Regulation and epigenetic control oftranscription at the nuclear peripherySara Ahmed and Jason H. Brickner

Department of Biochemistry, Molecular Biology and Cell Biology Northwestern University, Evanston, IL 60208, USA

Review TRENDS in Genetics Vol.23 No.8

Glossary

Mex: mRNA export

Mlp: Myosin-like protein

Mtor: Megator

Nic: Nuclear pore interacting complex

Nup: nucleoporin

Sac: Suppressor of actin

Thp: Tho/Hpr1 phenotype

TPR: Translocated promoter region

The localization of DNA within the nucleus influencesthe regulation of gene transcription. Subnuclear environ-ments at the nuclear periphery promote gene silencingand activation. Silenced regions of the genome, such ascentromeres and telomeres, are statically tethered to thenuclear envelope. Recent work in yeast has revealed thatcertain genes can undergo dynamic recruitment to theperiphery upon transcriptional activation. For such genes,localization to the periphery has been suggested toimprove mRNA export and favor optimal transcription.In addition, maintenance of peripheral localization con-fers cellular memory of previous transcriptional acti-vation, enabling cells to adapt rapidly to transcriptionalcues.

Localization at the nuclear periphery promotestranscriptional silencing and activationTheeukaryoticnucleushasdifferent compartments, suchasthenucleolus, nuclearenvelopeandnuclearpores, eachwithdistinct structures and functions. The nuclear pore providesa gateway to the nucleus, enabling exchange of proteins andmRNAwith the cytoplasm, whereas the nucleolus serves asthe site for ribosomal component assembly and synthesis[1,2]. Subnuclear compartments or domains have also beenimplicated in regulation of transcription. Although tran-scription is regulatedmainly throughDNA-bindingproteinsthat affect RNA polymerase recruitment or local chromatinstructure, there is also a functional relationship betweengene expression and nuclear organization. Chromosomesare nonrandomly arranged within the nucleus in diverseeukaryotic organisms, suggesting that subnuclear domainsmight have specialized roles in chromatin organization andtranscription. In many metazoan cells, chromosomes foldback onto themselves to create distinct subnuclear terri-tories [3]. Transcriptionally active genes frequently localizeat the edge of such territories, and it has been proposed thatthis localization enables better access to stable transcrip-tional ‘factories’ between territories [4]. The arrangement ofthese chromosome territories within the nucleus is uniformincellswithin the same tissueand canbe conservedbetweenspecies [5].

One of the best-characterized subnuclear domains is thenuclear periphery. Localization of parts of the genome tothe nuclear periphery has important effects on transcrip-tion. Constitutive heterochromatin localizes to the nuclearperiphery in many cell types [6,7], as do other silenced loci,

Corresponding author: Brickner, J.H. (j-brickner@northwestern.edu).Available online 12 June 2007.

www.sciencedirect.com 0168-9525/$ – see front matter � 2007 Elsevier Ltd. All rights reserve

such as the immunoglobulin genes in hematopoieticprogenitors of B lymphocytes [8]. Localization of repressedparts of the genome to the nuclear periphery has beenthoroughly explored in the budding yeast Saccharomycescerevisiae, in which regions of transcriptionally silent chro-matin, such as telomeres and the mating type loci, associ-ate with the nuclear envelope [9]. Proximity to the nuclearperiphery promotes efficient silencing of genes near telo-meres [9]. Conversely, artificially tethering mating-typeloci with crippled silencing elements to the nuclear envel-ope promotes silencing [10].

Recent work, however, indicates that transcriptionalactivation also takes place at the nuclear periphery inyeast. Several dynamically regulated genes are randomlydistributed in the nucleoplasm when repressed but arerecruited to the nuclear periphery when activated. Thesegenes include many highly expressed genes such as INO1(encoding an enzyme involved in phospholipid biosyn-thesis), HSP104 (a molecular chaperone), HXK1 (hexoki-nase), SUC2 (invertase), GAL1 (galactokinase), GAL2 (ahexose transporter), GAL10 (glucose epimerase) and mat-ing pheromone-induced genes [11–17]. The recruitmentof active genes to the nuclear periphery in yeast is remi-niscent of the observation made over 20 years ago byHutchison and Weintraub that in mouse fibroblastsDNase I-sensitive (andpresumably transcriptionallyactive)regionsof thegenomewere found localizedalong thenuclearrim [18]. This suggests that transcriptional activation at thenuclear periphery might not be a yeast-specific phenom-enon. Themouseb-globin locus is transcriptionally active atthe nuclear periphery before its relocalization toward thenuclear interior during erythroid maturation [19]. Thisindicates that localization at the nuclear periphery is notincompatible with transcription in mammalian cells. Also,the transcriptional upregulation of the X chromosome inmales inDrosophila requires nuclearpore componentsMtor

TREX: transcription and export complex, a complex involved in cotranscrip-

tional mRNA processing and transport, composed of the THO complex (Hpr1,

Tho2, Mft1 and Thp2) and the Yra1–Sub2 complex

d. doi:10.1016/j.tig.2007.05.009

Review TRENDS in Genetics Vol.23 No.8 397

(also called TPR) and Nup153 (see Glossary) and the Xchromosome localizes at the nuclear periphery [20].

