(2.5.16)--ATP-DependentChromatinRemodeling.pdf
Int.J.Mol.Sci.2011,12,6544-6565;doi:10.3390/ijms12106544 International Journal of Molecular Sciences ISSN 1422-0067 Review ATP-Dependent Chromatin Remodeling Factors and Their Roles in Affecting Nucleosome Fiber Composition Paolo Piatti,Anette Zeilner and Alexandra Lusser*Division of Molecular Biology,Innsbruck Medical University,Biocenter,Fritz-Pregl Strasse 3,6020 Innsbruck,Austria;E-Mails:paolo.piattii-med.ac.at(P.P.);anette.zeilneri-med.ac.at(A.Z.)*Author to whom correspondence should be addressed;E-Mail:alexandra.lusseri-med.ac.at;Tel.:+43-512-9003-70210;Fax:+43-512-9003-73100.Received:22 July 2011;in revised form:20 September 2011/Accepted:28 September 2011/Published:6 October 2011 Abstract:ATP-dependent chromatin remodeling factors of the SNF2 family are key components of the cellular machineries that shape and regulate chromatin structure and function.Members of this group of proteins have broad and heterogeneous functions ranging from controlling gene activity,facilitating DNA damage repair,promoting homologous recombination to maintaining genomic stability.Several chromatin remodeling factors are critical components of nucleosome assembly processes,and recent reports have identified specific functions of distinct chromatin remodeling factors in the assembly of variant histones into chromatin.In this review we will discuss the specific roles of ATP-dependent chromatin remodeling factors in determining nucleosome composition and,thus,chromatin fiber properties.Keywords:chromatin;histone variant;chromatin remodeling factor;centromere;linker histone;chromatin assembly 1.Introduction Chromatin is an extremely complex structure that serves to compact eukaryotic DNA in order to comply with the size restrictions of the nucleus.In addition,the way in which chromatin is organized and in which its arrangement is modulated endows it with an extraordinary regulatory potential.At its most basic level of organization,chromatin consists of repeating spherical particles termed OPEN ACCESS Int.J.Mol.Sci.2011,12 6545 nucleosomes.Nucleosomes are formed by the wrapping of 147 bp of DNA in 1.7 left-handed superhelical turns around a core of small,evolutionary conserved,highly basic histone proteins 1.Two molecules each of the histones H3 and H4 interact via the so-called“histone-fold”domains to generate a protein tetramer,which associates with two heterodimers of the histones H2A and H2B to form the nucleosome core 1.Nucleosomes are connected by short stretches of linker DNA resulting in a fiber with a diameter of 10 nm that has a beads-on-a-string-like appearance 2,3.Although this structure may seem uniform from a superficial perspective,a tremendous amount of research during the past decades has provided ample evidence that nucleosomes can differ from each other with respect to their structure,the type of histones that they contain as well as the nature and extent of chemical modifications on both the DNA and histones.In addition,the positioning of the nucleosomes along the DNA can show striking variation,including regular arrangements with constant spacing (e.g.,in constitutive heterochromatin),irregular arrays of nucleosomes(typically in active genes)or regions that are devoid or depleted of nucleosomes(e.g.,at enhancers and promoters)4,5.Importantly,chromatin structure is not static.On the contrary,the organization and composition of chromatin is constantly changing thereby facilitating or preventing access for DNA-utilizing proteins to their substrate.In this review we will discuss some of the mechanisms that contribute to the shaping of chromatin structure not only at the level of the 10 nm fiber but also in higher-order levels of chromatin organization.We will give special attention to the ATP-dependent chromatin remodeling machines and their diverse roles in modulating the composition of nucleosomes and chromatin fibers.2.Chromatin Remodeling Machines and Their Impact on Nucleosome Structure Chromatin organization is regulated on various levels and by a multitude of diverse proteins and non-coding RNAs.On one hand,enzyme complexes that use DNA for transcription,replication,recombination or repair actively contribute to changing chromatin structure.For instance,RNA and DNA polymerases travel along the DNA double helix and by doing so introduce torsional stress that can promote the loss of histones ahead of them and facilitate the reassembly of nucleosomes in their wake 6.Although most of this stress is constantly released by the action of topoisomerases,it is likely that DNA-utilizing processes exert distinct effects on local as well as regional chromatin structure.Other mechanisms that profoundly affect chromatin structure are posttranslational modifications of nucleosomal histones,the incorporation of so-called variant histone proteins and of other non-histone architectural proteins,such as high mobility group(HMG)proteins,as well as the energy-consuming remodeling of nucleosomes