Chromosomal biology involves a dynamic balance between genome packaging and genome access. Chromosomes must actively balance two opposing needs: the need to condense and organize (topologically) nearly 2 m of DNA—against the need for access to the genome by the factors that conduct transcription, replication, recombination, repair, and other chromosomal processes. The proteins involved in DNA packaging and condensation (as well as those that reverse these processes) are termed chromatin, and the most abundant constituents are histone proteins, which come together to form nucleosomes. The majority of chromatin assembly occurs during DNA replication, in coordination with the DNA replisome. This process involves histone delivery to nascent DNA, and also the action of chromatin Remodelers—which ensure proper density and spacing of nucleosomes after replication. Access to the DNA within chromatin involves the cooperative action of DNA sequence, site-specific transcription factors, histone modification enzymes, and a set of chromatin remodeling complexes. Chromatin remodeling complexes are a set of complexes with central and specialized roles in either the assembly of chromatin, the access of factors to chromatin, or the restructuring of nucleosomes.
The wrapping of DNA into nucleosomes contributes to transcriptional repression, as nucleosomes inhibit the binding of transcription factors and the progress of RNA polymerases. Therefore, transcriptional activation often requires the repositioning or ejection of repressive nucleosomes. These activities are performed by large multiprotein complexes termed remodelers, which are grouped into five classes.
To enable dynamic access to packaged DNA and to tailor nucleosome composition in chromosomal regions, cells have a set of specialized chromatin remodeling complexes (remodelers). Remodelers use the energy of ATP hydrolysis to move, destabilize, eject, or restructure nucleosomes 23
Why Do Cells Need Remodelers?
Specialized remodelers help to provide following solutions:
(a) The different outcomes of chromatin remodeling. Remodelers ( green) can assist in chromatin assembly by moving already deposited histone octamers, generating room for additional deposition .
(b) Remodeler action on a nucleosome array results in various products that can be classified in two categories:
(c) site exposure, in which a site (red ) for a DNA-binding protein (DBP), initially occluded by the histone octamer, becomes accessible by nucleosomal sliding (repositioning), or nucleosomal eviction (ejection), or localized unwrapping, and altered composition, in which the nucleosome content is modified by dimer replacement [exchange of H2A-H2B dimer with an alternative dimer containing a histone variant (blue)] or through dimer ejection.
- Following replication, nucleosomes must be deposited and properly spaced genome-wide. Specialized remodelers are utilized to correctly space nucleosomes following replication
- Densely packed nucleosomes can hide important cis DNA elements as most DNA-binding factors cannot bind their cognate site if one face of the DNA is wrapped on the nucleosome surface. Solution: There are two methods for element exposure: (a) position the cis-elements in nucleosome-free regions or in the DNA linker between nucleosomes, and (b) utilize a specialized remodeler to slide the nucleosome, or to expose the element transiently on the nucleosome surface
- DNA repair requires access to all DNA base pairs, and recombination requires access to long stretches of DNA. Thus, nucleosomes must be mobilized or ejected to provide rapid access. Solution: Specialized remodelers assist in nucleosome removal, sliding, and restructuring during repair and recombination.
- The progress of RNA and DNA polymerases can be impeded by nucleosomes. Also, transcription can release nucleosomes, which need replacement and proper positioning. Solution: Remodeling factors either eject or chaperone
the histone octamer around the advancing polymerase. Furthermore, remodelers may help the replication-independent chromatin assembly machinery fill in gaps where nucleosomes have been ejected.
Thus, remodelers are needed for nucleosome dynamics to move, eject, or restructure the composition of nucleosomes.
Remodeler Families, defined by their ATPase.
All remodeler families contain a SWI2/SNF2-family ATPase subunit characterized by an ATPase domain that is split in two parts: DExx (red ) and HELICc (orange). What distinguishes each family are the unique domains residing within, or adjacent to, the ATPase domain. Remodelers of the SWI/SNF, ISWI, and CHD families each have a distinctive short insertion ( gray) within the ATPase domain, whereas remodelers of INO80 family contain a long insertion ( yellow). Each family is further defined by distinct combinations of flanking domains: Bromodomain (light green) and HSA (helicase-SANT) domain (dark green) for SWI/SNF family, SANT-SLIDE module (blue) for ISWI family, tandem chromodomains (magenta) for the CHD family, and HSA domain (dark green) for the INO80 family.
Chromatin remodelers in nucleosome dynamics.
Chromatin remodelers use ATP hydrolysis to alter nucleosomes and are specialized for certain tasks. SWI/SNF-family remodelers provide access to binding sites in nucleosomal DNA, mainly through nucleosome movement or ejection. ISWI family members conduct chromatin assembly and organization, in order to provide consistent spacing of nucleosomes. This organization can cover a binding site for a transcription factor. INO80 remodelers reconstruct nucleosomes by inserting the histone variant H2A.Z into nucleosomes, specializing their composition
Phylogenetic and functional analyses have classified all remodeller ATPases within the RNA/DNA helicase superfamily, which can be divided into following subfamilies of chromatin-remodeling enzymes:
- imitation switch (ISWI),
- chromodomain helicase DNA-binding (CHD),
- switch/sucrose nonfermentable (SWI/SNF) and
Shared Remodeler Properties
All remodelers share five basic properties:
(a) an affinity for the nucleosome, beyond DNA itself;
(b) domains that recognize covalent histone modifications;
(c) a similar DNA-dependent ATPase domain, required for remodeling and serving as a DNA-translocating motor to break histone-DNA contacts;
(d) domains and/or proteins that regulate the ATPase domain; and
(e) domains and/or proteins for interaction with other chromatin or transcription factors. Together, these shared properties allow nucleosome engagement, selection, and remodeling. However, distinctive targeting and tasks require remodeler specialization.
