The PHD finger, a nuclear protein-interaction domain

The PHD finger, a nuclear protein-interaction domain

Review TRENDS in Biochemical Sciences Vol.31 No.1 January 2006 The PHD finger, a nuclear protein-interaction domain Mariann Bienz LMB Laboratory of...

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Review

TRENDS in Biochemical Sciences

Vol.31 No.1 January 2006

The PHD finger, a nuclear protein-interaction domain Mariann Bienz LMB Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK

The PHD finger is a common structural motif found in all eukaryotic genomes. It is a Zn2C-binding domain and its closest structural relative is the RING domain. Many RING fingers bind to E2 ligases to mediate the ubiquitination of proteins. Whether PHD fingers share a common function is unclear. Notably, many if not all PHD fingers are found in nuclear proteins whose substrate tends to be chromatin. Some PHD fingers bind to specific nuclear protein partners, apparently through the same surface that is used by RING domains to bind their cognate E2 ligases. New evidence also suggests that some PHD fingers bind to nucleosomes, raising the possibility that chromatin might be a common nuclear ligand of PHD fingers. Introduction The PHD finger was discovered over a decade ago by Schindler et al. [1], who noted a stretch of sequence conservation with regularly spaced cysteines between two plant homeodomain proteins. They remarked on the similarity between this sequence and metal-binding domains such as the RING finger and named it the plant homeodomain (PHD) finger, proposing that similar fingers would be found in other proteins. This turned out to be true, and a landmark paper published in Trends in Biological Sciences 2 years later established the PHD finger as a bona fide domain that is present in a wide variety of eukaryotic proteins [2]. This raised questions – which remain open – concerning the role of this domain and whether different PHD fingers might share a common function. The answers are likely to be found in the molecules that interact with them, given that other zinc fingers bind to proteins or nucleic acids. The quest for a common role of PHD fingers was fuelled considerably by the discovery that many RING fingers function in the ubiquitin pathway, where they bind to E2 ligases to mediate ubiquitination [3]. It thus seemed possible that PHD fingers might also bind to a common set of ligands that would reveal an intrinsic function of this domain. PHD fingers tend to be found in nuclear proteins that have a role in regulating chromatin [2]. Here, I examine this further by considering whole genomic complements of PHD fingers, and conclude that PHD fingers are likely to present in nuclear proteins without exception. Furthermore, by focusing on their ligands, I discuss ideas Corresponding author: Bienz, M. ([email protected]). Available online 16 December 2005

regarding the function of PHD fingers. These ligands include specific protein partners and, according to recent work, nucleosomes. It is thus conceivable that chromatin might be a common ligand of PHD fingers and that PHD fingers could tether their protein partners to chromatin by binding simultaneously to both. The relationship between PHD and RING fingers PHD fingers comprise w60 amino acids. They typically show a C4HC3 signature (four cysteines, one histidine, three cysteines) with a characteristic cysteine spacing and with additional conserved residues, most notably a tryptophan or other aromatic amino acid preceding the final cysteine pair [2] (Figure 1). It was noted early on that the PHD finger resembles the RING domain [1,2], which typically has a C3HC4 signature and binds two Zn2C ions. This resemblance was confirmed by the structure determinations of four different canonical PHD fingers, WSTF, KAP-1, Mi-2b and AIRE1 [4–7] (Figure 1): like RING fingers, these structures show the same interleaved (‘cross-brace’) topology of the Zn2C-coordinating residues (Figure 2); in addition, they share some similarity with RING fingers in their structural cores. However, there are also considerable differences between the two types of finger (see later). The similarity between PHD and RING domains prompted the idea that PHD fingers might also bind to E2 ubiquitin ligases. Indeed, the zinc fingers of both MEKK1 [8] and the MIR proteins [9–11] were shown to do just this and to act as E3 ubiquitin ligases [12]. Two independent groups [13,14] subsequently pointed out, however, that these zinc fingers had been misclassified as PHD fingers, and that they were in fact unambiguous, if slightly deviant, RING domains. This controversy highlighted the need for better criteria and tools for zinc finger classification, such as similarity profiles [13] that can distinguish between different classes of zinc finger. Structural analysis has confirmed that there are crucial differences between PHD and RING fingers, especially in their surface areas. Indeed, the overall structure of the MIR K3 zinc finger looks like a RING rather than a PHD finger [15]. Furthermore, the RING domain surface that docks E2 ligases contains a conserved a-helix [15–17] that is absent from the equivalent surface of PHD fingers [4–7] (Figure 2, loop 2). Finally, although it was claimed that the PHD finger of AIRE1 functions as an E3 ligase [18], these results were not reproduced in a subsequent study, which found that this finger neither bound to E2 ligases nor