In yeast, gene recruitment to the periphery changes thesubnuclear distribution of genes and reduces theirmobilityto a constrained, two-dimensional movement near thenuclear envelope [13,21]. Genome-wide chromatin immu-noprecipitation studies reveal that many transcriptionallyactive genes physically interact with components of thenuclear pore complex (NPC) and associated factors [14,15].Intriguingly, the nuclear pore component Nup2 is necess-ary and sufficient (when tethered toDNAdirectly) to createboundary elements that block the spread of heterochroma-tin [22–24]. Nup2 also interacts with transcriptionallyactive loci [15,25], suggesting that the protein might helpto shield these regions from neighboring silenced DNA (seebelow). The nuclear periphery could represent a subnuc-lear domain that is itself composed of distinct microenvir-onments with roles in either gene silencing or activation.This review focuses on the mechanism of gene recruitmentto the nuclear periphery in yeast. In addition, we highlightthe potential functional significance of localizing genes tothe nuclear periphery, particularly in promoting rapidtranscriptional activation of recruited genes and in estab-lishing novel epigenetic states.

The mechanism of gene recruitment to the nuclearperipheryThe nuclear pore complex

One of themost fascinating features of gene recruitment isthat cells dynamically control the localization of particularparts of the genome. The mechanism(s) by which this isachieved are not only interesting in themselves, but alsocould have more general implications for our understand-ing of how genomes are spatially organized. The nuclearpore complex (NPC)has been identified as the site towhichthese genes are recruited [15]. The NPC is a large assem-bly of �30 core nucleoporin proteins and numerous acces-sory proteins [26] that perforates the nuclear envelope andserves essential roles in nucleocytoplasmic trafficking[27]. As articulated by Blobel’s ‘gene-gating’ hypothesis,the processes of transcription and mRNA export might becoupled through interactions with the NPC [28]. Accord-ing to this model, nuclear pore complexes might interactwith expanded, transcriptionally active portions of thegenome, promoting optimal export of the transcriptthrough the pore to which it is gated [28]. The observationthat many genes are recruited to the nuclear peripheryupon activation and that they physically interact withthe NPC has inspired a re-evaluation of this appealinghypothesis.

The yeast nucleoporins Nup2 [15,25], Nup60, Nic96,Nup116 and the myosin-like proteins Mlp1 and Mlp2[14,15] physically interact with active genes. The NPChas three distinct parts: the cytoplasmic filaments, thecore channel and the nucleoplasmic basket [29,30]. Thecomponents of the nucleoplasmic basket interact withseveral proteins implicated in mRNA export – such asMlp1, Mlp2, Sac3, Thp1 and Mex67 [31] – and transcrip-tion – such as the Spt–Ada–Gcn5 histone acetyltransferase(SAGA) complex [32] (Figure 1). Loss of many of theseproteins blocks gene recruitment, suggesting a general

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requirement for the nucleoplasmic basket and associatedfactors in this phenomenon (Table 1).

Although there is general agreement that the nuclearbasket is important for gene recruitment, it is unclear if allbasket proteins are essential. Although Nup2, a com-ponent of the nuclear basket [33], promotes boundaryactivity and physically interacts with the promoter ofGAL1 under activating conditions [14,15,34], the role ofthe protein in recruitment of GAL1 and other genesremains controversial. We found that Nup2 is essentialfor recruitment of both GAL1 and INO1 to the nuclearperiphery [35], whereas Cabal et al. reported that GAL1recruitment takes place normally in a nup2-D mutantusing a similar assay [13]. Likewise, they found that thegene is recruited in cells lacking Nup60 [13], which tethersNup2 to the nuclear pore basket [36]. Similarly, the Stutzgroup found that the basket-associated protein Mlp1 isessential for recruitment of GAL10 and HSP104 [37]whereas Cabal et al. found it to be dispensable [13]. There-fore, although the nuclear pore basket is implicated inrecruitment of several genes to the periphery, it is uncer-tain whether there are basket substructures that aresufficient for gene recruitment.

Does transcription drive peripheral localization?

When it was discovered that certain genes are recruited tothe nuclear pore complex upon activation, it was unclearwhether localization at the nuclear periphery is an activetargeting process, coordinated with transcription andmRNA export, or simply an effect of coupling mRNA pro-duction with mRNA export through the NPC. Could achange in gene localization and physical association withthe pore arise from association of nascent transcripts withthe mRNA export machinery and NPC? Most genes thatundergo recruitment are highly expressed [38,39]. There-fore, it is conceivable that the mRNA export machineryforms a bridge between the nascent message and theNPC, leading to peripheral localization of genes. Consistentwith this possibility, the association of Mlp1 with phero-mone-induced genes is sensitive to RNase treatment [14].Similarly, recruitment of HXK1 and GAL1 to the nuclearperiphery requires their 30 untranslated regions (UTRs),which are involved in efficientmRNA export and processing[11,16]. Finally, loss of Sac3 (part of the Sac3–Thp1–Cdc31mRNA export complex [40]) or Mex67 (an mRNA exportreceptor) blocks recruitment of the GAL1–10 locus [13,37].These results suggested that the nascent transcript andmRNA export machinery mediate gene recruitment.