by ATP-dependent remodeling machines 710.ATP-dependent chromatin remodeling factors typically are large protein complexes that contain an ATPase subunit,which belongs to the sucrose non-fermenting 2(SNF2)family of ATPases/helicases 11,12.SNF2-like ATPases can be grouped into 23 subclasses according to sequence differences in their ATPase domains and the presence of additional protein motifs 11.The best-studied chromatin remodeling factors belong to the SWI/SNF(switch/sucrose non-fermenting),the ISWI(imitation switch),the CHD(chromo helicase DNA binding)and the INO80(inositol auxotroph 80)subfamilies 10,1317.Int.J.Mol.Sci.2011,12 6546 2.1.The Role of ATP-Dependent Chromatin Remodeling Factors in Nucleosome Positioning Several recent studies that mapped the positions of nucleosomes at a genome-wide level in different organisms and cell types have reported the existence of rather well conserved patterns of nucleosome occupancy in particular at the 5 and 3 ends of genes(e.g.,1822).Using micrococcal digestion combined with deep-sequencing technology,it was shown for yeast,Drosophila and humans that promoters are commonly marked by a nucleosome-free or depleted region(NDR)upstream of the transcriptional start site(TSS).Furthermore,the first nucleosome downstream of the TSS (+1 nucleosome)usually occupies a distinct position,which is 50 bp downstream of the TSS in yeast and at +135 bp in Drosophila and humans 4,5.Another NDR appears to be distinctive of 3-ends of genes.Upstream of this NDR a positioned nucleosome is usually detected although the latter appears not to be universally conserved 4,5,23.Although DNA sequence is likely to influence some of the nucleosome positions,in particular the NDRs,it was postulated that ATP-dependent chromatin remodeling machines play an important role in determining nucleosome positions in vivo 4,5,24.This is especially likely for nucleosomes that occupy energetically unfavorable positions.Chromatin remodeling enzymes are well equipped to carry out this task.In many elegant in vitro studies,it has been demonstrated that by using the energy derived from hydrolyzing ATP,these enzymes can break and/or establish histone-DNA contacts.The results of these actions are manifold and dependent on the type of remodeler as well as on the functional context 10,2527.Numerous studies exploring the effects of deletion or knock-down of chromatin remodelers have found wide-spread gene regulation defects 28.These effects can at least in part be attributed to a role of these factors in positioning and remodeling of nucleosomes.Two SNF2 subfamilies in particular,the ISWI and the CHD families,have been shown to be able to move nucleosomes to different translational positions along the DNA(“sliding”)2934.Consistent with this function,ISWI and CHD type enzymes have been shown to be associated with active genes 3538.They have roles in remodeling nucleosomes in the vicinity of the TSS 3740,but they seem also involved in regulating nucleosome positioning at the 3-end of genes.In yeast it was observed that loss of Isw2 resulted in increased production of non-coding transcripts.These transcripts originated from mis-oriented transcription as a result of aberrant nucleosome positioning at the 3-end of Isw2 target genes 37.Likewise,yeast Chd1 was shown to be involved in organizing the nucleosomal fiber at the 3-end of genes,since deletion of CHD1 resulted in transcription termination defects and aberrant nucleosomal arrangements at the 3-ends of the CYC1 and ASC1 genes 41.Very recently,the Mi-2/CHD3-related ATPase Mit1(Mi2-like protein interacting with Clr three 1),which is part of the SHREC(Snf2/Hdac-containing Repressor Complex)complex in Schizosaccharomyces pombewas shown to profoundly affect nucleosome positioning globally and at specific heterochromatic sites 23,42.Chromatin remodeling complexes of the SWI/SNF family have also been extensively characterized in vitro and in vivo.One salient feature of this type of remodeler is its ability to disrupt nucleosome structure more profoundly than ISWI and CHD enzymes(e.g.,4346).SWI/SNF enzymes can eject histones from nucleosomes,they can transfer dimers and tetramers to other DNA molecules (e.g.,43,4749)and they can catalyze nucleosome sliding reactions 10,50.Thus,in vivo SWI/SNF ATPases have been identified as crucial regulators of gene activation,and they have been shown to be able to generate NDRs 51.Int.J.Mol.Sci.2011,12 6547 Almost all SNF2-type motors are part of(large)protein complexes.The accessory subunits can gravely impact on the biochemical properties of a remodeler complex.For instance,association of the ISWI motor protein with the ATP-dependent chromatin assembly factor 1(Acf1)subunit,strongly stimulates the efficiency by which it can assemble and remodel nucleosomes 52.In a similar manner the chromatin remodeling activity of the SWI/SNF ATPases BRG1(brahma related gene 1)and hBRM(human brahma)are significantly enhanced by the INI1(integrase interactor 1)and the