Remodeler Family Specialization
Although all remodeler catalytic subunits share a conserved ATPase domain, each family member bears unique flanking domains, allowing their separation into four distinct families. Individual families are conserved from yeast to human, although there is some variation in their detailed protein composition. However, ortholog complexes often conserve key domains, suggesting that conserved domains reflect conserved functions
Domains, proteins, and modifications that regulate remodelers.
Remodeler regulation is an area of increasing complexity. To capture these principles conceptually, we depict the ATPase domain itself (blue) along with the proteins, domains, and modifications that are involved in remodeler regulation. Regulatory (Reg.) modifications and proteins that positively impact remodeling activities are in green, those negatively affecting remodeling activities are in red, and those contributing to targeting are in purple. Yellow is used for features with unclear or unknown effect. Objects implicated in both activation and targeting are depicted as objects with a green-purple gradient. CHD remodelers can be monomeric or multimeric, with italicized text only for the monomeric form.
They have global and fundamental roles for remodeling complexes in shaping the epigenome during development. Embryonic development manifests as a series of changes in cellular programmes that mark the transitions from the totipotent zygote to increasingly more differentiated cells with specialized morphology and function. These programmes are best characterized by the distinct patterns of gene expression reflecting the selective usage of the genetic information. The initiation of differential gene expression is interwoven with changes in chromatin features; its maintenance is based on the existence of stable, heritable chromatin structure. Understanding developmental switches in gene expression requires detailed knowledge about the local and global changes in chromatin organization and their functional consequences. 22
Chromatin affects gene expression at several levels of structural organization: through the placement of single nucleosomes, the folding of the nucleosomal fibre, the assembly of higher-order structure by interacting proteins and the formation of nuclear compartments characterized by enrichment of specific regulators. The accessibility of DNA—genes and regulatory elements—can be tuned through differential packaging. Second, specific loci, areas or chromosomal domains may be earmarked as substrates for those enzymes that translate structure into function. Nucleosome remodeling factors are enzymes that are able to disrupt the tight ionic association of DNA with histones. Key to their action is an ATPase ‘motor’ subunit that belongs to the large SNF2 family of helicase-related proteins, many of which are able to translocate DNA. The simultaneous movement of DNA and binding to the histones leads to displacement of DNA segments relative to the histone surface. The conformational changes in the enzyme necessary for this action are supported by binding and hydrolysis of ATP.
The mammalian cell harbors numerous different remodeling complexes that possess distinct activities. These can translate a variety of signals into certain patterns of nucleosome positions with specific functions. 21
Certain remodeler classes have specialized tasks, all remodelers alter the position of DNA on the octamer. Remodeling requires ATP hydrolysis, and all remodeling complexes contain a conserved DNA-dependent ATPase subunit. For most remodeler classes, the ATPase subunit in isolation is capable of limited nucleosome remodeling and is therefore defined as the catalytic subunit. The similarity of the ATPase domain among all remodelers strongly suggests that all use the energy stored in ATP in a similar manner to alter nucleosome structure. A central question regarding remodelers is how ATP hydrolysis is converted into mechanical force that breaks histone-DNA contacts to mobilize nucleosomes.
Chromatin structure is a key determinant of gene regulation. The wrapping of the DNA around the histone octamer protein core in the nucleosome impedes the access of other protein factors to the DNA sequence information. To mediate access, a diverse chromatin-remodeling machinery exists in the eukaryotic cell nucleus to translocate, remove or assemble nucleosomes as needed. It is centered around numerous different types of ATP‐driven molecular machines that can move the nucleosomal DNA with respect to the histone octamer core via an ATP‐driven mechanism 19
Chromatin remodelers can facilitate many different modifications to chromatin by positioning or removing nucleosomes from promoters or by evenly spacing nucleosomes across sections of DNA. Chromatin remodelers accelerate the packaging of DNA by moving nucleosomes away from their sequence-directed binding locations into metastable positions. The mechanism by which these metastable nucleosomes relax back to their equilibrium locations represents an important process through which DNA sequence and chromatin dynamics are coupled. 20
Chromatin remodeling complexes (remodelers) are a set of diverse multi-protein machines that reposition and restructure nucleosomes. Remodelers are specialized, containing unique proteins that assist in targeting, interaction with modified nucleosomes and performing specific chromatin tasks. However, all remodelers contain an ATPase domain that is highly similar to known DNA translocases/helicases, suggesting that DNA translocation is a property common to all remodelers. 10
Access to DNA within nucleosomes is required for a variety of processes in cells including transcription, replication, and repair. Consequently, cells encode multiple systems that remodel nucleosomes. These complexes can be simple, involving one or a few protein subunits, or more complicated multi-subunit machines. Biochemical studies have placed the motor domains of several chromatin remodelers in the superhelical location region of the nucleosome. 33
As the basic packaging units of eukaryotic genomes, nucleosomes provide both a rich medium for accumulation of epigenetic marks and a physical barrier that restricts access to DNA. These two nucleosomal features – presenting epigenetic signatures and blocking DNA access – are integrated by a diverse group of protein machines called chromatin remodelers. 34
Chromatin processes and Remodeler involvement.
Remodelers can be classified by their involvement in particular chromatin processes.
( a ) Chromatin Assembly: Most of ISWI- and CHD- family Remodelers help in the process of histone deposition, the full maturation/formation of nucleosomes, and their spacing—which can result in the blockage of the cognate site ( red ) of a DNA-binding protein (DBP) (Note: spacing can also result in consistent site exposure.
( b ) Chromatin Editing: Remodelers of the INO80/SWR1 family (and others) modify the
composition of resident nucleosomes by performing histone exchange, either removing or replacing
noncanonical histone variants ( blue disk ).
