InteractiveFly: GeneBrief

polybromo: Biological Overview | References

Gene name - polybromo

Synonyms -

Cytological map position - 96A22-96A23

Function - chromatin component

Keywords - polybromo encodes a subunit of Polybromo-associated Brahma complex (PBAP). It is involved in chromatin remodeling together with Brahma complex - regulates gene transcription through DNA binding, which is dependent or independent of the PBAP complex.

Symbol - polybromo

FlyBase ID: FBgn0039227

Genetic map position - chr3R:24,799,967-24,805,259

Classification - Bromodomain, HMG box, BAH or Bromo Adjacent Homology domain

Cellular location - nuclear

NCBI links: EntrezGene, Nucleotide, Protein

Polybromo orthologs: Biolitmine

To regenerate, damaged tissue must heal the wound, regrow to the proper size, replace the correct cell types, and return to the normal gene-expression program. However, the mechanisms that temporally and spatially control the activation or repression of important genes during regeneration are not fully understood. To determine the role that chromatin modifiers play in regulating gene expression after tissue damage, ablation was induced in Drosophila melanogaster imaginal wing discs, and a screen was carried out for chromatin regulators that are required for epithelial tissue regeneration. Many of these genes are shown to be important for promoting or constraining regeneration. Specifically, the two SWI/SNF chromatin-remodeling complexes play distinct roles in regulating different aspects of regeneration. The PBAP (see Polybromo) complex regulates regenerative growth and developmental timing, and is required for the expression of JNK signaling targets and the growth promoter Myc. By contrast, the BAP complex (see Osa) ensures correct patterning and cell fate by stabilizing the expression of the posterior gene engrailed. Thus, both SWI/SNF complexes are essential for proper gene expression during tissue regeneration, but they play distinct roles in regulating growth and cell fate (Tian, 2021).

Regeneration is a complex yet highly elegant process that some organisms can use to recognize, repair, and replace missing or damaged tissue. Imaginal disc repair in Drosophila is a good model system for understanding regeneration, due to the high capacity of these tissues to regrow and restore complex patterning, as well as the genetic tools available in this model organism. Regeneration requires the coordinated expression of genes that regulate the sensing of tissue damage, induction of regenerative growth, repatterning of the tissue, and coordination of regeneration with developmental timing. Initiation of regeneration in imaginal discs requires known signaling pathways such as the Reactive oxygen species (ROS), Jun N-terminal kinase (JNK), Wingless (Wg), p38, Janus kinase/signal transducer and activator of transcription (Jak/STAT), and Hippo pathways. These pathways activate many regeneration genes, such as the growth promoter Myc and the hormone-like peptide ilp8, which delays pupariation after imaginal disc damage. However, misregulation of these signals can impair regeneration. For example, elevated levels of JNK signaling can induce patterning defects in the posterior of the wing, and elevated ROS levels can suppress JNK activity and regenerative growth. While the signals that initiate regeneration have been extensively studied, regulation of regeneration gene expression in response to tissue damage is not fully understood (Tian, 2021).

Such regulation could occur through chromatin modification. In Drosophila, chromatin modifiers include the Polycomb repressive complexes PRC1 and PRC2, which can be recruited to specific locations by the Pho repressor complex (PhoRC), the activating complexes Trithorax acetylation complex (TAC1), Complex of proteins associated with Set1 (COMPASS) and COMPASS-like, the nucleosome remodeling complex (NURF), and the switch/sucrose non-fermentable (SWI/SNF) chromatin remodelers Brahma-associated proteins (BAP) and Polybromo-associated proteins (PBAP). PRC2 carries out trimethylation of histone H3 at lysine 27, recruiting PRC1 to repress transcription of nearby genes. COMPASS-like and COMPASS carry out histone H3 lysine 4 monomethylation and di- and trimethylation, respectively, thereby activating the expression of nearby genes. TAC1 acetylates histone H3 lysine 27, also supporting activation of gene transcription. NURF, BAP, and PBAP alter or move nucleosomes to facilitate binding of transcription factors and chromatin modifiers. Rapid changes in gene expression induced by these complexes may help facilitate a damaged tissue's regenerative response (Tian, 2021).

A few chromatin modifiers and histone modifications have been reported to be important for regulating regeneration of Xenopus tadpole tails, mouse pancreas and liver, zebrafish fins, and Drosophila imaginal discs. Furthermore, components of Drosophila and mouse SWI/SNF complexes regulate regeneration in the Drosophila midgut and mouse skin, liver, and ear. However, little is known about how these complexes alter gene expression, signaling, and cellular behavior to regulate regeneration. Importantly, genome-wide analysis of chromatin state after Drosophila imaginal disc damage revealed changes in chromatin around a large set of genes, including known regeneration genes . Thus, chromatin modifiers likely play a key role in regulating activation of the regeneration program. However, it is unclear whether all regeneration genes are coordinately regulated in the same manner, or whether specific chromatin modification complexes target different subsets of genes that respond to tissue damage (Tian, 2021).