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hPygo1 hPygo2

YPCGMCHKEVNDNDEAVFCES-GCNF-FFHRTCVGLTEAAFQMLNKEVFAE-WCCDKCVS YPCGICTNEVNDDQDAILCEA-SCQK-WFHRICTGMTETAYGLLTAEASAV-WGCDTCMA YPCGACRSEVNDDQDAILCEA-SCQK-WFHRECTGMTESAYGLLTTEASAV-WACDLCLK

AIRE1 Mi-2 NURF301 WSTF KAP-1 ATRX

DECAVCRDGGELIC----CD—-GCPR-AFHLACLSPPLREIPSGT-------WRCSSCLQ EFCRVCKDGGELLC----CD—-ACPS-SYHLHCLNPPLPEIPNGE-------WLCPRCTC DHCRVCHRLGDLLC----CE—-TCPA-VYHLECVDPPMNDVPTED-------WQCGLCRS ARCKVCRKKGEDDKLIL-CD—-ECNK-AFHLFCLRPALYEVPDGE-------WQCPACQP TICRVCQKPGDLVM----CN—-QCEF-CFHLDCHLPALQDVPGEE-------WSCSLCHV EQCRWCAEGGNLIC----CD—-FCHN-AFCKKCILRNLGRKELSTIMDENNQWYCYICHP

ING2

TYC-LCNQVSYGEMIG—-CDNEQCPIEWFHFSCVSLTYKPKGK---------WYCPKCRG

ACF1-1 ACF1-2

SLCKVCRRGSDPEKMLL-CD—-ECNA-GTHMFCLKPKLRSVPPGN-------WYCNDCVK KVCQKCFYDGGEIK----CV—-QCRL-FFHLECVHLKRPPRTD---------FVCKTCKP

P300

HFCEKCFNEIQGES-32-CT—-ECGR-KMHQICVLHHEIIWPAG--------FVCDGCLK

Pygopus

Consensus

C—-C------------C----C-----H—-C-------------------W-C--C Loop 1 Loop 2

Figure 1. The sequence signature of PHD fingers. Sequence alignment of ten different canonical PHD fingers and two atypical ones (WSTF and p300), as discussed in this review (both PHD fingers of ACF1 are shown); all sequences are from human proteins, except for Pygopus, ACF1 and NURF301, which are from Drosophila. Note the characteristic spacing between the Zn2C-coordinating residues (bold) and the highly conserved aromatic residue, typically a tryptophan (bold), that are common to all canonical PHD fingers. Note also that additional residues are conserved in loop 1 (between C2 and C3) and loop 2 (between C5 and C6) among related PHD fingers, for example, among the Pygopus orthologues (top), or the KAP-1 group of PHD fingers (middle). These loops vary in length and, according to structural analysis [4–-7], constitute two different surfaces of the domain. Loop residues with functional relevance are highlighted, as indicated by their requirement for ligand binding (red) [41], activity in transcription assays (blue) [40,41], or mutation in disease (orange) [29,42,43]. Notably, most of these residues are in loop 2, suggesting that this loop constitutes a prime interaction surface of many PHD fingers.