( c ) Chromatin Access: SWI/SNF-family Remodelers (and others) alter nucleosomes by repositioning, ejecting the octamer, or evicting dimer(s), allowing exposure for a DNA-binding protein to its cognate site ( green )
Remodelers are distinguished from other chromatin factors by their use of the energy of ATP hydrolysis to promote these functions. Remodelers work with other chromatin factors to regulate both chromatin packaging and unpackaging, as the DNA elements that control chromosomal processes (enhancers, promoters, and replication origins) must be exposed in a regulated manner to properly regulate gene transcription, DNA replication, DNA repair, and recombination.
Chromatin presents a barrier to transcription factors and other proteins that must access DNA in eukaryotic cells. By altering the structure or positioning of nucleosomes, histone-modifying enzymes and ATP-dependent chromatin-remodeling factors play critical roles in modulating chromatin repression. Chromatin-remodeling enzymes use the energy of ATP to alter the structure or positioning of nucleosomes, thus modulating the access of regulatory proteins to DNA. The activity of chromatin-remodeling enzymes can be regulated by other proteins and they typically function as subunits of multiprotein complexes. The coordinated action of histone-modifying enzymes and chromatin remodeling complexes is critical for a wide variety of biological processes, including transcriptional activation and repression, differentiation, DNA replication, repair and recombination, and cell cycle progression. 13
Eugene Koonin: "The origin of eukaryotes and multicellularity involved invention of several fundamentally new functional systems. The eukaryotic chromatin remodeling machinery is such a major eukaryotic innovation, which does not appear to have direct prokaryotic predecessors analogs. " 15
Koonin, the author of the paper, attributes its origin to a momentous evolutionary transition. He remains to provide evidence for such claim.
Chromatin-structure dynamics are important for the regulation of gene expression and chromosome function. All chromatin-remodeling complex subfamilies contain an ATPase–translocase ‘motor’ that translocates DNA from a common location within the nucleosome. Each remodeller subfamily utilizes diverse specialized proteins and protein domains to assist in nucleosome targeting. These modules converge to regulate a common DNA translocation mechanism, to inform the conserved ATPase ‘motor’ on whether and how to apply DNA translocation, which together achieve the various outcomes of chromatin remodeling: nucleosome assembly, chromatin access, and nucleosome editing.
The basic components of chromatin are nucleosomes, which comprise octamers of histone proteins around which DNA is wrapped. The majority of nucleosome assembly occurs during DNA replication, directly in the wake of the replisome, and involves the delivery of histones to nascent DNA by histone chaperones. Chromatin dynamics involve the action of specialized ATP-dependent chromatin-remodeling complexes (herein termed remodellers). Remodellers include enzymes that ensure the proper density and spacing of nucleosomes and that can also contribute to gene repression. Another set of remodellers cooperates with site-specific transcription factors and histone-modification enzymes to move or to eject histones to enable the binding of transcription factors to DNA. Yet another set of remodellers is involved in creating specialized chromosomal regions where canonical histones are replaced by histone variants. Thus, genome-wide nucleosome occupancy and composition are tailored by specialized remodellers. Genetic experiments have revealed that ATP-dependent chromatin-remodeling enzymes are essential regulators of nearly every chromosomal process, and their deregulation leads to a variety of diseases, including cancer.
The composition of each subfamily of chromatin remodelers in Saccharomyces cerevisiae.
Chromatin remodeler complexes representing each subfamily are depicted: ISW1a, ISW1b and ISW2 of the ISWI subfamily, CHD1 of the CHD subfamily, SWI/SNF and RSC of the SWI/SNF subfamily and INO80C and SWR1C of the INO80 subfamily. All remodellers contain a ‘core’ or ’motor’ ATPase–translocase subunit (in red), additional ‘core’ or ’signature’ subunits that are conserved between distinct remodellers within a subfamily (for example Arp7 and Arp9 in the SWI/SNF subfamily; Rvb1-Rvb2 in the INO80 subfamily), as well as unique subunits. Complexes are organized in modules, and an example of modular construction is presented for the ISWI subfamily in the composition of ISW1a versus that of ISW1b.
Most remodelers are specialized to preferentially conduct one of the following three functions: nucleosome assembly and organization, chromatin access and nucleosome editing (installing or removing histone variants) Fig. a
Functions and domain organization of chromatin remodelers.
a | Functional classification of remodelers. The ATPase–translocase subunit of all remodellers is depicted in pink; additional subunits are depicted in green (imitation switch (ISWI) and chromodomain helicase DNA-binding (CHD)), brown (switch/sucrose nonfermentable (SWI/SNF)) and blue (INO80). Nucleosome assembly: particular ISWI and CHD subfamily remodellers participate in the random deposition of histones, the maturation of nucleosomes and their spacing. Chromatin access: primarily, SWI/SNF subfamily remodellers alter chromatin by repositioning nucleosomes, ejecting octamers or evicting histone dimers. Nucleosome editing: remodellers of the INO80 subfamily (INO80C or Swr1 complex (SWR1C)) change nucleosome composition by exchanging canonical and variant histones, for example, and installing H2A.Z variants (yellow). We note that this functional classification is a simplification, as INO80C, the ISWI remodeller nucleosome remodeling factor (NURF) and certain CHD remodellers can promote chromatin access.