To probe the role of chromatin modifiers in tissue regeneration systematically, a collection of pre-existing Drosophila mutants and RNAi lines targeting components of these complexes as well as other genes that regulate chromatin was collected, and these lines were screened for regeneration defects using the Drosophila wing imaginal disc. A spatially and temporally controllable tissue-ablation method was used that uses transgenic tools to induce tissue damage only in the wing primordium. This method ablates 94% of the wing primordium on average at the early third instar and allows the damaged wing discs to regenerate in situ. Previous genetic screens using this tissue ablation method have identified genes critical for regulating different aspects of regeneration, such as taranis, trithorax, and cap-n-collar, demonstrating its efficacy in finding regeneration genes (Tian, 2021).

Through this targeted genetic screen of chromatin regulators, it was found that mutations in Drosophila SWI/SNF components caused striking regeneration defects. The SWI/SNF complexes are conserved multi-subunit protein complexes that activate or repress gene expression by using the energy from ATP hydrolysis to disrupt histone-DNA contacts and remodel nucleosome structure and position. Brahma (Brm) is the only ATPase of the SWI/SNF complexes in Drosophila. Moira (Mor) serves as the core scaffold of the complexes. Other components contain domains involved in protein-protein interactions, protein-DNA interactions, or interactions with modified histones. There are two subtypes of SWI/SNF in Drosophila: the Brahma-associated proteins (BAP) and the Polybromo-associated BAP (PBAP) remodeling complexes. They share common core components, including Brm, Snf5-related 1 (Snr1), Mor, Brahma-associated protein 55kD (Bap55), Brahma-associated protein 60kD (Bap60), Brahma-associated protein 111kD (Bap111), and Actin, but contain different signature proteins. The PBAP complex is defined by the components Brahma-associated protein 170kD (Bap170), Polybromo, and Supporter of activation of yellow protein (Sayp) (Tian, 2021).

This study shows that the SWI/SNF complexes BAP and PBAP are required for regeneration, and that the two complexes play distinct roles. The PBAP complex is important for activation of JNK signaling targets such as ilp8 to delay metamorphosis and allow enough time for the damaged tissue to regrow, and for expression of Myc to drive regenerative growth. By contrast, the BAP complex functions to prevent changes in cell fate induced by tissue damage through stabilizing expression of the posterior identity gene engrailed. Thus, different aspects of the regeneration program are regulated independently by distinct chromatin regulators (Tian, 2021).

To address the question of how regeneration genes are regulated in response to tissue damage, a collection of mutants and RNAi lines were screened that affect a significant number of the chromatin regulators in Drosophila. Most of these mutants had regeneration phenotypes, confirming that these genes are important for both promoting and constraining regeneration and likely facilitate the shift from the normal developmental program to the regeneration program, and back again. The variation in regeneration phenotypes among different chromatin regulators and among components of the same multiunit complexes supports a previous finding that damage activates expression of genes that both promote and constrain regeneration. Such regulators of regeneration may be differentially affected by distinct mutations that affect the same chromatin-modifying complexes, resulting in different phenotypes (Tian, 2021).

This study has demonstrated that both Drosophila SWI/SNF complexes play essential but distinct roles during epithelial regeneration, controlling multiple aspects of the process, including growth, developmental timing, and cell fate. Furthermore, this work has identified multiple likely targets, including mmp1, Myc, ilp8, and en. Indeed, analysis of data from a recent study that identified regions of the genome that transition to open chromatin after imaginal disc damage showed such damage-responsive regions near Myc, mmp1, and ilp8. While previous work has suggested that chromatin modifiers can regulate regeneration, and that the chromatin near Drosophila regeneration genes is modified after damage, the results suggest that these damage-responsive loci are not all coordinately regulated in the same manner. The SWI/SNF complexes target different subsets of genes, and it will not be surprising if different cofactors or transcription factors recruit different complexes to other subsets of regeneration genes (Tian, 2021).

Is the requirement for the SWI/SNF complexes for growth and conservation of cell fate in the wing disc specific to regeneration? In contrast to tara, which is required for posterior wing fate only after damage and regeneration, loss of mor in homozygous clones during wing disc development caused loss of en expression in the posterior compartment, although this result was interpreted to mean that mor promotes rather than constrains en expression, which is the opposite of the current observations. Importantly, undamaged mor heterozygous mutant animals did not show patterning defects, while damaged heterozygous mutant animals did, indicating that regenerating tissue is more sensitive to reductions in SWI/SNF levels than normally developing tissue. Furthermore, osa is required for normal wing growth, but reduction of osa levels did not compromise growth during regeneration (Supplementary Figure S3, D-H), and instead led to enhanced regeneration. Thus, while some functions of SWI/SNF during regeneration may be the same as during development, other functions of SWI/SNF may be unique to regeneration (Tian, 2021).