Alternatively, post-transcriptional mRNAmight regulatemaintenance of GAL1 at the nuclear envelope [11]. Hetero-logous mRNA expressed from a GAL1 promoter accumu-lates at foci near the nuclear periphery and this localizationis modulated by the GAL1 30-UTR [11]. The localization ofthesemRNA foci is distinct from the localizationof theDNA,indicating that they represent post-transcriptional forms ofthe transcript. Furthermore, the foci persist at the nuclearperipheryafter transcriptional shutoff [11]. Thus, post-tran-scriptional events might also affect tethering of recruitedgenes to the NPC.

In contrast to these results, other findings argue thatgene recruitment is independent of transcription. Using a

Figure 1. A model for gene recruitment at multiple stages of transcription. Gene recruitment has been shown to require factors involved in transcription and mRNA export

(shown as blue proteins; see text and Table 1 for references). However, several groups have found that transcription is not required. The model proposes that there are

different phases of recruitment that require different factors. (a) Initial recruitment occurs upstream of transcription and involves nuclear pore–promoter interactions, which

are regulated by transcription factors. This can occur either after the association of nucleoplasmic transcription factors or through the interaction of the promoter with NPC-

associated transcription factors, like the Nup84-bound Rap1–Gcr1–Gcr2 transcription machinery [44]. (b) Following recruitment, the NPC-associated SAGA histone

acetyltransferase is recruited to the promoter, linking the DNA to the periphery through interactions involving the Sus1 and Sac3–Thp1 proteins. (c) Alternatively, the mRNA

export receptor Mex67 can be recruited through an initial RNA-independent interaction with the TREX complex [63] and subsequently be transferred to the mRNA. Mex67

also directly interacts with components of the NPC. Steps proposed in (b) and (c) are not mutually exclusive and can be coordinated in the same pathway, as represented by

the hatched arrow. Pol II, RNA polymerase II.

398 Review TRENDS in Genetics Vol.23 No.8

temperature-sensitive mutant in the large subunit of RNApolymerase II (rpb1–1), Schmid et al. showed that thenuclear pore protein Nup2 interacts with the promoterof GAL1–10 in the absence of RNA polymerase II function[25]. They also showed that Nup2 interaction was inde-pendent of the SAGA complex, suggesting that Nup2interaction occurs before the preinitiation complex isformed [25]. Because Nup2 is rapidly exchanged betweenits nucleoplasmic and NPC-associated pools [33], the inter-action of Nup2 with the promoter of GAL1 might not be aperfect indicator of gene relocalization to the nuclear

Table 1. Summary of yeast genes recruited to the nuclear periphe

Gene Genomic region implicated in

relocalization to the nuclear periphery

Pr

nu

GAL1–10, GAL7 Promoter, 30-UTR M

S

GAL2 Promoter M

INO1 – N

HXK1 30-UTR –

HSP104 – M

SUC2 – NaMlp1 was shown to be required for recruitment of GAL genes by Ref. [37] but found tbNup2 was shown to be required for recruitment of GAL genes by Ref. [35] but foundcH2A.Z is only required for retention of INO1 at the periphery after transcriptional reprdG. Santangelo, personal communication.

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periphery. However, using a chromatin localization assayin the rpb1–1 mutant, we found that INO1 recruitment tothe nuclear periphery occurs normally after global inacti-vation of RNA polymerase II [35]. Also, association of themRNA export factor Mex67 with GAL10 is RNA-indepen-dent, indicating thatMex67might function in gene recruit-ment by interacting with chromatin through adaptorproteins such as Hpr1 [37,41]. Furthermore, NPC com-ponents such as Nup2 interact preferentially with the 50

ends of active genes, rather than 30 ends, as would beexpected for RNA-mediated tethering [25,28]. Finally,

ry

oteins required for relocalization to the

clear periphery

Refs

lp1a, Mex67, Nup1, Nup2b, Nup60, Ada2, Sac3,

us1, Gal4

[13,25,35,37]

lp1, Mex67 [37]

up2, H2A.Zc [35]

[16]

lp1, Mex67 [37]

up84 complexd [17]

o be dispensable by Ref. [13].

to be dispensable by Ref. [13].

ession. It is not essential for recruitment in the activated state of the gene [35].

Review TRENDS in Genetics Vol.23 No.8 399

recruitment of GAL1 [11] and GAL2 [37] requiressequences in the promoter but is independent of the codingsequence. Therefore, although gene recruitment mightfunction to couple transcription and mRNA export, thelocalization event itself is an active process that can beseparated from transcription.