mediated ubiquitin transfer [7]. Thus, experimental evidence also argues against a possible link between PHD fingers and ubiquitination. PHD proteins are nuclear PHD fingers were discovered before genome sequences of eukaryotes were available. Since then, it has become possible to determine the full complement of PHD proteins in eukaryotic genomes, although their precise numbers depends, of course, on the definition of the PHD finger. Here, I consider mainly PHD fingers that are identified by both SMART and Pfam searches (‘canonical’ PHD fingers; Tables 1, 2), but I also touch on other ‘atypical’ PHDlike fingers. In the budding yeast Saccharomyces cerevisiae, SMART and Pfam searches identify 14 proteins with canonical PHD fingers (Table 1). Seven of these contain single or tandem PHD fingers as their only recognizable domains (Table 1, ‘nd’). Remarkably, 11 of the 14 yeast PHD proteins are known to be nuclear [19], and the remaining three are also expected to be nuclear on the basis of their additional domains, which have predicted roles in transcription elongation (TFS2M) or histone modification (SET [20] or JmjC [21]). Furthermore, except for one yeast PHD protein, for which informative functional evidence is lacking, each of the other 13 proteins has been implicated in the control of chromatin or transcription, either by direct functional analysis (Table 1, column 6) or on the basis of an additional domain (SANT [22] or JmjC [21]; Table 1, column 3). In the fruitfly Drosophila melanogaster, a SMART search identifies 80 PHD entries. After discarding redundant entries and counterscreening by Pfam, the number of different canonical PHD proteins is reduced to 38 (Table 2). Of these, only 12 (‘nd’) do not contain any additional recognizable domains. The best-known example of this group is Pygopus, a recently discovered nuclear component of the Wnt signalling pathway that interacts www.sciencedirect.com

with the transcriptional coactivator Armadillo (also known as b-catenin) through the adaptor Legless (also known as BCL9) [23] (see later). As in yeast, the fly PHD proteins are known, or expected, to be nuclear. For example, most of them (28/38) contain matches to a classical nuclear localization signal [24] (Table 2, column 4). As in yeast, many fly PHD proteins are known, or firmly predicted, to bind DNA or chromatin and/or to function in the control of chromatin or transcription (28/38; Table 2, column 5). It is

Binding to Lgs/BCL9

Loop 2

T L

E

L

A

G C4

C5

C1

W

E

Y P

A

C6 D

G

Zn

Zn R H1

C2

E

F

C7

C3 A

E V

D N D

Loop 1

Activity in transcription assay Ti BS

Figure 2. Cross-brace model of the PHD finger of Pygopus. A representation of the Pygopus PHD finger is shown, as predicted from the structural analysis of other PHD fingers [4–-7], showing the cross-brace topology of the Zn2C-coordinating residues. Residues conserved among the Pygopus orthologues are in green; red rings mark loop 1 and loop 2 residues with the indicated functional relevance (see also Figure 1); the blue bracket spans residues in loop 2 that in the RING finger of cCbl form a surface that docks its cognate E2 ligase [16]. Figure adapted, with permission, from Ref. [41].

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Table 1. Canonical PHD fingers in the genome of S. cerevisiaea ORF

Name

YKR029C YHR090C YER051W YJL105W YJR119C YNL097C YGL131C YPL138C YMR176W YMR075W YOR064C YPR031W YPL181W YKL005C

set3 yng2 set4 pho23 spp1 rco1 yng1 nto1 cti6 bye1

Additional domainsb SET nd JmjC SET JmjC nd SANT, BAH nd Bright, JmjC nd nd nd nd TFS2M

Nuclearc Yes Yes Unknown Unknown Yes Yes Yes Yes Yes Yes Yes Yes Yes Unknown

Related mammalian proteinsd MLL ING

Function

MLL SMCX ING Phf14 (CXXC1) SMCX Phf12 ING BRD1/BRPF1

Predicted histone methyltransferasee

Transcription elongation factor SII

Histone methyltransferase Subunit of NuA4 HAT complex

Associated with Rpd3 histone deacetylase Subunit of Set1C

Subunit of NuA3 HAT complex HAT component Binds to Cyc8–Tup1 co-repressor Regulator of transcription elongation

a

Only open reading frames (ORFs) with PHD fingers that were identified by both SMART and Pfam database searches are listed. Only domains that are known to be found in nuclear proteins are listed; nd, no additional domains were detected (‘PHD-finger-only’ proteins). ‘Yes’ indicates nuclear location of genomically tagged proteins [19]. d Only mammalian relatives whose sequence similarity extends significantly beyond the PHD finger are listed. e This function is predicted on the basis of its associated SET domain. Abbreviation: HAT, histone acetyltransferase. b c