SWI/SNF complexes help organisms respond rapidly to stressful conditions or changes in the environment. For example, SWI/SNF is recruited by the transcription factor DAF-16/FOXO to promote stress resistance in Caenorhabditis elegans, and the Drosophila BAP complex is required for the activation of target genes of the NF-κB signaling transcription factor Relish in immune responses. This study showed that the Drosophila PBAP complex is similarly required after tissue damage for activation of target genes of the JNK signaling transcription factor AP-1 after tissue damage. Interestingly, the BAF60a subunit, a mammalian homolog of Drosophila BAP60, directly binds the AP-1 transcription factor and stimulates the DNA-binding activity of AP-1, suggesting that this role may be conserved (Tian, 2021).

In summary, this study have demonstrated that the two SWI/SNF complexes regulate different aspects of wing imaginal disc regeneration, implying that activation of the regeneration program is controlled by changes in chromatin, but that the mechanism of regulation is likely different for subsets of regeneration genes. Future identification of all genes targeted by BAP and PBAP after tissue damage, the factors that recruit these chromatin-remodeling complexes, and the changes they induce at these loci will deepen our understanding of how unexpected or stressful conditions lead to rapid activation of the appropriate genes (Tian, 2021).

The Drosophila BEAF insulator protein interacts with the polybromo subunit of the PBAP chromatin remodeling complex
The Drosophila Boundary Element-Associated Factor of 32 kDa (BEAF) binds in promoter regions of a few thousand mostly housekeeping genes. This study shows that BEAF physically interacts with the polybromo subunit (Pbro) of PBAP, a SWI/SNF-class chromatin remodeling complex. BEAF also shows genetic interactions with Pbro and other PBAP subunits. The effect of this interaction on gene expression and chromatin structure was examined using precision run-on sequencing and micrococcal nuclease sequencing after RNAi-mediated knockdown in cultured S2 cells. The results are consistent with the interaction playing a subtle role in gene activation. Fewer than 5% of BEAF-associated genes were significantly affected after BEAF knockdown. Most were downregulated, accompanied by fill-in of the promoter nucleosome-depleted region and a slight upstream shift of the +1 nucleosome. Pbro knockdown caused downregulation of several hundred genes and showed a correlation with BEAF knockdown but a better correlation with promoter-proximal GAGA factor binding. Micrococcal nuclease sequencing supports that BEAF binds near housekeeping gene promoters while Pbro is more important at regulated genes. Yet there is a similar general but slight reduction of promoter-proximal pausing by RNA polymerase II and increase in nucleosome-depleted region nucleosome occupancy after knockdown of either protein. The possibility is discussed of redundant factors keeping BEAF-associated promoters active and masking the role of interactions between BEAF and the Pbro subunit of PBAP in S2 cells. Facilitates Chromatin Transcription (FACT) and Nucleosome Remodeling Factor (NURF) were identified as candidate redundant factors (McKowen, 2022).

Chromatin targeting of nuclear pore proteins induces chromatin decondensation

Nuclear pore complexes have emerged in recent years as chromatin-binding nuclear scaffolds, able to influence target gene expression. However, how nucleoporins (Nups) exert this control remains poorly understood. This study shows that ectopically tethering Drosophila Nups, especially Sec13, to chromatin is sufficient to induce chromatin decondensation. This decondensation is mediated through chromatin-remodeling complex PBAP, as PBAP is both robustly recruited by Sec13 and required for Sec13-induced decondensation. This phenomenon is not correlated with localization of the target locus to the nuclear periphery, but is correlated with robust recruitment of Nup Elys. Furthermore, this study identified a biochemical interaction between endogenous Sec13 and Elys with PBAP, and a role for endogenous Elys in global as well as gene-specific chromatin decompaction. Together, these findings reveal a functional role and mechanism for specific nuclear pore components in promoting an open chromatin state (Kuhn, 2019).

Functionally, several Nups were found to be required for the transcriptional output and regulation of at least a subset of their target genes. In metazoans, Nup targets include genes important for tissue-specific development, regulation of the cell cycle, and antiviral responses. One conserved regulatory mechanism that requires Nups is transcriptional memory, a process by which genes are marked as recently transcribed to allow more robust transcriptional responses to future activation. Loss-of-function studies have demonstrated that specific Nups are required for multiple molecular steps involved in transcription and transcriptional memory, including binding of poised RNA polymerase (RNAP) II, H3K4 methylation, chromatin remodeling, and formation of activation-induced genomic loops. However, while Nups have been shown to be required for these molecular events, it remains unclear which specific steps of the transcriptional or epigenetic processes Nups are sufficient to induce (Kuhn, 2019).

