Structural basis for high-affinity binding of LEDGF PWWP to mononucleosomes

Eidahl, Jocelyn O.; Crowe, Brandon L.; North, Justin A.; McKee, Christopher J.; Shkriabai, Nikoloz; Feng, Lei; Plumb, Matthew R.; Graham, R.L.; Gorelick, Robert J.; Hess, Sonja; Poirier, Michael G.; Foster, Mark P.; Kvaratskhelia, Mamuka

doi:10.1093/nar/gkt074

Cited by 182 publications

(210 citation statements)

References 52 publications

(95 reference statements)

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“…The site selectivity of HIV-1 integration is controlled by cellular protein LEDGF/p75 (9,11,12), which functions as a bimodal tether. The LEDGF/p75 C-terminal region directly engages lentiviral INs, whereas its N-terminal region containing the PWWP domain recognizes trimethylated H3 tails in chromatin (36)(37)(38) and, accordingly, directs HIV-1 integration into actively transcribed genes (9)(10)(11)(12).…”

Section: Discussionmentioning

confidence: 99%

BET proteins promote efficient murine leukemia virus integration at transcription start sites

Sharma¹,

Larue²,

Plumb³

et al. 2013

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

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180

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The selection of chromosomal targets for retroviral integration varies markedly, tracking with the genus of the retrovirus, suggestive of targeting by binding to cellular factors. γ-Retroviral murine leukemia virus (MLV) DNA integration into the host genome is favored at transcription start sites, but the underlying mechanism for this preference is unknown. Here, we have identified bromodomain and extraterminal domain (BET) proteins (Brd2, -3, -4) as cellular-binding partners of MLV integrase. We show that purified recombinant Brd4(1-720) binds with high affinity to MLV integrase and stimulates correct concerted integration in vitro. JQ-1, a small molecule that selectively inhibits interactions of BET proteins with modified histone sites impaired MLV but not HIV-1 integration in infected cells. Comparison of the distribution of BET protein-binding sites analyzed using ChIP-Seq data and MLV-integration sites revealed significant positive correlations. Antagonism of BET proteins, via JQ-1 treatment or RNA interference, reduced MLV-integration frequencies at transcription start sites. These findings elucidate the importance of BET proteins for MLV integration efficiency and targeting and provide a route to developing safer MLV-based vectors for human gene therapy. (1-4). The selection of chromosomal targets for retroviral integration varies markedly, tracking with the genus of the retrovirus studied (5-7). For example, the γ-retroviruses favor integration near transcription start sites, whereas lentiviruses favor integration within transcription units. These observations have suggested that different cellularbinding partners of retroviral integrases are likely to be responsible for integration target-site selection. However, to date, only one example has been reported: lens epithelium-derived growth factor (LEDGF/p75), which functions as a bimodal tether that engages HIV-1 intasomes and navigates them to active genes (8-14). Cellular cofactors of other retroviral genera are currently unknown.The molecular mechanisms of γ-retroviral murine leukemia virus (MLV) integration are of particular significance because MLV-based vectors are used for human gene therapy. In clinical trials, the use of γ-retroviral vectors to correct primary immunodeficiencies has been curative, but adverse events have occurred associated with insertion of MLV-based vectors near protooncogenes (reviewed in refs. 15-18). The identification of cellular factors for γ-retroviruses may provide mechanistic clues to facilitate the development of safer gene-therapy vectors.In this report, we have identified the bromodomain and extraterminal domain (BET) proteins (Brd2, -3, -4) as the cellularbinding partners of MLV IN and demonstrate their significance for stimulating and targeting MLV integration at transcription start sites. (Table 1, Table S1, and Fig. S1). Of these, Brd4 and Brd3 were the top hits in NIH 3T3 and Sup-T1 cells, respectively. Differential pull-down levels of these proteins (Table 1) could be attributable to the varying expression le...

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Section: Discussionmentioning

confidence: 99%

BET proteins promote efficient murine leukemia virus integration at transcription start sites