It is worth pointing out that the gene-gating model doesnot demand that mRNA tethers genes to the NPC; proxi-mity of genes to the nuclear pore might improve nuclearexport regardless of the mechanism of localization. In thiscase, export and translation of mRNAs from genes with thesame basal transcription rate would be improved by proxi-mity to the pore. The recruited gene could therefore betethered physically through sequences in the promoter andthis tethering could still promote export of mRNA to thecytoplasm.

The SAGA complex

The SAGA (Spt–Ada–Gcn5 acetyltransferase) complex is atranscriptional coactivator that alters gene expression byacetylating histones in the promoters of target genes [42].Gcn5 is the catalytic subunit of this complex [42]. TheSAGA complex has been proposed to associate physicallywith the NPC through a bridging interaction involving theSac3 and Sus1 proteins [32], and several studies havesuggested a role for this complex in promoting gene recruit-ment to the nuclear periphery (Figure 1b; [13,43]). Cabalet al., using gene localization experiments, found thatmutants lacking the SAGA components Sus1 and Ada2were defective for GAL1 recruitment [13].

A recent study by Luthra et al. [43] described a linkbetween the SAGA complex and the NPC-associatedprotein Mlp1. Chromatin immunoprecipitation exper-iments demonstrate that Mlp1 interacts with active genesat the nuclear periphery [14,15]. Furthermore, mutantslacking Mlp1 fail to recruit GAL1 to the nuclear periphery[37]. Luthra et al. found that Mlp1 interacts directly withSAGA. Similar to Nup2 [25], bothMlp1 and SAGA interactwith the upstream activating sequence (UAS) elements inthe GAL1–10 promoter [43]. The interaction of Mlp1 withthe promoter requires the SAGA complex [43]. Intrigu-ingly, the interaction of Nup2 with the GAL UAS is inde-pendent of SAGA [25]. Therefore, Nup2 and Mlp1 interactwith the GAL locus by distinct mechanisms, perhapsrepresenting distinct stages of recruitment (Figure 1).Nup2 interactions with the GAL UAS might representan early event, preceding recruitment of the SAGA com-plex to the activated promoter. Because Nup2 dynamicallyexchanges between the nucleoplasm and the NPC [33], it isan attractive candidate for a shuttle protein that mediatesthe initial relocalization event. Mlp1 association mightrepresent a second stage in the process, downstream ofSAGA recruitment to the promoter and perhaps down-stream of transcription [14] (Figure 1c).

Functional significanceGene recruitment as a means of optimal expression

Why are active genes recruited to the nuclear periphery?When INO1 gene recruitment was initially discovered, weshowed that artificially tethering the gene to the nuclearenvelope bypassed the requirement for a transcription

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factor in its activation [12]. Subsequent work from ourlaboratory has shown that tethering results in more rapidactivation of INO1 [35]. Likewise, LexA fusions to nucleo-porins of the Nup84 subcomplex activate reporter genes,suggesting that localization at the NPC is sufficient toactivate transcription [17,44]. In addition, transcriptionof the HXK1 gene is enhanced by tethering to the nuclearperiphery [16]. Thus, localization at the nuclear peripherypromotes enhanced transcription.

Peripheral localization might promote transcription inseveral ways. Expression of genes could be enhancedthrough recruitment and proper assembly of the transcrip-tion initiationmachinery.Recruitment ofRap1–Gcr1–Gcr2-activatedgenes to theNup84subcomplexhas beenproposedto provide a platform for assembly of the transcriptionmachinery [44]. Intriguingly, Rap1-binding sites are enri-ched in thepromoters of genes that interactwith theNPCbychromatin immunoprecipitation [15]. Alternatively, chro-matin-remodeling events important for transcriptional acti-vation might be promoted by localization at the nuclearperiphery. This model is particularly intriguing in light of arequirement for theSAGAcomplex ingenerecruitment [13].SAGA is required for full transcriptional activation ofGAL1[45], INO1 [46] and SUC2 [47]. Thus, gene recruitmentmight directly or indirectly affect formation of the transcrip-tion preinitiation complex. Consistent with this possibility,upstream activating sequences control the interactions ofcertain genes with nuclear pore components [25]. Theseresults suggest that gene recruitment is coordinated withthe activation event and that localization at the peripherypromotes transcription initiation, but is not absolutelyrequired for transcription under steady-state conditions[13,37].

Despite coupling of transcription to peripheral localiza-tion, loss of Nup2, Mlp1 and SAGA components that arerequired for gene recruitment does not dramatically affectsteady-state transcriptional activity of GAL1 [13,43]. Sim-ilarly, GAL10 expression is not disrupted in mlp1D cells[37]. Therefore, although gene recruitment might enhancethe rate of transcriptional activation, it is not absolutelyrequired for transcriptional activation.