In Drosophila melanogaster, Nups such as Nup98, Sec13, and Nup62 have been detected at a large number of active genes via DNA adenine methyltransferase identification, chromatin immunoprecipitation (ChIP), and imaging studies. Depletion of Sec13 or Nup98 in fly culture cells or in salivary gland tissues has been shown to lead to more compact chromatin, decreased levels of active RNAP II, and reduced mRNA production at select target genes. Nup98 has been extensively implicated in maintaining transcriptional memory of its target genes in yeast, fly, and mammalian cells, and it has been recently reported that Nup98 is involved in stabilization of enhancer-promoter contacts of ecdysone-inducible genes. However, the molecular functions performed by other transcription-associated Nups such as Sec13 and Nup62 at Nup-chromatin contacts remain unknown. Additionally, many of the Nup-chromatin contacts can occur off-pore in the nuclear interior, as these Nups have been found to shuttle NPCs on and off and/or have distinct intranuclear pools. However, it remains unclear if gene regulatory functions of Nups are independent of nuclear localization (Kuhn, 2019).

To examine these functions and to identify which chromatin- or transcription-associated changes Nups are sufficient to induce, a gain-of-function approach was used. A tethering system was generated to create ectopic chromatin-binding sites of Sec13 and Nup62 in the genome of transgenic Drosophila strains. Using this system, it was observed that NPC component Sec13 consistently induces robust chromatin decondensation at multiple genomic locations. In dissecting the mechanism of this phenomenon, Nup Elys was implicated as the primary mediator of chromatin decompaction, and a robust interaction was identified of Sec13 and Elys with the ATP-dependent chromatin-remodeling complex polybromo-containing Brahma (Brm)-associated proteins (PBAP), as well as a role of Elys in endogenous chromatin decondensation. These findings suggest that promoting chromatin decondensation is a critical and previously underappreciated molecular function of specific Nups in the process of gene regulation (Kuhn, 2019).

The presented findings, combined with previous findings in the field demonstrating functional roles for Nups in regulating gene expression, lead to a model whereby certain Nups primarily influence chromatin state, which in turn can affect downstream gene expression. It is proposed that chromatin-bound Nups, such as Elys and Sec13, recruit factors associated with formation of open chromatin, specifically GAF and components of PBAP. This results in a permissive, open-chromatin state, which, in the right cellular contexts, may allow for binding of appropriate transcription factors, for RNAP II recruitment, and subsequently in an increase in downstream gene expression. Together, these results and model suggest a specific chromatin-decondensing function of certain Nups, particularly Elys, as an early step in the process of gene activation (Kuhn, 2019).

Evidence is provided that Nups facilitate chromatin decondensation. The resulting 'holes' in DNA stain that appear upon Nup tethering and the associated loss of IF signal from antibodies against both core histone H3 (Fig. 2, A and B) and histone modifications favor this notion. This interpretation is further supported by the observed recruitment and functional involvement of the chromatin-remodeling PBAP complex and by additional biochemical data showing global and gene-specific defects in nucleosome occupancy upon Elys depletion. Furthermore, the robust biochemical interaction between Nups and components of PBAP and the correlation between the amount of Brm recruitment by Nups and the level of observed decondensation at lacO 96C further suggest that Nups have the capacity to promote chromatin decondensation. One interesting outstanding question is whether these Nup-induced changes in chromatin structure can occur entirely de novo (or rapidly after Nup binding) or require the process of chromatin assembly during replication to take effect. The current experiments have not differentiated between these possibilities. Further experiments, perhaps in blocking replication and assaying for similar Nup functions, could differentiate between these mechanisms further. Regardless, the findings strongly support the function of Nups in regulating compaction states of chromatin, while the particular cell cycle stage and the dynamic time frame at which this process takes place remain to be elucidated (Kuhn, 2019).

As transcription and chromatin decompaction are intimately intertwined, it was of interest to know if the Nup-induced changes in chromatin were primary or secondary to transcriptional regulation. Increased transcription of the gene directly downstream from the lacO 96C integration, dan, was observed upon tethering of Sec13, which also promoted decondensation here. However, since Brm recruitment and chromatin decondensation appear to be much more robustly detected than the presence of RNAP II upon Sec13 tethering, it is believed that decondensation is likely the primary effect of Sec13 tethering, and increased gene expression a secondary consequence. This is supported by the fact that Nup62 is able to induce a small amount of detectable decondensation at 96C lacO, associated with low-level recruitment of Elys and Brm, but does not result in significant levels of RNAP II recruitment. Further evidence that the primary effect of Nup targeting is decondensation rather than transcriptional activation is the increased nucleosome occupancy at both Hph and B52 genes upon Elys knockdown, but a transcriptional change is detected only at Hph. The differential effect of Elys depletion on Hph and B52 transcription again suggests that the primary chromatin-associated role of certain Nups is to facilitate the step of chromatin decondensation (Kuhn, 2019).