Table 2. Canonical PHD fingers in the genome of D. melanogastera ORF

Name

CG9594 CG2662 CG8103 CG8651 CG8887 CG5109 CG12238 CG10042 CG1070 CG32346 CG7036 CG8677 CG9293 CG10897 CG4976 CG15439 CG17440 CG1966 CG2009 CG5206e CG1845 CG 4903 CG2682 CG11518 CG5491 CG7379 CG6525 CG9088 CG2926

Chd3

CG9007 CG6632 CG5591 CG17446 CG3815 CG10414 CG11290 CG1815 CG7376 a

Mi-2 Trx Ash1 Polycomblike SAYP/e(y)3 MBD-R2 Alhambra NURF301 Rhinoceros

Toutatis Mes-4

CHRAC/ACF1 TAF155/Bip2 Bonus MESR4 D4/Dd4 Pygopus

Lid

Ing3

Additional domainsb Chromo Chromo SET SET, BAH nd MBD nd BRD nd nd nd BRD SET nd nd BRD BRD BRD nd nd nd nd TFS2M Bright, JmjC

SET nd HMG

KKxK Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes

FHA Enoki mushroom

SAS2 BRD

Yes Yes

Related mammalian proteinsc CHD4 MLL3 CHD4 Trx2, MLL4 Ash1-like Phf19 Phf10 Phf20 AF10/MLLT10 Falz Phf16 RSF1 ING5 hWALp4 WHSC1 Phf14 CXXC1 WSTF ING3, TAF140 TIF1, TRIM33 BRPF1/BRD1 – Requiem/ubi-D4 hPygo1, hPygo2 Phf22 p33ING1 DATF1 RBP2,Smcx CTD-binding SR-like protein MLL5 p47ING3 MLL3 CXXC1 Phf12 CSRP2 binding protein MYST3 PRKCBP1 SNF2 histone linker PHD RING helicase

Function Chromatin remodelling Chromatin remodelling Histone methyltransferase Histone methyltransferase Chromatin binding Chromatin binding Methyl-CpG bindingd Transcription factord Chromatin remodelling Chromatin remodellingd Chromatin remodellingd Histone methyltransferase CpG bindingd Chromatin remodelling Transcription factor IID Transcriptional activationd Chromatin bindingd Transcription factord Transcriptional activation

Transcription elongation factord

Histone methyltransferased DNA bindingd CpG bindingd Transcription factord Histone acetyltransferased Chromatin bindingd

Only ORFs with PHD fingers that were identified by both SMART and Pfam database searches are listed (in addition, the following six ORFs were identified by SMART, but not by Pfam: CG6677, CG15141, CG11534, CG13928, CG5354 and CG3848). b Only domains that are known, or firmly predicted, to function in the nucleus are listed; nd, no additional domains were detected (‘PHD-finger-only’ proteins). c Only mammalian relatives whose sequence similarity extends significantly beyond the PHD finger are listed. d These functions are inferred from an additional domain (column 3), or from a mammalian relative (column 5). e Also called CG15687. www.sciencedirect.com