b | Domain organization of remodeller subfamilies. The ATPase–translocase domain (Tr) of all the remodellers is sufficient to carry out DNA translocation. It is comprised of two RecA-like lobes (lobe 1 and lobe 2, which are separated by a short or long (such as in the INO80 subfamily) insertion (grey)). Remodellers can be classified into four subfamilies based on the length and function of the insertion and on their domain organization. c | ‘Inchworming’ mechanism of DNA translocation. An ATP binding–hydrolysis-dependent conformational cycle of the RecA-like lobes (‘mittens’) drives DNA translocation. Mittens are depicted closed when lobes have high affinity for DNA and open when lobes have low affinity for DNA (Supplementary information S3 (movie)). Although the DNA can be double-stranded, only the tracking strand of DNA is depicted, along which the lobes move in the 3ʹ–5ʹ direction (validated by single-stranded DNA studies53). Steps are depicted as sequential, but they may be concerted, and a similar model with mitten/lobe 1 being stationary is equally supported. The yellow arrows represent remodeller movement; the green arrow represents DNA translocation. The precise step in which inorganic phosphate (Pi) is released is not known. NegC* is a region with structural similarity to the ISWI negative regulator of coupling (NegC) domain. AutoN, autoinhibitory N‑terminal; Bromo, bromodomain; DBD, DNA-binding domain; HSA, helicase/SANT-associated; HSS, HAND–SANT–SLIDE; SnAC, Snf2 ATP coupling.
The Impact of Chromatin Remodeling
The packing of genomic DNA around nucleosomes provides topological order but hides one face of the DNA, thus nucleosomes often block the access of transcription factors to genomic DNA. Binding sites located near the middle of a nucleosome are generally inaccessible to transcription factors, those near the edge are partially accessible, and only those in the linker are fully accessible. This inaccessibility of a larger part of the genome leads to a dependence of major parts of transcription on chromatin remodeling. To maintain topological order and also to allow rapid and regulated access to the DNA, cells have a set of chromatin remodeling complexes that alter nucleosome position, presence and structure. Repositioning a nucleosome by as little as a few bp can be sufficient to change the accessibility of a regulatory genomic region, such as a promoter or an enhancer. In the same way that most transcription factors form homo- or heterodimeric complexes, in order to synergistically activate gene expression, transcription factors also co-operate with chromatin remodeling proteins. Genome-wide studies have indicated that transcription factors and chromatin remodelers are often found at the same genomic location.
Chromatin modifiers and remodelers affect the structure of chromatin at all levels, they can modulate local structures on the few 100 bp of an active core promoter but also organize millions bp of genomic DNA into specialized structures, such as the centromere and surrounding constitutive heterochromatin. In addition, to block transcription factor binding, chromatin also compromises transcriptional elongation. RNA polymerases can transcribe genomic DNA even when it is covered by nucleosomes, but the process is slow. Interestingly, the nucleosome does not leave the genomic DNA template, when the RNA polymerase moves during elongation, but transfers directly to a more upstream position. Chromatin remodeling complexes help to construct the initial chromatin states and catalyze the transition to alternative states, using the energy from ATP hydrolysis. In general, chromatin remodelers make DNA regulatory sequences more or less accessible to the transcriptional apparatus, thereby allowing transcription factors to activate or repress the transcription of their target genes. When acting together, these processes allow a large and dynamic range in the regulation of specific genes: when chromatin is condensed the transcription is fully “off”, with little nonspecific transcription, whereas the combination of fully open chromatin, low nucleosome density and transcription factor binding results in extremely high levels of mRNA transcript accumulation. Intermediate levels of transcription can be achieved by producing accessible chromatin that has relatively high nucleosome density, which allows transcription factor binding and transcriptional activation, but a slower rate of transcriptional initiation.
Coordination between chromatin remodelers and transcription factors.
The action of chromatin remodeling complexes in coordination with chromatin-modifying complexes make genomic DNA more or less accessible to transcription factors. This determines the ability of the latter to activate transcription at a given genomic locus. Silent chromatin ( top) is transcriptionally inactive and inaccessible to transcription factors. Open chromatin ( center), created through the action of chromatin remodelers and modifiers, is accessible to transcription factors, allowing them to activate transcription. Further removal of nucleosomes by chromatin remodelers creates fully open chromatin, which allows high rates of transcription, for example, of housekeeping genes. The
structure of chromatin is dynamic and can be easily reversed to the transcriptionally silent state through chromatin remodelers, for example, in developmentally regulated genes
ATP-Dependent Remodeling Complexes
ATP-dependent remodeling is crucial for both the assembly of chromatin structures and their dissolution. About 30 human genes encode for subunits of these complexes. Many chromatin remodeling complexes are assembled combinatorially, thereby greatly expanding the potential for various gene expression patterns. The ATPases in the core of the chromatin remodeling complexes are genetically non-redundant, but they all increase nucleosome mobility. The investment of energy for this process is necessary since both sliding and ejection of nucleosome from genomic DNA has to dissolve all histone-DNA contacts requiring approximately 12–14 kcal/mol. The remodeling processes involve the dissociation of genomic DNA at the edge of the nucleosome and form a DNA bulge on the histone octamer surface. The DNA loop then propagates across the surface of the nucleosome in a wave-like manner, resulting in the repositioning of DNA without changes in the total number of histone- DNA contacts.
Chromatin remodeling complexes affect nucleosomes in at least four ways:
Mobility and stability of nucleosomes.