Although this study found tethering of Sec13 to elicit chromatin decondensation in the ectopic context, the data suggest that Elys may be the Nup primarily responsible for facilitating decondensation. As discussed above, there is a striking correlation between levels of Elys recruitment and level of decondensation at multiple lacO loci, and endogenous Elys appears to interact much more robustly with components of PBAP in S2 cells than Sec13. Significantly, Elys depletion shows a defect in global genomic MNase digestion, whereas Sec13 depletion does not. The latter experiment also suggests that the role of Elys in chromatin decondensation is independent of NPC integrity, as both Elys and Sec13 (which is a core component of the Nup107-Nup160 complex) are required for nuclear pore assembly. Therefore, a lack of phenotype of Sec13 RNAi in the MNase assay suggests that the observed reduction in nucleosomal accessibility in Elys RNAi conditions does not stem from a defect in NPC assembly. This conclusion is supported by the previously published observation that inhibiting transport capabilities of the NPC with WGA treatment does not lead to chromatin decondensation defects. It is further hypothesize that since Elys exhibits a particularly robust genome-wide binding while Sec13 appears to bind fewer loci, Elys has a stronger and more detectable effect on global chromatin decompaction. It remains to be determined whether Sec13 and Elys share a subset of target genes, and whether chromatin-bound Sec13 co-functions with Elys in chromatin decompaction of such targets (Kuhn, 2019).

The data presented in this study provide functional and mechanistic evidence for the long-standing visual correlation between NPCs and open chromatin and validates the hypothesized relationship between them. Interestingly, previous genetic and proteomic experiments have reported interactions between the Caenorhabditis elegans homologue of Elys, MEL-28, and chromatin-remodeling complexes, including the SWI/SNF complex subunit SWSN-2.2, suggesting an evolutionarily conserved role for Elys in regulating chromatin state. Furthermore, genetic and physical interactions between yeast NPC components and the chromatin-remodeling RSC complex have also been reported. Elys is known to bind condensed postmitotic chromatin to nucleate NPC assembly during nuclear envelope reformation, and recent work has reported a defect in global postmitotic chromatin decompaction associated with depletion of Elys from chromatin (Aze, 2017). Thus, an intriguing possibility is that in addition to NPC assembly, postmitotic chromatin binding of Elys may also play a role in postmitotic chromatin decompaction through mechanisms similar to those described in this study. A role for Nups in facilitating the formation or maintenance of open chromatin is also consistent with the evolutionarily conserved phenomenon of viral genome integration into open/active chromatin regions that are associated with NPCs. Finally, the interaction of Nups with developmentally critical GAF and PBAP suggests that this relationship may be relevant to the establishment of tissue-specific open chromatin regions or the global genome decompaction during organismal development. It is possible that the potential role of Elys and possibly other Nups in postmitotic chromatin decondensation has extended to regulation of chromatin structure in the context of interphase transcription, thus contributing to regulation of developmental transcriptional programs (Kuhn, 2019).

Modular organization and assembly of SWI/SNF family chromatin remodeling complexes

Mammalian SWI/SNF (mSWI/SNF) ATP-dependent chromatin remodeling complexes are multi-subunit molecular machines that play vital roles in regulating genomic architecture and are frequently disrupted in human cancer and developmental disorders. To date, the modular organization and pathways of assembly of these chromatin regulators remain unknown, presenting a major barrier to structural and functional determination. This study elucidates the architecture and assembly pathway across three classes of mSWI/SNF complexes-canonical BRG1/BRM-associated factor (BAF), polybromo-associated BAF (PBAF), and newly defined ncBAF complexes-and define the requirement of each subunit for complex formation and stability. Using affinity purification of endogenous complexes from mammalian and Drosophila cells coupled with cross-linking mass spectrometry (CX-MS) and mutagenesis, three distinct and evolutionarily conserved modules, their organization, and the temporal incorporation of these modules into each complete mSWI/SNF complex class were uncovered. Finally, human disease-associated mutations were mapped within subunits and modules, defining specific topological regions that are affected upon subunit perturbation (Mashtalir, 2018).

ATP-dependent chromatin remodeling complexes are multimeric molecular assemblies that regulate chromatin architecture. These complexes are grouped into four major families, including switching (SWI)/sucrose fermentation (sucrose non-fermenting [SNF]), INO80, ISWI (imitation SWI), and CHD/M-2 (chromodomain helicase DNA-binding) groups), all of which contain Snf2-like ATPase subunits but differ substantially via the incorporation of distinct subunits and in their targeting and activity on chromatin (Mashtalir, 2018).

SWI/SNF complexes were originally discovered and characterized in yeast, later in Drosophila, and most recently in mammals. Mammalian SWI/SNF (mSWI/SNF) complexes are ∼1- to 1.5-MDa entities combinatorially assembled from the products of 29 genes, including multiple paralogs, generating extensive diversity in composition. All complexes contain an ATPase subunit, either SMARCA4 (BRG1) or SMARCA2 (BRM), that catalyzes the hydrolysis of ATP. The roles of most other accessory subunits in complex assembly and stability as well as targeting and function remain unknown (Mashtalir, 2018).

Over the past several years, mSWI/SNF complexes have emerged as a major focus of attention because of the striking mutational frequencies in the genes encoding their subunits across a range of human diseases, from cancer to neurologic disorders. Indeed, recent exome sequencing studies have revealed that over 20% of human cancers bear mutations in the genes encoding mSWI/SNF subunits. In addition, heterozygous point mutations in mSWI/SNF genes have been implicated as causative events in intellectual disability and autism spectrum disorders (Mashtalir, 2018).