Gene localization as a source of transcriptional

memory

The INO1 and GAL1 genes are randomly localized whenrepressed and peripherally localized when activated.Analysis of the localization of INO1 andGAL1 upon shiftingfrom activating to repressing conditions, however, revealedan unexpected result. Although both genes are transcrip-tionally repressedwithinminutes, they linger at thenuclearperiphery for hours after repression [35]. Localization at thenuclear periphery is a heritable trait; after shifting fromactivating conditions, cells maintain INO1 andGAL1 at thenuclear periphery through multiple cell divisions [35]. Per-ipheral localization therefore represents a novel epigeneticstate. This suggests a stable and active mechanism forretention of these genes at the nuclear periphery, even inthe absence of ongoing transcription.

The maintenance of genes at the nuclear peripheryafter repression suggests that repressed INO1 and GAL1are present in two states: a long-term repressed form

Figure 2. Chromatin-mediated transcriptional memory at the nuclear periphery. In

their long-term repressed state, certain genes localize randomly within the

nucleoplasm. Upon activation, relocalization to the nuclear periphery is mediated

through interactions with the nuclear pore complex (NPC) and associated

components. Following repression, incorporation of histone variant H2A.Z

(red nucleosomes) marks these genes, leading to their retention at the nuclear

periphery and promoting rapid reactivation. Adapted with permission from Ref. [35].

400 Review TRENDS in Genetics Vol.23 No.8

distributed randomly in the nucleoplasm and a recentlyrepressed form localized at the nuclear periphery(Figure 2). This suggests that localizationmight enable cellsto distinguish recently repressed genes from long-termrepressed genes. This difference represents a form of cellu-lar memory of recent transcription. This memory is adap-tive; recently repressed GAL1 is activated much morerapidly than the long-term repressed form, even after manygenerations of repression [35]. Furthermore, reactivation ofINO1 is delayed in a mutant lacking the Nup2 protein [35].Considering that artificial tethering of INO1 causes morerapid activation, these results suggest that localization ofgenes at the periphery promotes more rapid activation orreactivation. This form of transcriptional memory requiresthe histone variant H2A.Z, which is frequently found innucleosomes in the promoters of repressed genes and hasbeen proposed to promote rapid activation [48–51].Mutantslacking H2A.Z fail to retain INO1 and GAL1 at the nuclearperiphery after repression and show a dramatic defect inreactivation of these genes [35]. Importantly, this effect isspecific to thememory state.Mutants lackingH2A.Z recruitINO1 and GAL1 normally under activating conditions andhave no defect in activation of long-term repressed forms ofthese genes [35].

Three important conclusions of this study are: (i) therepressed forms of certain genes assume two differentdistributions, enabling cells to ‘mark’ previously transcribedgenes; (ii) transcriptional memory is an epigenetic phenom-enon, being inherited for 3–4 generations for INO1 and>65generations for GAL1; and (iii) memory is adaptive, enhan-cing the rateof reactivationof INO1andGAL1. In the case oftheGAL1 gene, reactivation rate ismuchmore rapid follow-ing repression for 12 h than in long-term repressed cells.After12 h, cellshaveundergone6–7doublingsand thusonly�1% of the cells have ever directly experienced growth ingalactose. Therefore, this phenomenon is a type of adaptive

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learning that canaffect the responsiveness of a population ofcells to changes in growth conditions for many generations.

Recent work in Drosophila has shown that anotherhistone variant, H3.3, can also serve as a marker of tran-scriptionally active regions of the genome [52]. This varianthistone differs from histone H3 at four amino acids [52].Unlike histone H3, histone H3.3 is incorporated into chro-matin through a replication-independent mechanism, per-haps coupled to transcription [52]. Genome-wide chromatinimmunoprecipitation has revealed two sites of enrichmentof incorporation of H3.3: transcriptionally active genes andregulatory elements [53,54]. H3.3 is enriched in the dosage-compensated male X chromosome, which localizes to thenuclear periphery [20,53]. The incorporation of H3.3 intothese regions seems to be the result of a greater turnover ofthese nucleosomes and the replacement of H3 with H3.3[54]. Therefore, the incorporation of H3.3, like H2A.Z, couldserve to mark active or poised parts of the genome. Thesemarkscouldbe faithfully replicatedduringDNAreplication,enabling their epigenetic inheritance.

Concluding remarks and future directionsRecruitment of activated genes to the nuclear periphery inyeast is a new and exciting example of the relationshipbetween subnuclear localization and transcriptionalstate. Although dynamic recruitment of activated genesto the nuclear periphery has not been described in otherorganisms, the conventional role of the periphery as asilencing environment needs revision. Examples frommice and Drosophila indicate that localization at theperiphery is compatible with transcriptional activation[19,20,55]. Localization of genes at the nuclear pore mightalso have important medical relevance; several forms ofacute myeloid leukemia result from the fusion of DNA-binding domains to nuclear pore proteins, presumablyleading to relocalization of target genes to the nuclearperiphery and altered gene expression [56,57]. A funda-mental understanding of how subnuclear positioningaffects normal regulation is essential to understandingsuch disease states.