Chromatin remodelers enable access to genomic DNA through sliding, ejection or H2A-H2B dimer removal from nucleosomes. Nucleosome mobility is influenced by thermal motion and the activity of ATP-dependent nucleosome remodeling complexes. Nucleosome stability is affected by the octamer composition and modification pattern of histones. Incorporation of histone variants alters the interactions with histone and nonhistone proteins
For an exposure of genomic DNA that was initially covered by nucleosomes they either mediate:
1. Movement (sliding) of the histone octamer to a new position,
2. Complete displacement (ejection) of the histone octamer,
3. Removal of the pair of H2A-H2B dimers, leaving only the central H3-H4 tetramer,
which destabilizes the nucleosome and/or
4. Replacement of regular histones by their variant forms, such as H2A.Z.
ISWI chromatin remodelers are highly conserved in eukaryotes and are important for the assembly and spacing of nucleosomes, thereby controlling transcription initiation and elongation. ISWI is typically associated with different subunits, forming specialized complexes with discrete functions. Chromatin remodelers in the ISWI family are highly conserved among eukaryotes and play a critical role in nucleosome assembly and spacing as well as in the organization of chromatin at a higher level in the cell. ISWI has a highly conserved SWI2/SNF2 family ATPase domain, which provides the motor for chromatin remodeling, and characteristic HAND-SANT-SLIDE domains with DNA binding activity 21
Using DNA-dependent ATPase activity, ISWI remodelers change nucleosome spacing to promote chromatin assembly, which often results in the repression of transcription. In addition to their role in remodeling existing nucleosomes, they can also facilitate the de novo assembly of nucleosomes in concert with core histone chaperones. ISWI invariably functions as part of a complex, and different eukaryotes have a diverse array of ISWI complexes, each with a discrete function. It is becoming increasingly clear that the ISWI partner subunits have a regulatory role and determine ISWI complex function. In Saccharomyces cerevisiae, there are two different ISWI variants (Isw1 and Isw2), which in combination with different subunits, form a total of four different complexes. ISWI (Isw1) together with the Ioc3 subunit forms the Isw1a complex, which binds Pol4 II promoters and excludes the basal Pol II transcription machinery, thereby preventing transcription initiation. In contrast, Isw1 partnered with the Ioc2 and Ioc4 subunits forms the Isw1b complex, which regulates Pol II transcription elongation and termination. In mammalian cells (where the ISWI equivalents are referred to as SNF2H or SNF2L/SMARCA1), at least seven different ISWI complexes have a similar broad range of functions, including facilitating DNA repair.
Activities of ISWI chromatin remodelers
The ISWI (imitation switch) family remodelers contain 2 to 4 subunits. dNURF, dCHRAC, and dACF complexes were initially purified from Drosophila melanogaster, with hWICH or hNoRC identified subsequently. Most eukaryotes build multiple ISWI family complexes using one or two different catalytic subunits, with specialized attendant proteins. A characteristic set of domains reside at the C terminus of ISWI family ATPases: a SANT domain (ySWI3, yADA2, hNCoR, hTFIIIB) adjacent to a SLIDE domain (SANT-like ISWI), which together form a nucleosome recognition module that binds to an unmodified histone tail and DNA. Specialized attendant proteins impart many domains, including DNA-binding histone fold motifs (in hCHRAC 15-17), plant homeodomain (PHD), bromodomains (hBPTF and hACF1), and additional DNA-binding motifs [HMGI(Y), for dNURF301]. Many ISWI family complexes (ACF, CHRAC) optimize nucleosome spacing to promote chromatin assembly and the repression of transcription. However, certain complexes (NURF) can randomize spacing, which can assist RNAPII activation, showing the diversity that can be imparted by attendant subunits.
One of the best‐conserved ATPase families involved in chromatin remodeling is the imitation switch (ISWI) family. Chromatin remodelers have been linked to various biological functions. Although only a limited number of motor ATPases are involved in chromatin remodeling, the combination of these motors with different accessory subunits generates a large variety of remodeling complexes. ISWI chromatin remodellers are involved in important genome‐associated processes and are instrumental for DNA replication, DNA repair, transcriptional regulation and maintenance of chromosome structure. These activities seem to be highly regulated on different levels. Via specific subunit composition and post‐translational modifications, distinct targeting of their activity is achieved in response to different stimuli, such as the metabolic state of the cell, a specific cell cycle phase, hormone treatment or the presence of DNA damage21
DNA replication is one of the biological processes associated with extensive chromatin remodeling. Chromatin structure is rearranged during DNA duplication and has to be restored afterward. Histones are deposited on the nascent DNA, and their modification status, as well as their positioning pattern, has to be adjusted in an appropriate way.
Mammalian cells have a dedicated pathway to respond to DNA lesions; this pathway is referred to as the DNA damage response (DDR). The repair process is typically accompanied by local alterations of the chromatin structure. During DDR, lesions are first recognized by certain sensor proteins and afterwards bound by catalytic effector proteins that mediate the repair process. Among the factors recruited to DNA damage sites are many different types of remodelers, including the ISWI complexes. In summary, ISWI complexes seem to have important functions at DNA repair sites that are not restricted to nucleosome repositioning but include recruitment of other factors and post‐translational modification of histones.
ISWI chromatin remodellers not only play a role during chromatin (dis)assembly, as is the case in DNA repair or replication, but they can also switch nucleosome positions to block or clear promoters. This can directly change the expression level of the corresponding gene. These switching processes are triggered in the cell by different signals (e.g. hormone‐dependent stimulation or metabolic changes)
Some ISWI complexes have functions connected to the regulation of chromosome structure.
ISWI slides nucleosomes along DNA, enabling the structural changes of chromatin required for the regulated use of eukaryotic genomes.
Chromatin organization endows eukaryotic genomes with stability and regulates gene expression. Arrays of nucleosomes are further folded to accommodate the genome in the nuclear volume. Tight packaging inevitably leads to the occlusion of DNA sequences that can no longer be accessed by regulatory proteins. However, chromatin has to be dynamic to permit cells to respond to environmental or developmental challenges. Crucial to a dynamic and regulated use of the genome are the actions of ATP-consuming nucleosome-remodeling enzymes. Nucleosome-remodeling enzymes use energy from ATP hydrolysis to weaken or disrupt histone-DNA contacts in the otherwise extremely stable nucleosome particle. They thereby catalyze histone exchange, partial or complete nucleosome disassembly and formation of new nucleosomes or repositioning of existing ones. The precise outcome of a remodeling reaction is frequently determined by regulatory subunits that associate with the ATPase. They share a strategic interaction site on the nucleosome. Their ATPase ‘motor’ domain engages the nucleosomal DNA about two helical turns off the nucleosomal dyad at superhelix location 2 (SHL2).