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also striking that the fly (like the yeast) PHD proteins lack transmembrane domains or other domains that are known to function outside the nucleus. In the human genome, a SMART search identifies more than 300 PHD proteins, but this is clearly an overestimate (see earlier), and the number of truly different human PHD proteins is likely to be less than 150. To identify them is beyond the scope of this review; it suffices to say that many of the human PHD proteins have counterparts in Drosophila (Table 2). Like the fly and yeast PHD proteins, they tend to be nuclear and/or function in the control of chromatin. This tendency is illustrated by the human PHD proteins that have been implicated in disease: for example, the William–Beuren syndrome transcription factor (WSTF) is a constituent of ISWI- and SWI/SNF-based chromatin remodelling complexes [25,26], the Mi-2 dermatomyositis-specific autoantigen is a subunit of NuRD chromatin remodelling complexes [27], and the autoimmune regulator protein AIRE1 is also thought to be involved in transcriptional control [28]. Another well-studied human disease-related PHD protein is the transcriptional regulator ATRX [29], a constituent of a SWI/SNF2-like chromatin remodelling complex [30], but the PHD finger in this protein is atypical in that its Zn2C-coordinating residues are all cysteines (Figure 1). PHD fingers can have nucleosome-binding activity Many if not all PHD proteins are nuclear, raising the issue of whether they bind to a common nuclear ligand. An obvious candidate for such a ligand is chromatin. Indeed, one of the initial ideas was that PHD fingers might bind to histones or their exposed tails [2], a notion that has been supported by two recent studies. First, in an electrophoretic mobility shift assay, nucleosome-binding activity was observed for the isolated PHD finger of p300 [31], a transcriptional coactivator with histone acetyltransferase activity [32]. Furthermore, in a stringent nucleosome retention assay, this PHD finger cooperated with the adjacent bromo domain (BRD) to confer a robust association with native hyperacetylated nucleosomes (isolated from mammalian cells treated with a histone deacetylase inhibitor [31]; note that BRDs can bind to acetylated histone residues in histone tails and are thought to be part of the machinery that recognizes stable marks on chromatin [20]. It is worth bearing in mind, however, that this finger is an atypical one that is not identified by SMART and Pfam searches, probably because its loop 1 is unusually large, comprising 42 instead of the typical 8–12 residues (Figure 1). Its substitution by heterologous canonical PHD fingers results in loss of nucleosome binding [31], suggesting that this activity could be a property of this slightly unusual BRD–PHD module. Second, Eberharter et al. [33] found that the two PHD fingers of ACF1, a subunit of an ATP-dependent ISWIbased nucleosome remodelling complex [34], binds to the central domains of all four core histones and increases the efficiency of the nucleosome sliding activity of ISWI. These authors thus proposed that these fingers might tether the associated ISWI factor to histones to provide a ‘grip’ on www.sciencedirect.com

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the core nucleosome against which ISWI can push to achieve the ATP-dependent displacement of nucleosomal DNA [33]. It might be significant that in both these proteins, p300 and ACF1, the PHD fingers seem to cooperate with an adjacent BRD to constitute a functional nucleosomebinding module [31,33]. Another example of a nucleosome-binding PHD–BRD module seems to be present in NURF301, a protein related to ACF1 and a constituent of the ISWI-containing NURF chromatin remodelling complex [35]. It is thus conceivable that a subset of the PHD fingers form PHD–BRD modules, designed to target or to tether chromatin remodelling complexes to acetylated stretches of nucleosomes. The role of the PHD fingers in these proteins seems to be to consolidate, or to strengthen, a separate chromatin-binding activity of either the same or an associated protein [31,33]. It will be interesting to see whether PHD fingers that are unlinked to BRDs or other chromatin-binding domains can also bind to nucleosomes. This is an attractive idea with regard to Pygopus and its putative function in the nuclear capture of the Armadillo coactivator [36]. A study has provided evidence that PHD fingers from proteins such as ING2 can bind to phosphoinositides, an association that might mediate their nuclear location [37]. This idea seemed plausible, given the structural similarity between the PHD finger and the FYVE domain [4], which binds to phosphatidylinositol 3-phosphate (PtdIns3P) to target cytoplasmic proteins to the plasma membrane [38]. In contrast to the latter domain, whose binding preference and affinity for PtdIns3P are well established [38], however, the PHD fingers that have been tested show neither clear binding preferences nor consistently strong binding affinities for specific phosphoinositides [37]. In addition, although binding of the ING2 finger to PtdIns5P was found to be dependent on several positively charged residues, these residues were not found to be significantly conserved among other PHD fingers; indeed, the residues most crucial for PtdIns5P binding were outside the finger motif. Notably, the PtdIns3P binding activity observed for the AIRE1 PHD finger [37] could not be confirmed by sensitive NMR binding experiments that can measure weak interactions with dissociation constants in the millimolar range [7]. Therefore, the proposal that PHD fingers might be nuclear phosphoinositide receptors remains without further experimental support. Binding of PHD fingers to specific protein ligands PHD fingers also bind to proteins other than histones, as originally proposed [2], but so far there is no evidence for robust binding to DNA (e.g. see Refs [31,33]). Here I consider only protein interactions if they have been shown to depend on the structural integrity of the PHD finger, either by mutagenesis of conserved structural residues or by treatment with Zn2C-chelating agents. These interactions encompass the PHD fingers of Polycomblike, which are involved in binding to the SET domain protein Enhancer of Zeste [39]; the PHD–BRD module of the KAP-1 repressor, which can bind to an isoform of Mi-2a [40]; and the PHD finger of Pygopus,