A major barrier to understanding of the functions, tissue-specific roles, and effect of mutations on mSWI/SNF complex mechanisms lies in the lack of information regarding subunit organization, assembly, and 3D structure. Several factors pose major challenges to such studies. Individually expressed subunits are often unstable or incorrectly folded without their appropriate binding partners, and minimal complexes pieced together via in vitro co-expression may not represent endogenous, physiologically relevant complexes in cells. Large quantities of purified endogenous complexes with minimal heterogeneity are required for downstream analyses, and selection of appropriate purification strategies cannot be informed without understanding modular architecture and assembly order. For these reasons and others, to date only low-resolution maps have been achieved using cryoelectron microscopy (cryo-EM) approaches (Mashtalir, 2018).

To establish a comprehensive structural framework for mSWI/SNF complexes, this study used a multifaceted series of approaches involving complex and subcomplex purification, mass spectrometry (MS), crosslinking mass spectrometry (CX-MS), systematic genetic manipulation of subunits and subunit paralog families, evolutionary analyses, and human disease genetics. These studies reveal that mSWI/SNF complexes exist in three non-redundant final form assemblies: BRG1/BRM-associated factor complexes (BAFs), polybromo-associated BAF complexes (PBAFs), and non-canonical BAFs (ncBAFs), for which this study established the assembly requirements and modular organization. This study defines the full spectrum of endogenous combinatorial possibilities and the effect of individual subunit deletions and mutations, including recurrent, previously uncharacterized missense and nonsense mutations, on complex architecture. These studies provide important insights into mSWI/SNF complex organization, structure, and function and the biochemical consequences of a wide range of human disease-associated mutations (Mashtalir, 2018).

This study presents a comprehensive architectural framework for the mSWI/SNF chromatin remodeler complex family, including the assembly pathways and inter- and intra-module linkages across three distinct complexes. Integrating multiple complex purifications with size fractionation, mutagenesis, and cross-linking mass spectrometry, this study defined intra-complex modular architecture, stoichiometry, and evolutionary relationships and explored the effects of disease-associated mutations on complex architecture and assembly. One particularly unexpected result is that the initial core for all three mSWI/SNF family complexes is a heterotrimer consisting of two SMARCC subunits (as a dimer) and one SMARCD subunit. Although previous in vitro subunit co-purifications had suggested a 'minimal BAF complex' consisting of SMARCA4, SMARCC1, SMARCC2, and SMARCB1, this study found that neither complex assembly pathways nor cross-linking mass spectrometry profiles of full BAF or PBAF complexes implicated this tetramer as a physiologic core in mammalian cells. Indeed, these results may begin to explain the challenges that have been faced in obtaining high-resolution structural information on this complex and in using such minimal complexes for small molecule screening efforts. Importantly, the mSWI/SNF initial core is required for global complex stability and the interaction of the majority of subunits in all three mSWI/SNF complexes. Notably, the newly identified ncBAF complex assembles exclusively around a SMARCC1 and SMARCD1 initial core and lacks SMARCE1 and SMARCB1 subunits, indicating fundamental differences and/or compensation in biochemical activity (Mashtalir, 2018).

Interestingly, network modularity analyses of cross-linking mass spectrometry data place SMARCB1 in the ATPase module, whereas biochemical purification of SMARCB1 demonstrates its presence in the BAF core module. This suggests that SMARCB1 may be involved in functionally linking the core and ATPase modules, potentially modulating ATPase or remodeling activity. Indeed, SNF5 regulates the chromatin remodeling activity of the yeast complex. Although the SNF5 and SMARCB1 subunits are largely dispensable for complex integrity in both yeast and human settings, respectively, we observed that these orthologs exhibit different module associations in distantly related eukaryotes, suggesting that SMARCB1 may play a dynamic role in regulating SWI/SNF complex activity (Mashtalir, 2018).

ARID subunits (ARID1A, ARID1B, and ARID2) are among the most frequently mutated subunits in human disease. Importantly, this study found that ARID subunits are the major determinants of assembly pathway branching toward BAF or PBAF complexes. ARID subunits bind the BAF core module through the CBR regions on the C terminus and N terminus of ARID1 and ARID2, respectively, likely leading to the formation of a large interaction interface and forging a structurally essential bridge between the core and ATPase modules. SMARCD subunits in particular play a major role in ARID subunit binding as their loss substantially affects ARID and subsequent ATPase module assembly. The critical role for ARID subunits is further illustrated by their interaction with the ATPase module subunits SMARCA and ACTL6A. Finally, the absence of any ARID subunits in the newly identified ncBAF complex suggests an alternative, ARID-independent mode of binding the ATPase module (likely mediated by GLTSCR1 and GLTSCR1L subunits) (Mashtalir, 2018).