ISWI-containing complexes exist in many organisms, from yeast and humans, highlighting the conserved function of this ATPase in chromatin remodeling. In addition to highly conserved ATPase domains, ISWI contains SANT and SLIDE domains: DNA and nucleosome binding motifs found in a variety of proteins that interact with chromatin
ISWI family of chromatin-remodeling complexes
SANT domains are found in many proteins known to be components of complexes that play a role in both transcriptional activations. The SANT-related SLIDE motif is believed to play an important role in nucleosome recognition. ISWI can facilitate chromatin assembly by transforming a disordered array of nucleosomes into an evenly spaced nucleosome array, a process known as nucleosome spacing. Using its nucleosome-mobilizing activity, recombinant ISWI can also assist transcription factors and other proteins to bind to their target sites.
Nucleosome-remodeling enzymes may th ave evolved directly from ancestral helicase-type motors, and peripheral domains have furnished regulatory capabilities that bias the remodeling reaction toward different structural outcomes. 14
Coordinated actions, regulation, and strategic interactions are crucial and must be pre-programmed by intelligence and require foreknowledge of distant needs. Were these peripheral domains not precisely structured and specialized to perform the task right from the beginning, they could not perform properly. Random, unguided non-intelligent natural processes would need to promote a future functional outcome with intermediate non-functional stages, and both 1. evolving the right physical properties of these peripheral domains, finely tuned to perform a conjoined co-operative action and correct regulation tasks once the system was fully set up. Furthermore, transcription activation is life-essential and could not occur, if the process was not fully implemented. Even more, coordination and regulation are required for these biological processes since it indicates that when both are not existent or fully implemented, the life-essential processes like transcription activation cannot occur properly, and in cases of malfunction, causing cancer.
SWI/SNF family remodelers
The SWI/ SNF (switching defective/sucrose nonfermenting) family remodelers are composed of 8 to 14 subunits. Most eukaryotes utilize two related SWI/SNF family remodelers, built around two related catalytic subunits. The catalytic ATPase includes an HSA (helicase-SANT), a post-HSA, and a C-terminal bromodomain. A pair of actin-related proteins (ARPs) is present in fungal complexes, whereas a dimer of actin and an ARP (hBAF53a/b) are present in higher orthologs. Other conserved subunits bear additional conserved domains; examples include hBAF155/170 (SANT, SWIRM), hBAF60 (SwiB), and human polybromo (multiple bromodomains). This family has many activities, and it slides and ejects nucleosomes at many loci and for diverse processes but lacks roles in chromatin assembly
The Swi2/Snf2 ATPase: A versatile motor
“Remodelers” are diverse molecular machines that use the energy of ATP to disrupt or remodel protein: nucleic acid ( histones / DNA ) complexes, most notably nucleosomes but also others such as transcription factors and RNA polymerase. The shared chemo-mechanical “engine” of remodelers is a Swi2/Snf2 ATPase, which possesses a Swi2/Snf2 ATPase domain along with other domains that target, regulate and/or mechanistically couple the ATPase domain with the substrate in the remodeling reaction 31 INO80 and the related SWR1 complex are large (megadalton) modular complexes that carry out intricate editing reactions.
CHD family remodelers
The CHD family remodelers, among which Mi-2, combine 1 to 10 subunits and were first purified from Xenopus laevis. Characteristic features include two tandemly arranged chromodomains on the N terminus of the catalytic
subunit. The catalytic subunit is monomeric in lower eukaryotes but can be in large complexes in vertebrates. Attendant proteins often bear DNA-binding domains and PHD, BRK, CR1-3, and SANT domains. Certain CHD remodelers slide or eject nucleosomes to promote transcription. However, others have repressive roles.
INO80 family remodelers
The INO80 family remodelers contain more than 10 subunits, include the SWR1-related complexes. INO80 has diverse functions, including promoting transcriptional activation and DNA repair. Although highly related to INO80,
SWR1 is unique in its ability to restructure the nucleosome by removing canonical H2A-H2B dimers and replacing them with H2A.Z-H2B dimers, thereby inserting the histone H2A variant H2A.Z.
Chromatin modifiers and remodelers work in concert to direct nucleosome dynamics.
The position and histone composition of nucleosomes is governed by ATP-dependent chromatin remodelers such as the 15-subunit INO80 complex. 32 INO80 regulates gene expression, DNA repair, and replication by sliding nucleosomes, the exchange of histone H2A.Z with H2A, and the positioning of+1 and −1 nucleosomes at promoter DNA. An Rvb1/Rvb2 AAA+ ATPase heterohexamer is an assembly scaffold for the complex and acts as a ‘stator’ for the motor and nucleosome-gripping subunits. Nucleosome sliding requires extensive inter-subunit coordination and a clear mechanistic framework explaining these activities is currently not available. Biochemical evidence indicates that INO80 translocates and loops DNA at the H2A–H2B interface, suggesting that sliding and editing may be facets of a common, complex chemo-mechanical reaction. The complex comprises subunits conserved ( unchanged ) from yeast to man. INO80core embraces one entire gyre of the nucleosome and binds in a multivalent fashion to nucleosomal DNA and histones 32
Model of INO80 nucleosome remodeling.