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which binds to Legless/BCL9 (which in turn binds to the Armadillo/b-catenin transcriptional coactivator) [23]. The latter is the best-characterized physical interaction [41], and its functional relevance to Wnt signalling during normal development has been clearly established [23,41]. The binding between the Pygopus PHD finger and Legless/BCL9 is abolished if the structural C2 residue is mutated, but it also depends on four individual residues in the predicted surface loop 2 [41] (Figure 2). Three of these residues are conserved among all known Pygopus proteins, but not among other PHD fingers (Figure 1), which implies that they provide specificity for the interaction with Legless/BCL9. Similarly, indirect evidence from transcriptional repression assays suggests that binding between the KAP-1 PHD finger and Mi-2a depends partly on a residue in the loop 2 surface [5] that is conserved among the KAP-1 family of PHD fingers, including WSTF, AIRE1 and Mi-2 itself [40] (Figure 1). Furthermore, disease-linked point mutations have been identified in the PHD fingers of ATRX [29] and AIRE1 [42,43] that are predicted to affect the surface rather than the structural integrity of the domain: these mutations invariably affect loop 2 residues (Figure 1). Notably, in all of these proteins, the mutated loop 2 residues are located in a portion of the PHD finger (Figure 2) that corresponds to the surface of E3 RING domains that docks their cognate E2 ligases [15–17]. Although PHD fingers and RING domains differ significantly in their structures of this surface (see earlier), this nevertheless indicates that they use the same surface for binding to specific protein partners. Can PHD fingers simultaneously bind to two ligands? PHD fingers have a second flexible loop (Figure 2, loop 1) that forms an alternative surface area [4–7]. Although several of the loop 1 residues are conserved between related PHD fingers (Figure 1), as yet there is no indication of a loop 1 ligand. A hint of a function for loop 1 has come from Pygopus, given that four of its conserved loop 1 residues contribute to activity in a cell-based transcription assay [41] (Figures 1, 2). In addition, although rescue assays of pygo mutants argue against a function for these loop 1 residues in development [23,41], these assays are based on overexpression of the rescuing protein and thus cannot exclude functions that provide efficiency (because these manifest themselves only at low protein concentration). It thus remains possible that the putative loop 1 surface of Pygopus mediates binding to an unknown ligand [41]. Unfortunately, it is not known which surface of the nucleosome-binding PHD fingers mediates the binding to nucleosomes or histones [33,35]. One might expect this surface to have a negative potential compatible with that of the positively charged histones. Indeed, one of the PHD fingers of AIRE1 shows a surface with negative potential contributed in part by two negatively charged residues of loop 1 [7] (Figure 3). Furthermore, the Pygopus proteins have three or four negatively charged residues in the same loop, two of which are completely conserved (Figure 1). In the absence of www.sciencedirect.com

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180 E11 D8

Figure 3. Electrostatic surface potential of the PHD finger of AIRE1. Surface plots of two different views of the first PHD finger of AIRE1 show predominantly positive (blue, left-hand view) or negative (red, right-hand view) surface potential; the two acidic loop 1 residues that contribute to the latter are indicated (for residue numbers, see Figure 1). Figure adapted, with permission, from Ref. [7].

a known structure, however, it is difficult to know whether these residues do indeed contribute to a putative binding surface. In future studies, it will be interesting to test whether either of these PHD fingers can participate in chromatin binding.