Assembly of multiprotein complexes often occurs in a directed modular manner with defined and evolutionarily conserved subcomplexes. Indeed, analysis of cross-linking mass spectrometry-identified linkages within SWI/SNF complexes of two other eukaryotic species reveals evolutionary conservation of the complex modularity identified in mammalian cells. The conserved structural properties of these complexes suggest separation and divergence of complex functions. Although the ATPase domain has been implicated in nucleosome sliding, the role of the other modules and subunits in both ATPase activity and nucleosome remodeling remains poorly understood. Extensive DNA binding surfaces, particularly on the BAF core module, may play critical roles in directing forces from the ATPase-nucleosome-DNA interaction. Further studies will be required to define the role of each subunit and domain in complex targeting and in the modulation of ATPase-driven nucleosome remodeling. Finally, the current findings suggest that BAF inter- and intra-modular interactions are altered by mutations found in many human cancers and other diseases and that these mutations disrupt the normal complex assembly pathway or subunit protein stability. A prime example of this lies in the extensively mutated ARID1A subunit, including both nonsense mutations and missense mutations that are disproportionately skewed to the C-terminal domain that we found is required for BAF complex binding (Mashtalir, 2018).

Taken together, these studies present new opportunities for structural and functional characterization of this family of mammalian chromatin remodeling complexes that exhibits outsized roles in human disease. Understanding the architecture and modular organization of mSWI/SNF complexes greatly potentiates the ability to assign density to subunits and modules using cryo-EM in efforts to achieve 3D structure, to link structure to binding and biochemical activity on chromatin, and to develop physiologically meaningful small-molecule screening strategies, collectively serving as a critical foundation in the quest to define mechanisms of mSWI/SNF-mediated chromatin remodeling in normal and disease states (Mashtalir, 2018).

The transcriptional coactivator SAYP is a trithorax group signature subunit of the PBAP chromatin remodeling complex

SWI/SNF ATP-dependent chromatin remodeling complexes (remodelers) perform critical functions in eukaryotic gene expression control. BAP and PBAP are the fly representatives of the two evolutionarily conserved major subclasses of SWI/SNF remodelers. Both complexes share seven core subunits, including the Brahma ATPase, but differ in a few signature subunits; POLYBROMO and BAP170 specify PBAP, whereas OSA defines BAP. This study shows that the transcriptional coactivator and PHD finger protein SAYP is a novel PBAP subunit. Biochemical analysis established that SAYP is tightly associated with PBAP but absent from BAP. SAYP, POLYBROMO, and BAP170 display an intimately overlapping distribution on larval salivary gland polytene chromosomes. Genome-wide expression analysis revealed that SAYP is critical for PBAP-dependent transcription. SAYP is required for normal development and interacts genetically with core- and PBAP-selective subunits. Genetic analysis suggested that, like BAP, PBAP also counteracts Polycomb silencing. SAYP appears to be a key architectural component required for the integrity and association of the PBAP-specific module. It is concluded that SAYP is a signature subunit that plays a major role in the functional specificity of the PBAP holoenzyme (Chalkley, 2008).

Gene expression control is one of the most fundamental biological processes and, to a large extent, occurs at the transcriptional level. The transcription of a single protein-encoding eukaryotic gene involves a stunning plethora of regulating factors comprising some 100 or so distinct polypeptides. These can be classified as sequence-specific DNA-binding transcription factors that initiate the recruitment of positive or negative coregulatory complexes and the basal transcription machinery. Coactivators include a variety of proteins performing distinct functions during the transcription cycle such as the opening up of chromatin structure, mediating posttranslational histone modifications or bridging between activators and the basal transcription machinery. It has become clear that the diversity among gene-specific activators and repressors is complemented by functional specification among coregulatory complexes and even the core transcription machinery. One important class of coregulators is formed by the ATP-dependent chromatin-remodeling factors (remodelers) (Chalkley, 2008).

Remodelers are large multisubunit complexes defined by the presence of an ATPase 'engine' subunit. These proteins act like DNA translocases and use the energy derived from ATP hydrolysis to change the DNA-histone contacts, thus remodeling chromatin structure. Based on the identity of their central ATPase, four major classes of remodelers have been recognized: SWI/SNF, ISWI, CHD/Mi2, and Ino80/Swr1 (Lall, 2007). Different remodelers are not exchangeable; rather, each executes unique biological functions. An early example of functional diversification was the finding that the Drosophila SWI/SNF class Brahma (BRM) remodelers, but not the ISWI remodelers, act as chromatin-specific coactivators for the transcription factor Zeste (Kal, 2000; Chalkley, 2008 and references therein).

SWI/SNF class remodelers perform broad yet gene-selective transcription regulatory functions during development, cell cycle control, and tumor suppression. There are two major SWI/SNF subclasses, conserved evolutionarily from yeast to humans. The first subclass includes yeast SWI/SNF (ySWI/SNF), fly BAP, and mammalian BAF, whereas the second subfamily includes yeast RSC, fly PBAP, and mammalian PBAF (Mohrmann, 2005). The corresponding multiprotein complexes are composed of highly related paralogs or identical subunits and a limited number of subclass-specific proteins. For example, Drosophila BAP and PBAP share seven core subunits, but each is defined by unique signature subunits: the BAP-specific OSA and the PBAP-specific POLYBROMO and BAP170. In this study the term SWI/SNF is used when making general statements that apply to both subcomplexes (Chalkley, 2008).