The unified model integrates our structural data with previous biochemical8 data. The functional architecture of INO80 with motor, grip and grappler suggests that processive nucleosome sliding proceeds via a ratchet mechanism. Transient generation of loops between the motor and the grip could expose H2A–H2B for editing. Direct binding of H2A–H2B by the grappler sensor foot could regulate variant- or modification-specific editing.
The motor, stator and multivalent grip of INO80 enable highly processive sliding without release and large-scale reconfigurations such as editing while keeping the remainder of the nucleosome intact. The proposed ratchet mechanism explains DNA loop formation that results in large translocation steps, as well as the means for ATP-dependent H2A.Z → H2A exchange.
The ARP5–IES6 module of INO80 makes additional contacts on the opposite side of the nucleosome. This arrangement enables the histone H3 tails of the nucleosome to have a role in the regulation of the activities of the INO80 motor domain—unlike in other characterized remodellers, for which H4 tails have been shown to regulate the motor domains.
Human INO80-nucleosome complex.
a, INO80 subunit with functional domains labelled.
b, Three-dimensional INO80–nucleosome complex reconstruction with RUVBL1–RUVBL2, INO80, ARP5, IES2 and nucleosome structural models fitted.
c, INO80– nucleosome interactions with histones and nucleosome positions labelled. INO80 contacts the nucleosome at SHL −6 and SHL −3. The locations of the histone tails are also shown. NTD, N-terminal domain; HSA, helicase-SANT-associated domain; HN, N-terminal helicase domain; HC, C-terminal helicase domain; I, INO80 insert domain; C, C-terminal domain.
Structures of remodellers
For ISWI, elegant cross-linking studies show interactions of the ATPase two turns from the nucleosomal dyad (Figure a,b)
Model of DNA movement during a remodeling event.
(a) At left, a nucleosome side view emphasizing the left-handed wrapping of DNA (orange then red ) around the histone octamer ( gray transparent cylinder). DNA color changes from orange to red when passing the nucleosomal dyad axis. At right (and also in part b), the nucleosome is rotated 90◦ according to the axis and depicted in two dimensions. After passing the dyad axis, the second gyre of DNA is presented in red dots instead of orange to reinforce the perspective of DNA wrapping. An asterisk (∗) provides a reference point on the DNA, useful for following the translocation of DNA along the octamer surface.
(b) States 1 to 4 represent the successive steps occurring during a remodeling event. The concerted action of a DNA-binding domain (DBD) located on the linker DNA and a translocation domain (Tr) located near the dyad generates a small DNA loop that propagates on the nucleosome surface. The remodeler undergoes a conformational change in its DBD when DNA loop is generated (State 1 to State 2), followed by the translocation of the DNA through the Tr domain, which passes the DNA loop to the dyad (State 2 to State 3). The DNA loop continues its propagation on the second half of the nucleosome surface by one-dimensional diffusion (see text). Loop propagation then resolves into the distal linker, resulting in nucleosome repositioning (State 3 to State 4). The remodeler resets its conformation with original binding contacts, ready for a new remodeling cycle (State 4 to State 1).
and important interactions of the SLIDE domain of ISWI with the linker DNA. This is depicted in Figure b, where the SLIDE domain is the DBD and the ATPase domain is the translocation domain (Tr). Nuclease protection and
other assays support a similar site of interaction (∼2 turns from the dyad) for the catalytic ATPase of RSC, as well as extensive enveloping of the nucleosome by the rest of the complex. Structural studies using electron microscopy
(EM) with RSC show a very large cavity of nucleosome dimensions and the presence of two conformations, which may be influenced by tail modifications. Recent EM studies with ySWI/SNF suggest nucleosome binding in a large depression on the remodeler surface, with cross-linking studies revealing component-nucleosome interactions. For SWI/SNF family remodelers, biochemical and structural studies suggest that the unit of remodeling is one remodeler and one nucleosome. However, two copies of the ISWI family complex ACF may bind one nucleosome, and these two copies may physically interact with one another, raising the possibility that each ISWI catalytic subunit moves the DNA over the octamer in the opposite direction, providing a back-and-forth motion. Although considerable progress has been made, one limitation of all published studies is the lack of a remodeled nucleosome complex; all current structures involve the modeling of the nucleosome into the remodeler.
Transcriptional regulation by Polycomb group proteins
Polycomb group (PcG) proteins are epigenetic regulators of transcription that have key roles in stem-cell identity, differentiation and disease. Mechanistically, they function within multiprotein complexes, called Polycomb repressive complexes (PRCs), which modify histones (and other proteins) and silence target genes. 20
The DNA of eukaryotic cells is organized in chromatin fibers, with the nucleosome forming the basic repeating unit. Each nucleosome comprises 145–147 bp of DNA wrapped in 1.8 helical turns around an octamer of four highly conserved histone proteins—H2A, H2B, H3 and H4. Histone H1 binds the linker DNA between two adjacent nucleosomes, causing further compaction of the chromatin fibers into higher-order structures, often referred to as solenoids. Analysis of the crystal structure of the nucleosome revealed that N-terminal histone tails are flexible and protrude outward from the nucleosome core1. Histone tails undergo numerous posttranslational modifications (PTMs) that influence a large number of nuclear processes, including transcription, replication, DNA repair, chromosome compaction, and localization. Two main functions have been ascribed to histone PTMs so far. First, lysine acetylation neutralizes the positive charge of histone tails and can thereby alter histone-DNA interactions and/or decrease interactions between different histones in adjacent nucleosomes. Second, several PTMs can generate docking sites or modulate the affinity of nuclear proteins for chromatin. The specific recognition of histone PTMs is achieved by a dozen protein domains, which are present in a large number of chromatin-associated proteins.