Concluding remarks PHD proteins seem to be found universally in the nucleus, and their functions tend to lie in the control of chromatin or transcription. Increasing evidence indicates that PHD fingers bind to specific nuclear protein partners, for which they apparently use their loop 2 surface. Perhaps each PHD finger has its own cognate nuclear ligand, much like RING fingers have their cognate E2 ligases. No doubt the list of specific PHD finger ligands will grow, and the set of these ligands is likely to reveal whether PHD fingers have a common function in the nucleus. Evidence is also beginning to emerge that some PHD fingers can bind to nucleosomes. It will be interesting to see whether chromatin binding is a more widespread property of PHD fingers and, if so, how this might contribute to the function of PHD proteins. Obviously, the interactions between PHD fingers and chromatin need further biochemical characterization. For example, it will be important to identify the residues of the PHD finger surfaces that are involved in the nucleosome binding. This might reveal whether PHD fingers can interact simultaneously with nucleosomes and specific protein ligands, thereby tethering these ligands to chromatin [31,33]. Acknowledgements I thank Giovanna Musco and Fiona Townsley for figure material; Marc Fiedler, Kay Hofmann and Giovanna Musco for discussion; and Karen Spillard for help with the tables.

References 1 Schindler, U. et al. (1993) HAT3.1, a novel Arabidopsis homeodomain protein containing a conserved cysteine-rich region. Plant J. 4, 137–150 2 Aasland, R. et al. (1995) The PHD finger: implications for chromatinmediated transcriptional regulation. Trends Biochem. Sci. 20, 56–59 3 Weissman, A.M. (2001) Themes and variations on ubiquitylation. Nat. Rev. Mol. Cell Biol. 2, 169–178 4 Pascual, J. et al. (2000) Structure of the PHD zinc finger from human Williams–Beuren syndrome transcription factor. J. Mol. Biol. 304, 723–729

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5 Capili, A.D. et al. (2001) Solution structure of the PHD domain from the KAP-1 corepressor: structural determinants for PHD, RING and LIM zinc-binding domains. EMBO J. 20, 165–177 6 Kwan, A.H. et al. (2003) Engineering a protein scaffold from a PHD finger. Structure (Camb.) 11, 803–813 7 Bottomley, M.J. et al. (2005) NMR structure of the first PHD finger of autoimmune regulator protein (AIRE1). Insights into autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) disease. J. Biol. Chem. 280, 11505–11512 8 Lu, Z. et al. (2002) The PHD domain of MEKK1 acts as an E3 ubiquitin ligase and mediates ubiquitination and degradation of ERK1/2. Mol. Cell 9, 945–956 9 Coscoy, L. et al. (2001) A novel class of herpesvirus-encoded membrane-bound E3 ubiquitin ligases regulates endocytosis of proteins involved in immune recognition. J. Cell Biol. 155, 1265–1273 10 Boname, J.M. and Stevenson, P.G. (2001) MHC class I ubiquitination by a viral PHD/LAP finger protein. Immunity 15, 627–636 11 Mansouri, M. et al. (2003) The PHD/LAP-domain protein M153R of myxomavirus is a ubiquitin ligase that induces the rapid internalization and lysosomal destruction of CD4. J. Virol. 77, 1427–1440 12 Coscoy, L. and Ganem, D. (2003) PHD domains and E3 ubiquitin ligases: viruses make the connection. Trends Cell Biol. 13, 7–12 13 Scheel, H. and Hofmann, K. (2003) No evidence for PHD fingers as ubiquitin ligases. Trends Cell Biol. 13, 285–287 14 Aravind, L. et al. (2003) Scores of RINGS but no PHDs in ubiquitin signaling. Cell Cycle 2, 123–126 15 Dodd, R.B. et al. (2004) Solution structure of the Kaposi’s sarcomaassociated herpesvirus K3 N-terminal domain reveals a novel E2binding C4HC3-type RING domain. J. Biol. Chem. 279, 53840–53847 16 Zheng, N. et al. (2000) Structure of a c-Cbl–UbcH7 complex: RING domain function in ubiquitin-protein ligases. Cell 102, 533–539 17 Dominguez, C. et al. (2004) Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches. Structure (Camb) 12, 633–644 18 Uchida, D. et al. (2004) AIRE functions as an E3 ubiquitin ligase. J. Exp. Med. 199, 167–172 19 Huh, W.K. et al. (2003) Global analysis of protein localization in budding yeast. Nature 425, 686–691 20 Jenuwein, T. and Allis, C.D. (2001) Translating the histone code. Science 293, 1074–1080 21 Trewick, S.C. et al. (2005) Methylation: lost in hydroxylation? EMBO Rep. 6, 315–320 22 Boyer, L.A. et al. (2004) The SANT domain: a unique histone-tailbinding module? Nat. Rev. Mol. Cell Biol. 5, 158–163 23 Kramps, T. et al. (2002) Wnt/wingless signaling requires BCL9– legless-mediated recruitment of pygopus to the nuclear b-catenin– TCF complex. Cell 109, 47–60 24 Conti, E. et al. (1998) Crystallographic analysis of the recognition of a nuclear localization signal by the nuclear import factor karyopherin a. Cell 94, 193–204 25 Bozhenok, L. et al. (2002) WSTF–ISWI chromatin remodeling complex targets heterochromatic replication foci. EMBO J. 21, 2231–2241