In their activated state, certain genes relocalize to thenuclear periphery by a rapid, active process that is inde-pendent of transcription. At the periphery, these genesinteract with components of the nuclear pore and SAGAcomplex. Robust transcription occurs after these genes loca-lize to the periphery [35], and artificially localizing genes tothe periphery promotes stronger transcription [16,35].Thus, recruitment might provide an optimal environmentfor expression and mRNA export. Localization is main-tained longafter transcriptional repression, promotingreac-tivation by a memory mechanism that requires the histonevariant H2A.Z. Adaptive memory might enable genes tobypass rate-limiting steps in their activation, leading tomore rapid reactivation when exposed to activating con-ditions once again.

Recent studies have provided valuable insights into themechanism and functional significance of gene recruit-ment. There are still many missing pieces to the puzzle.To date, nuclear pore, mRNA export and SAGA complexcomponents have been shown to have a role in gene relo-calization. However, because the histone variant H2A.Z is

Box 1. Important future questions about adaptive

transcriptional memory

� What controls H2A.Z incorporation in the recently repressed

promoter?

� How does this incorporation promote faster transcriptional

reactivation of genes that have been active in the recent past?

� What is the mechanism of H2A.Z-dependent targeting of recently

repressed genes to the nuclear periphery?

� How widespread and conserved is the phenomenon of adaptive

transcriptional memory? What determines the duration of mem-

ory?

� Do all loci at which H2A.Z is found localize to the nuclear

periphery?

Review TRENDS in Genetics Vol.23 No.8 401

required to maintain genes at the nuclear periphery, it isclear that nonperipheral proteins can also be involved.The mechanism of gene recruitment depends on bothperipheral proteins that target genes to the NPC andcis-acting DNA elements in the vicinity of recruited genes.GAL1 reporter constructs exhibited similar relocalizationbehavior when placed at a nonendogenous locus [11]. Thesereporters contained only the GAL promoter and 30-UTRencompassing a green fluorescent protein open readingframe, indicating that the GAL1 ORF and neighboringsequences are dispensable for recruitment to the nuclearperiphery [11]. Studying the role of promoters and30-UTRs in recruitment of genes to the nuclear peripherywill reveal whether their role is based onmRNA export andprocessing or in recruitment of proteins involved in genelocalization.

It is possible that microenvironments at the nuclearperiphery are exploited by gene recruitment to the NPC.It remains unclear if recruitment occurs to any of thenuclear pores within the nuclear envelope, or to particularnuclear pores. In other words, can a gene be recruited toany nuclear pore or do constraints on mobility imposed bythe position of a gene within the chromosome define whichnuclear pores it can visit? Along these lines, are all NPCsequal or is there some specialization of function amongthe pores in a nucleus? Several results hint that not allNPCs are identical and that genes are recruited to asubset of pores. The myosin-like proteins Mlp1 andMlp2, which have a role in gene recruitment [14,15,37,43], localize in a crescent-shaped distribution at thenuclear periphery, colocalizing only with those nuclearpores on the side of the nucleus opposite the nucleolus[58,59]. Therefore, only a subset of NPCs are associatedwith Mlp1 and Mlp2. Intriguingly, the mating phero-mone-induced gene FIG2 is recruited to the nuclear per-iphery in a polarized manner [14], localizing to a regionclose to the spindle pole body [60–62]. Therefore, acti-vated genes might be recruited to distinct locations at thenuclear periphery, defined by the subset of pores to whichthe genes have access.

The discovery that H2A.Z has a key role in maintainingperipheral localization of genes, and hence their fasterreactivation after a short period of repression, raises sev-eral fascinating questions (Box 1). The answers to thesequestions will provide crucial insights into how the local-ization and history of a locus have long-lasting effects on itstranscriptional regulation.

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AcknowledgementsWe thank Rick Gaber and Eric Weiss, in addition to members of theBrickner laboratory, for helpful comments on the manuscript. We alsothank George Santangelo for communicating unpublished results.

References1 Olson, M.O. et al. (2002) Conventional and nonconventional roles of the

nucleolus. Int. Rev. Cytol. 219, 199–2662 Fatica, A. and Tollervey, D. (2002) Making ribosomes. Curr. Opin. Cell

Biol. 14, 313–3183 Zink, D. et al. (1998) Structure and dynamics of human interphase

chromosome territories in vivo. Hum. Genet. 102, 241–2514 Branco, M.R. and Pombo, A. (2006) Intermingling of chromosome

territories in interphase suggests role in translocations andtranscription-dependent associations. PLoS Biol. 4, e138

5 Cremer, T. and Cremer, C. (2001) Chromosome territories, nucleararchitecture and gene regulation in mammalian cells. Nat. Rev. Genet.2, 292–301

6 Comings, D.E. (1980) Arrangement of chromatin in the nucleus. Hum.Genet. 53, 131–143

7 Haaf, T. and Schmid, M. (1991) Chromosome topology in mammalianinterphase nuclei. Exp. Cell Res. 192, 325–332

8 Kosak, S.T. et al. (2002) Subnuclear compartmentalization ofimmunoglobulin loci during lymphocyte development. Science 296,158–162

