play during viral infections.Viruses 2020, 12, 181 2 of 15 helicases to particular RNAs or proteins; the diversity of these regions accounts for the breadth of function observed within this protein family [7]. As a result of their diversity of binding and function, DEAD-box RNA helicases are involved in all aspects of cellular RNA metabolism, including transcription, splicing, microRNA biogenesis, ribosomal RNA processing, RNA export, translation, RNP granule formation, and decay [10]. Moreover, they are also involved in cellular stress responses, contributing to double-strand break (DSB) repair [11], stress granule formation, and antimicrobial responses [12]. DEAD-Box Helicases in Canonical Innate Immune SensingInnate immune defenses depend upon the recognition of invading pathogens by the host, and viral infections, including RNA viruses, are largely sensed through nucleic acid recognition. RNA viruses present a host cell with various foreign RNA features, such as unique ends, structured RNA elements, or dsRNA replication intermediates, which can be recognized as hallmarks of infection. RNA binding proteins thus play important roles in the sensing of viral infection, and DExD/H helicases are well-suited to recognize structural features characteristic of viral RNAs.The canonical cytoplasmic sensors of viral RNA, the RIG-I-like receptors (RLRs) RIG-I and MDA-5, contain DExD/H-box helicase domains [13]. RIG-I recognizes uncapped viral RNAsand short dsRNAs containing a 5 triphosphate, while MDA-5 binds longer dsRNA replication intermediates [13][14][15]. In addition to the helicase core domain, these proteins contain caspase activation and recruitment domains (CARDs).RNA recognition by these RLRs leads to oligomerization of ...

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“…DDX17 and its close homolog DDX5 play an important role in various contexts, including processing of primary microRNA transcripts (pri-miRs) in the nucleus (Kao et al, 2019;Li et al, 2017;Mori et al, 2014), pre-mRNA alternative splicing Hö nig et al, 2002), ribosome biogenesis (Jalal et al, 2007), mRNA export (Montpetit et al, 2011), and coregulation of transcription Fuller-Pace, 2013a;Lambert et al, 2018;Samaan et al, 2014). DDX17 has also been implicated in immunity by affecting viral infectivity (Lorgeoux et al, 2013;Moy et al, 2014;Sithole et al, 2018). Dysregulated expression of DDX17 has been associated with many cancers, including those in colon, prostate, breast, brain, lung, stomach, and blood (Cai et al, 2017;Fuller-Pace and Moore, 2011).…”

Section: Introductionmentioning

confidence: 99%

RNA Specificity and Autoregulation of DDX17, a Modulator of MicroRNA Biogenesis

2019

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Graphical Abstract Highlights d Crystal structures of human DDX17 core domains in multiple states are determined d DDX17 core domains exhibit RNA sequence preference via the RMFQ motif d DDX17 can enhance processing of pri-miRs by remodeling the 3 0 flanking region d N-terminal tail of DDX17 can regulate the ATPase activity In Brief Ngo et al. reveal crystal structures of DEAD-box 17 (DDX17) and show that the core catalytic domains recognize RNA sequence motifs in primary transcripts of microRNAs, to regulate processing by Drosha. DDX17 also has a unique N-terminal tail that can attenuate the ATPase activity. SUMMARY DDX17, a DEAD-box ATPase, is a multifunctional helicase important for various RNA functions, including microRNA maturation. Key questions for DDX17 include how it recognizes target RNAs and influences their structures, as well as how its ATPase activity may be regulated. Through crystal structures and biochemical assays, we show the ability of the core catalytic domains of DDX17 to recognize specific sequences in target RNAs. The RNA sequence preference of the catalytic core is critical for DDX17 to directly bind and remodel a specific region of primary microRNAs 3 0 to the mature sequence, and consequently enhance processing by Drosha. Furthermore, we identify an intramolecular interaction between the N-terminal tail and the DEAD domain of DDX17 to have an autoregulatory role in controlling the ATPase activity. Thus, we provide the molecular basis for how cognate RNA recognition and functional outcomes are linked for DDX17. À . We identify several mutations of DDX17 that affect ATP 4024 Cell Reports 29, 4024-4035, December 17, 2019 ª 2019 The Author(s). This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). domains. STAR+METHODSDetailed methods are provided in the online version of this paper and include the following:TABLE d LEAD CONTACT AND MATERIALS AVAILABILITY d EXPERIMENTAL MODEL AND SUBJECT DETAILS d METHOD DETAILS B Materials B in vitro RNA transcription and purification B Protein purification B RNA Unwinding Assay B Size-exclusion chromatography-Multiangle light scattering B Electrophoretic Mobility Shift Assay B in vitro ATP hydrolysis Assay B Differential Scanning Fluorimetry B Crystallization and Data Collection B Structure determination and refinement B in vitro pri-miR processing assays B Hydroxyl radical footprinting B Selective hydroxyl acylation followed by primer extension (SHAPE) B Cell Culture and quantitative real-time PCR (qPCR)

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DDX17 Specifically, and Independently of DDX5, Controls Use of the HIV A4/5 Splice Acceptor Cluster and Is Essential for Efficient Replication of HIV

Cited by 12 publications

References 72 publications

Intragenic recruitment of NF-κB drives splicing modifications upon activation by the oncogene Tax of HTLV-1

Intragenic recruitment of NF-κB drives splicing modifications upon activation by the oncogene Tax of HTLV-1

DEAD-Box Helicases: Sensors, Regulators, and Effectors for Antiviral Defense

RNA Specificity and Autoregulation of DDX17, a Modulator of MicroRNA Biogenesis

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