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26 Kitagawa, H. et al. (2003) The chromatin-remodeling complex WINAC targets a nuclear receptor to promoters and is impaired in Williams syndrome. Cell 113, 905–917 27 Becker, P.B. and Ho¨rz, W. (2002) ATP-dependent nucleosome remodeling. Annu. Rev. Biochem. 71, 247–273 28 Villasenor, J. et al. (2005) AIRE and APECED: molecular insights into an autoimmune disease. Immunol. Rev. 204, 156–164 29 Gibbons, R.J. et al. (1997) Mutations in transcriptional regulator ATRX establish the functional significance of a PHD-like domain. Nat. Genet. 17, 146–148 30 Xue, Y. et al. (2003) The ATRX syndrome protein forms a chromatinremodeling complex with Daxx and localizes in promyelocytic leukemia nuclear bodies. Proc. Natl. Acad. Sci. U. S. A. 100, 10635–10640 31 Ragvin, A. et al. (2004) Nucleosome binding by the bromodomain and PHD finger of the transcriptional cofactor p300. J. Mol. Biol. 337, 773–788 32 Ogryzko, V.V. et al. (1996) The transcriptional coactivators p300 and CBP are histone acetyltransferases. Cell 87, 953–959 33 Eberharter, A. et al. (2004) ACF1 improves the effectiveness of nucleosome mobilization by ISWI through PHD–histone contacts. EMBO J. 23, 4029–4039 34 Eberharter, A. et al. (2001) Acf1, the largest subunit of CHRAC, regulates ISWI-induced nucleosome remodelling. EMBO J. 20, 3781–3788 35 Xiao, H. et al. (2001) Dual functions of largest NURF subunit NURF301 in nucleosome sliding and transcription factor interactions. Mol. Cell 8, 531–543 36 Townsley, F.M. et al. (2004) Pygopus and Legless target Armadillo/bcatenin to the nucleus to enable its transcriptional co-activator function. Nat. Cell Biol. 6, 626–633 37 Gozani, O. et al. (2003) The PHD finger of the chromatin-associated protein ING2 functions as a nuclear phosphoinositide receptor. Cell 114, 99–111 38 Misra, S. and Hurley, J.H. (1999) Crystal structure of a phosphatidylinositol 3-phosphate-specific membrane-targeting motif, the FYVE domain of Vps27p. Cell 97, 657–666 39 O’Connell, S. et al. (2001) Polycomblike PHD fingers mediate conserved interaction with Enhancer of zeste protein. J. Biol. Chem. 276, 43065–43073 40 Schultz, D.C. et al. (2001) Targeting histone deacetylase complexes via KRAB-zinc finger proteins: the PHD and bromodomains of KAP-1 form a cooperative unit that recruits a novel isoform of the Mi-2a subunit of NuRD. Genes Dev. 15, 428–443 41 Townsley, F.M. et al. (2004) Pygopus residues required for its binding to Legless are critical for transcription and development. J. Biol. Chem. 279, 5177–5183 42 Bjorses, P. et al. (2000) Mutations in the AIRE gene: effects on subcellular location and transactivation function of the autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy protein. Am. J. Hum. Genet. 66, 378–392 43 Saugier-Veber, P. et al. (2001) Identification of a novel mutation in the autoimmune regulator (AIRE-1) gene in a French family with autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy. Eur. J. Endocrinol. 144, 347–351

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