9 Cockell, M. and Gasser, S.M. (1999) Nuclear compartments and generegulation. Curr. Opin. Genet. Dev. 9, 199–205

10 Andrulis, E.D. et al. (1998) Perinuclear localization of chromatinfacilitates transcriptional silencing. Nature 394, 592–595

11 Abruzzi, K.C. et al. (2006) 30-end formation signals modulate theassociation of genes with the nuclear periphery as well as mRNPdot formation. EMBO J. 25, 4253–4262

12 Brickner, J.H. et al. (2004) Gene recruitment of the activated INO1locus to the nuclear membrane. PLoS Biol. 2, e342

13 Cabal, G.G. et al. (2006) SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelope. Nature 441,770–773

14 Casolari, J.M. et al. (2005) Developmentally induced changes intranscriptional program alter spatial organization across chrom-osomes. Genes Dev. 19, 1188–1198

15 Casolari, J.M. et al. (2004) Genome-wide localization of the nucleartransport machinery couples transcriptional status and nuclearorganization. Cell 117, 427–439

16 Taddei, A. et al. (2006) Nuclear pore association confers optimalexpression levels for an inducible yeast gene. Nature 441, 774–778

17 Sarma, N.J. et al. (2007) Glucose-responsive regulators of geneexpression in Saccharomyces cerevisiae function at the nuclearperiphery via a reverse recruitment mechanism. Genetics 175, 1127–1135

18 Hutchison, N. and Weintraub, H. (1985) Localization of DNAaseI-sensitive sequences to specific regions of interphase nuclei. Cell 43,471–482

19 Ragoczy, T. et al. (2006) The locus control region is requiredfor association of the murine beta-globin locus with engagedtranscription factories during erythroid maturation. Genes Dev. 20,1447–1457

20 Mendjan, S. et al. (2006) Nuclear pore components are involved in thetranscriptional regulation of dosage compensation in Drosophila. Mol.Cell 21, 811–823

21 Taddei, A. et al. (2005) Multiple pathways tether telomeres and silentchromatin at the nuclear periphery: functional implications for sir-mediated repression. Novartis Found. Symp. 264, 140–156, discussion156–165, 227–130

22 Ishii, K. et al. (2002) Chromatin boundaries in budding yeast: thenuclear pore connection. Cell 109, 551–562

23 Dilworth, D.J. et al. (2005) The mobile nucleoporin Nup2p andchromatin-bound Prp20p function in endogenous NPC-mediatedtranscriptional control. J. Cell Biol. 171, 955–965

24 Burgess-Beusse, B. et al. (2002) The insulation of genes from externalenhancers and silencing chromatin. Proc. Natl. Acad. Sci. U. S. A. 99(Suppl. 4), 16433–16437

25 Schmid, M. et al. (2006) Nup-PI: the nucleopore-promoter interaction ofgenes in yeast. Mol. Cell 21, 379–391

402 Review TRENDS in Genetics Vol.23 No.8

26 Rout, M.P. and Aitchison, J.D. (2001) The nuclear pore complex as atransport machine. J. Biol. Chem. 276, 16593–16596

27 Lim, R.Y. and Fahrenkrog, B. (2006) The nuclear pore complex upclose. Curr. Opin. Cell Biol. 18, 342–347

28 Blobel,G. (1985)Genegating: ahypothesis.Proc.Natl. Acad. Sci.U.S.A.82, 8527–8529

29 Suntharalingam, M. and Wente, S.R. (2003) Peering through the pore:nuclear pore complex structure, assembly, and function. Dev. Cell 4,775–789

30 Tran, E.J. andWente, S.R. (2006) Dynamic nuclear pore complexes: lifeon the edge. Cell 125, 1041–1053

31 Fischer, T. et al. (2002) ThemRNA exportmachinery requires the novelSac3p-Thp1p complex to dock at the nucleoplasmic entrance of thenuclear pores. EMBO J. 21, 5843–5852

32 Rodriguez-Navarro, S. et al. (2004) Sus1, a functional component of theSAGA histone acetylase complex and the nuclear pore-associatedmRNA export machinery. Cell 116, 75–86

33 Dilworth, D.J. et al. (2001) Nup2p dynamically associates with thedistal regions of the yeast nuclear pore complex. J. Cell Biol. 153, 1465–1478

34 Schmid, M. et al. (2004) ChIC and ChEC; genomic mapping ofchromatin proteins. Mol. Cell 16, 147–157

35 Brickner, D.G. et al. (2007) H2A.Z-mediated localization of genesat the nuclear periphery confers epigenetic memory of previoustranscriptional state. PLoS Biol. 5, e81

36 Denning, D. et al. (2001) The nucleoporinNup60p functions as aGsp1p-GTP-sensitive tether for Nup2p at the nuclear pore complex. J. CellBiol. 154, 937–950

37 Dieppois, G. et al. (2006) Cotranscriptional recruitment to the mRNAexport receptor Mex67p contributes to nuclear pore anchoring ofactivated genes. Mol. Cell. Biol. 26, 7858–7870