Epigenetics is one of the hottest fields in the life sciences. It’s a phenomenon with wide-ranging, powerful effects on many aspects of biology. Epigenetics is essentially additional information layered on top of the sequence of letters (strings of molecules called A, C, G, and T) that makes up DNA. If you consider a DNA sequence as the text of an instruction manual that explains how to make a human body, epigenetics is as if someone's taken a pack of highlighters and used different colors to mark up different parts of the text in different ways. For example, someone might use a pink highlighter to mark parts of the text that needs to be read the most carefully, and a blue highlighter to mark parts that aren't as important.
There are different types of epigenetic marks, and each one tells the proteins in the cell to process those parts of the DNA in certain ways. For example, DNA can be tagged with tiny molecules called methyl groups that stick to some of its C letters. Other tags can be added to proteins called histones that are closely associated with DNA. There are proteins that specifically seek out and bind to these methylated areas, and shut it down so that the genes in that region are inactivated in that cell. So methylation is like a blue highlighter telling the cell "you don't need to know about this section right now." The really interesting thing about epigenetics is that the marks aren’t fixed in the same way the DNA sequence is: some of them can change throughout your lifetime and in response to outside influences. Some can even be inherited, just like some highlighting still shows up when text is photocopied. 12
Genes are regulated by epigenetic factors, which includes heritability, as it defines a nongenetic memory of function that is transmitted from generation to generation. Histone modifications are involved in epigenetic processes. The question is, do modifications pass on the memory of a given chromatin state or do they merely implement the memory, once the memory is passed on via a distinct process? If epigenetic memory is mediated by one or more of the histone modifications, then there should be a mechanism for the transmission of such modifications onto the chromatin of the replicating DNA. Such a mechanism has been proposed for H3K9 methylation in the transmission of the heterochromatin ( Heterochromatin is a tightly packed form of DNA or condensed DNA ) : recruitment of HP1 brings in further H3K9-methylating activity that modifies nucleosomes on the daughter strand, thus ensuring the transmission of the H3K9me mark. This mechanism of transmission, along with the observation that H3K4me3 patterns persist, have given lysine methylation an epigenetic status. The issue that remains, however, is whether the modification pattern inherited by the daughter chromatin is sufficient to impose the correct chromatin structure originating from the mother cell. Is methylation of lysines dictating the memory of chromatin structure? 2
ATP-dependent chromatin remodeling during mammalian development
Precise gene expression ensures proper stem and progenitor cell differentiation, lineage commitment and organogenesis during mammalian development. ATP-dependent chromatin-remodeling complexes utilize the energy from ATP hydrolysis to reorganize chromatin and, hence, regulate gene expression. These complexes contain diverse subunits that together provide a multitude of functions, from early embryogenesis through cell differentiation and development into various adult tissues. 1 Gene expression programs operate within the confines of chromatin and hence chromatin organization influences key aspects of mammalian development. Major factors that affect chromatin organization are:
(1) DNA methylation;
(2) covalent modification of histones; and
(3) ATP-dependent alterations to chromatin.
ATP-dependent chromatin alteration is accomplished by several multi-subunit chromatin-remodeling complexes that utilize energy derived from ATP hydrolysis to alter nucleosome structure or conformation and, thereby, regulate the access of transcription factors to their cognate DNA binding sites. These chromatin-remodeling complexes are primarily made up of a single ATPase and multiple associated subunits. The ATPase subunit binds and hydrolyzes ATP, while the associated subunits modulate the catalytic activity of the ATPase subunit and provide specificity to genome binding. Thus, combinatorial assembly of different ATPase and associated subunits gives rise to a diverse set of chromatin-remodeling complexes with cell- and tissue-specific functions. Chromatin-remodeling complexes facilitate the transcription of a group of genes while simultaneously inhibiting inappropriate expression of other genes to establish a specific cell identity.
Tissue-specific chromatin-remodeler subunits often form a unique complex that collaborates with lineage-specific transcription factors for recruitment to regulatory sites in the genome, where they remodel chromatin to favor transcription factor binding and regulate lineage-specific gene transcription.
Chromatin Remodeling BAF (SWI/SNF) Complexes
The ATP-dependent BRG1/BRM associated factor (BAF) chromatin remodeling complexes are crucial in regulating gene expression by controlling chromatin dynamics. During neural development in mammals, distinct ontogenetic stage-specific BAF complexes derived from combinatorial assembly of their subunits are formed in neural progenitors and post-mitotic neural cells. Proper functioning of the BAF complexes plays critical
roles in neural development, including the establishment and maintenance of neural fates and functionality. Indeed, human exome sequencing and genome-wide association studies have revealed that mutations in BAF complex subunits are linked to neurodevelopmental disorders, like schizophrenia - amongst many others.
The developmental processes that lead to formation of the central nervous system (CNS) are intricately regulated to ensure proper cellular architecture and functionality. Mammalian neural structures are functionally made up of neural cells that develop under strict molecular and cellular instructions to confer cell subtype differentiation. Highly ordered gene expression programs regulate the establishment of various cell fate status during neural development. Many factors, including epigenetic and chromatin regulators act in concert to determine and sustain cell-specific transcriptional programs. The establishment of specific epigenetic landscapes provides strong evidence that link chromatin state with gene expression profiles. Thus, regions of DNA compaction (heterochromatin) are transcription-repressed sites, whereas less compact or open regions (euchromatin) have active transcriptional activity. Chromatin regulators are capable of reordering chromatin state (heterochromatin/euchromatin) and hence are critical determinants of access to genomic loci by the transcriptional machinery . Consequently, a coordinated deployment of chromatin regulators, along with the recruitment of transcription factors, are essential for establishing gene expression patterns in response to various cellular cues and physiological states in health and disease.
8. Molecular biology of the Cell, 6th ed. page 405
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