brahma-associated factors BAF155 and BAF170 complex subunits 53.Nevertheless,a recent study demonstrated that the ATPases themselves exhibit strikingly different characteristics with respect to their nucleosome sliding properties.When Drosophila ISWI and CHD1 as well as human Snf2H,Brg1 and Mi-2(dermatomyositis specific autoantigen Mi-2)were tested side by side in an in vitro sliding assay,each remodeler moved the nucleosome to different positions although the underlying DNA sequence was the same in all cases 34.Hence,it is conceivable that in vivo different chromatin remodeling factors may establish specific local nucleosome positions in addition to histone displacement.The action of these enzymes,therefore,will not only facilitate but also impede the access of factors to their binding sites on the DNA.2.2.Chromatin Remodeling Factorsin Replication-Coupled Nucleosome Assembly During S-phase,when the DNA is replicated,chromatin is completely disassembled and nucleosomes are reformed at the nascent daughter strands.Thereby,newly synthesized histones must be incorporated to complement the“old”histones that are reused in the newly established nucleosomes 54,55.ATP-dependent factors are likely to adopt a critical position within the DNA replication process.They are known to not only slide and restructure existing nucleosomes but also to mediate the formation of new nucleosomes or change the histone composition of nucleosomes 8,56.ISWI-containing remodeling complexes,such as ACF(ATP-dependent chromatin assembly and remodeling factor)and RSF(remodeling and spacing factor),and CHD1 have been demonstrated to be able to generate nucleosome arrays in vitro from purified histones and DNA.ACF and CHD1 perform this reaction in conjunction with the histone chaperone NAP-1(nucleosome assembly protein 1),while RSF does not require a chaperone 52,5760.Despite the well-characterized biochemical activities of chromatin remodeling factors it is rather surprising that information about their involvement in replication-coupled chromatin assembly in vivo is still limited.To date,only ISWI-type enzymes have been linked to nucleosome formation during S-phase.In Drosophila the inactivation of the ACF complex by deletion of its Acf1 subunit resulted in an acceleration of S-phase caused by a shortening of heterochromatin replication timing 61.Similarly,the human ISWI homolog SNF2h was proposed to play a role in replication-coupled heterochromatin assembly 6264.In this case,two different SNF2h-containing complexes appear to be important,since knock-down of the ACF1 subunit of the human ACF complex inhibited progression through S-phase 63,while a complex containing Snf2h and the Williams syndrome transcription factor(WSTF)targeted SNF2h to heterochromatin by interaction with proliferating cell nuclear antigen(PCNA),which is a processivity factor of DNA polymerase 62,64.Thus,ISWI enzymes appear to be involved in replication-coupled heterochromatin assembly.However,in light of more recent studies implicating ISWI in the incorporation of the linker histone H1(see below),the Int.J.Mol.Sci.2011,12 6548 above-mentioned observations might not fully support this conclusion.A recent report identified the mammalian SNF2-type ATPase SMARCAD1 as an important regulator of global DNA replication-associated histone deacetylation.As a consequence of SMARCAD1 knock-down,heterochromatin establishment,in particular histone H3 lysine 9 trimethylation and HP1 binding was perturbed 65.Thus,while SMARCAD1 appears to play a crucial role in thedeacetylation of newly incorporated histones,which are acetylated,it seems not to be directly involved in histone deposition.Therefore,to date no chromatin remodeler has been unequivocally demonstrated to mediate the reassembly of either heterochromatin or euchromatin in the course of DNA replication in vivo.2.3.Incorporation of Linker Histone H1 The linker histone H1 associates with DNA at nucleosome entry/exit sites and thereby affects the folding of the 10 nm nucleosomal fiber into higher-order structures with a diameter of about 30 nm 66,67.It is assumed that the 30 nm fiber makes chromatin less accessible to DNA binding factors and is thus largely refractory for processes such as transcription.Although several recent studies have made considerable progress in elucidating the structure of in vitro reconstituted 30 nm fibers 6871,their in vivo organization appears to be heterogeneous and is still poorly understood 72,73.This may be due in part to the highly dynamic behavior of H1 in vivo.While the core histones H3 and H4 typically remain bound to the chromatin over several cell generations,H1 turn-over occurs within seconds 7477.Several lines of evidence point to a critical role for ATP-dependent chromatin remodelers in H1 assembly.First,it was shown that in vitro ACF and ISWI but not the CHD-type factor CHD1 can generate periodic H1-containing nucleosome arrays 58,78,79.Second,in Drosophila,deletion of ISWI resulted in global decond