38 Hirsch, J.P. and Henry, S.A. (1986) Expression of the Saccharomycescerevisiae inositol-1-phosphate synthase (INO1) gene is regulated byfactors that affect phospholipid synthesis.Mol. Cell. Biol. 6, 3320–3328

39 St John, T.P. and Davis, R.W. (1981) The organization andtranscription of the galactose gene cluster of Saccharomyces. J. Mol.Biol. 152, 285–315

40 Fischer, T. et al. (2004) Yeast centrin Cdc31 is linked to the nuclearmRNA export machinery. Nat. Cell Biol. 6, 840–848

41 Gwizdek, C. et al. (2006) Ubiquitin-associated domain of Mex67synchronizes recruitment of the mRNA export machinery withtranscription. Proc. Natl. Acad. Sci. U. S. A. 103, 16376–16381

42 Grant, P.A. et al. (1997) Yeast Gcn5 functions in two multisubunitcomplexes to acetylate nucleosomal histones: characterization of anAda complex and the SAGA (Spt/Ada) complex. Genes Dev. 11, 1640–1650

43 Luthra, R. et al. (2006) Actively transcribed GAL genes can bephysically linked to the nuclear pore by the SAGA chromatinmodifying complex. J. Biol. Chem. 282, 3042–3049

44 Menon, B.B. et al. (2005) Reverse recruitment: the Nup84 nuclear poresubcomplex mediates Rap1/Gcr1/Gcr2 transcriptional activation. Proc.Natl. Acad. Sci. U. S. A. 102, 5749–5754

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45 Larschan, E. and Winston, F. (2005) The Saccharomyces cerevisiaeSrb8-Srb11 complex functions with the SAGA complex duringGal4-activated transcription. Mol. Cell. Biol. 25, 114–123

46 Lo, W.S. et al. (2001) Snf1 – a histone kinase that works in concert withthe histone acetyltransferase Gcn5 to regulate transcription. Science293, 1142–1146

47 Roberts, S.M. and Winston, F. (1997) Essential functional interactionsof SAGA, a Saccharomyces cerevisiae complex of Spt, Ada, and Gcn5proteins, with the Snf/Swi and Srb/mediator complexes. Genetics 147,451–465

48 Guillemette, B. et al. (2005) Variant histone H2A.Z is globally localizedto the promoters of inactive yeast genes and regulates nucleosomepositioning. PLoS Biol. 3, e384

49 Li, B. et al. (2005) Preferential occupancy of histone variant H2AZat inactive promoters influences local histone modifications andchromatin remodeling.Proc. Natl. Acad. Sci. U. S. A. 102, 18385–18390

50 Raisner, R.M. et al. (2005) Histone variant H2A.Z marks the 50 ends ofboth active and inactive genes in euchromatin. Cell 123, 233–248

51 Zhang, H. et al. (2005) Genome-wide dynamics of Htz1, a histone H2Avariant that poises repressed/basal promoters for activation throughhistone loss. Cell 123, 219–231

52 Ahmad, K. and Henikoff, S. (2002) The histone variant H3.3 marksactive chromatin by replication-independent nucleosome assembly.Mol. Cell 9, 1191–1200

53 Mito, Y. et al. (2005) Genome-scale profiling of histone H3.3replacement patterns. Nat. Genet. 37, 1090–1097

54 Mito, Y. et al. (2007) Histone replacement marks the boundaries ofcis-regulatory domains. Science 315, 1408–1411

55 Buscaino, A. et al. (2006) X-chromosome targeting and dosagecompensation are mediated by distinct domains in MSL-3. EMBORep. 7, 531–538

56 Nakamura, T. et al. (1996) Fusion of the nucleoporin gene NUP98 toHOXA9 by the chromosome translocation t(7;11)(p15;p15) in humanmyeloid leukaemia. Nat. Genet. 12, 154–158

57 Lawrence, H.J. et al. (1999) Frequent co-expression of the HOXA9 andMEIS1 homeobox genes in human myeloid leukemias. Leukemia 13,1993–1999

58 Galy, V. et al. (2004) Nuclear retention of unspliced mRNAs in yeast ismediated by perinuclear Mlp1. Cell 116, 63–73

59 Strambio-de-Castillia, C. et al. (1999) Proteins connecting the nuclearpore complex with the nuclear interior. J. Cell Biol. 144, 839–855

60 Baba, M. et al. (1989) Three-dimensional analysis of morphogenesisinduced by mating pheromone alpha factor in Saccharomycescerevisiae. J. Cell Sci. 94, 207–216

61 Yang, C.H. et al. (1989) Higher order structure is present in the yeastnucleus: autoantibody probes demonstrate that the nucleolus liesopposite the spindle pole body. Chromosoma 98, 123–128

62 Snyder, M. et al. (1991) Studies concerning the temporal and geneticcontrol of cell polarity in Saccharomyces cerevisiae. J. Cell Biol. 114,515–532

63 Strasser, K. et al. (2002) TREX is a conserved complex couplingtranscription with messenger RNA export. Nature 417, 304–308

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