Sharma¹,

Larue²,

Plumb³

et al. 2013

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

Self Cite

180

259

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“…L ens epithelium-derived growth factor (LEDGF/p75) is an epigenetic reader recognizing H3K36me3 histone marks via its N-terminal PWWP domain 1,2 . Knockout of the gene encoding LEDGF/p75 and its splice variant p52 (Psip1) leads to perinatal mortality and severe homeotic skeletal transformations reminiscent of those seen in mice with Hox mutations 3 .…”

mentioning

confidence: 99%

Multiple cellular proteins interact with LEDGF/p75 through a conserved unstructured consensus motif

et al. 2015

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Lens epithelium-derived growth factor (LEDGF/p75) is an epigenetic reader and attractive therapeutic target involved in HIV integration and the development of mixed lineage leukaemia (MLL1) fusion-driven leukaemia. Besides HIV integrase and the MLL1-menin complex, LEDGF/p75 interacts with various cellular proteins via its integrase binding domain (IBD). Here we present structural characterization of IBD interactions with transcriptional repressor JPO2 and domesticated transposase PogZ, and show that the PogZ interaction is nearly identical to the interaction of LEDGF/p75 with MLL1. The interaction with the IBD is maintained by an intrinsically disordered IBD-binding motif (IBM) common to all known cellular partners of LEDGF/p75. In addition, based on IBM conservation, we identify and validate IWS1 as a novel LEDGF/p75 interaction partner. Our results also reveal how HIV integrase efficiently displaces cellular binding partners from LEDGF/p75. Finally, the similar binding modes of LEDGF/p75 interaction partners represent a new challenge for the development of selective interaction inhibitors.

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“…Recently, the structure of the PWWP domain from LEDGF/ p75 revealed a C-terminal region with less helical content than its counterparts. LEDGF/p75 PWWP contains a shorter helix α3, which leads to a longer connecting loop (Eidahl et al 2013;van Nuland et al 2013). Despite the lack of sequence conservation, one α-helix is virtually identical in all PWWP structures determined so far (Fig.…”

Section: Structural Features Of Pwwp Domainsmentioning

confidence: 92%

“…To date, several three-dimensional structures of PWWP domains have been reported, including those of DNMT3a, DNMT3b, Pdp1, Pdp2, HDGF, HDGF2, HDGF-related protein 3 (HRP-3), Bromo and plant homeodomain (PHD) finger-containing protein 1 (BRPF1), BRPF2, BRPF3, LEDGF/ p75, Mutated melanoma-associated antigen 1 (MUM1), MutS homolog 6 (MSH6), and Zinc finger MYND domaincontaining protein 11 (ZMNYD11) (Qiu et al 2002;Slater et al 2003;Sue et al 2004Sue et al , 2007Nameki et al 2005;Lukasik et al 2006;Laguri et al 2008;Vezzoli et al 2010;Wu et al 2011;Eidahl et al 2013;van Nuland et al 2013;Wang et al 2014;Wen et al 2014). Table 1 summarizes the structural data currently available in the literature.…”

Section: Structural Features Of Pwwp Domainsmentioning

confidence: 99%

“…In addition, mutations on the PWWP domains of DNMT3a and DNMT3b abolish their interaction with heterochromatin and inhibit their ability to methylate DNA Ge et al 2004). From that time until now, numerous PWWP domains have been shown to exhibit DNA-binding activity, including those of LEDGF/p75 (Singh et al 2006;Eidahl et al 2013;van Nuland et al 2013), HDGF (Lukasik et al 2006;Yang and Everett 2007), MSH6 (Laguri et al 2008), DNMT3a (Purdy et al 2010), Pdp1 (Qiu et al 2012), and the Bromo-ZnF-PWWP domain of human ZMNYD11 . For most proteins, DNA binding occurs in a nonspecific manner, without sequence selectivity.…”

Section: Structural Features Of Pwwp Domainsmentioning

confidence: 99%

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PWWP domains and their modes of sensing DNA and histone methylated lysines

2016

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Chromatin plays an important role in gene transcription control, cell cycle progression, recombination, DNA replication and repair. The fundamental unit of chromatin, the nucleosome, is formed by a DNA duplex wrapped around an octamer of histones. Histones are susceptible to various post-translational modifications, covalent alterations that change the chromatin status. Lysine methylation is one of the major post-translational modifications involved in the regulation of chromatin function. The PWWP domain is a member of the Royal superfamily that functions as a chromatin methylation reader by recognizing both DNA and histone methylated lysines. The PWWP domain three-dimensional structure is based on an N-terminal hydrophobic β-barrel responsible for histone methyl-lysine binding, and a C-terminal α-helical domain. In this review, we set out to discuss the most recent literature on PWWP domains, focusing on their structural features and the mechanisms by which they specifically recognize DNA and histone methylated lysines at the level of the nucleosome.

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Structural basis for high-affinity binding of LEDGF PWWP to mononucleosomes

Cited by 182 publications

References 52 publications

BET proteins promote efficient murine leukemia virus integration at transcription start sites

BET proteins promote efficient murine leukemia virus integration at transcription start sites

Multiple cellular proteins interact with LEDGF/p75 through a conserved unstructured consensus motif

PWWP domains and their modes of sensing DNA and histone methylated lysines

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