Previous structure-function dissection of fly SWI/SNF revealed that the common core subunits play architectural and enzymatic roles, whereas the signature subunits are key to the functional specificity of BAP and PBAP holoenzymes. In particular, BRM and MOR are critical for the structural integrity of both BAP and PBAP (Moshkin, 2007). Regulation of the majority of target genes required the signature subunit OSA, PB, or BAP170, suggesting that SWI/SNF remodelers function mostly as holoenzymes (Moshkin, 2007). BAP and PBAP regulate distinct but overlapping transcriptional circuitries, acting either independently, similarly, or antagonistically. Likewise, BAP and PBAP direct convergent as well as distinct biological processes. BAP, but not PBAP, is required for cell cycle progression through mitosis. BAP mediates G2/M transition through direct regulation of the cell cycle regulator string/cdc25. OSA is required for targeting BAP to the string/cdc25 promoter (Chalkley, 2008).

The genes encoding BRM, MOR, and OSA were originally discovered in screens for dominant suppressors of Polycomb (Pc) mutations and therefore were classified as trithorax group (trxG) proteins. The trxG of activators, together with their antagonists, the Pc group (PcG) of repressors, maintain correct expression of many developmental regulators. So far, no other core- or PBAP-selective subunits have been identified as trxG proteins. Thus, whether PBAP, like BAP, acts as a trxG suppressor of Pc remains unclear (Chalkley, 2008).

SAYP is a chromatin-associated transcriptional coactivator that was originally identified as the enhancer of yellow, e(y)3, gene (Shidlovskii, 2005). SAYP contains two PHD fingers, an AT hook and a highly conserved SAY domain that is essential for transcription coactivation. Analysis of mutants revealed that SAYP is essential for oogenesis and early development (Shidlovskii, 2005). However, the molecular functioning of SAYP remained completely unclear (Chalkley, 2008).

Because distinct SWI/SNF subunits each provide unique functionalities, the complete determination of the BAP and PBAP composition is an important objective. In this study PBAP was purified and the coactivator SAYP was identified as a novel subunit. SAYP was found to be an essential and distinctive subunit of PBAP, which is absent from BAP. A variety of genomic, biochemical, and genetic approaches were used to dissect the role of SAYP. It is concluded that the transcriptional coactivator SAYP is a novel signature subunit that is essential for the functional specificity of the PBAP holoenzyme (Chalkley, 2008).

This study shows that SAYP is a novel PBAP signature subunit. The human homologue of SAYP has been shown to be a subunit of PBAF. Moreover, genes homologous to sayp were identified in the genomes of sequenced metazoans, but no clear homologues were detected in, e.g., Neurospora spp., Saccharomyces cerevisiae, or Schizosaccharomyces pombe, suggesting that SAYP might be a metazoan-specific subunit (Chalkley, 2008).

Immunodepletion of a nuclear extract using antibodies directed against MOR led to the concomitant loss of SAYP in the unbound fraction. This result suggests that the majority of SAYP exists as part of the PBAP complex. Previous results have suggested that SWI/SNF subunits that are not incorporated in a complex are unstable and degraded. Moreover, this study established that particular subunits, e.g., MOR, are essential for the architectural integrity of BAP and PBAP. This analysis found that SAYP is required for the incorporation of BAP170 and POLYBROMO into PBAP. This relationship was not reciprocal: neither BAP170 nor POLYBROMO was required for SAYP assembly (Chalkley, 2008).

Whereas the BAP and PBAP signature modules require the core, removal of the PBAP signature subunits or OSA depletion did not affect the core complex. However, in the absence of the signature subunits, the SWI/SNF core alone turned out to be largely dysfunctional in global gene expression control. This finding highlights the interesting issue that untargeted chromatin remodeling, which can be mediated efficiently by the SWI/SNF core by itself does not suffice for transcription control. Therefore, it is suggested that SWI/SNF remodelers act as holoenzymes, in which the core subunits provide key architectural and enzymatic functions, but the signature subunits determine most of the transcriptional specificity (Chalkley, 2008).

Another interesting outcome from this analysis is that there is no evidence for BAP/PBAP hybrid complexes. Thus, the docking of OSA and the PBAP signature module appear to be mutually exclusive. Although there are likely to be additional sites of contact, SAYP appears to be particularly important for the stable association of POLYBROMO and BAP170 with the core complex. BAP170 stabilizes POLYBROMO binding (Moshkin, 2007). Most likely, there is a hierarchy of incorporation in which SAYP and OSA compete for an overlapping docking site within the core complex. The association of POLYBROMO and BAP170 is stabilized by SAYP but blocked by OSA, preventing the formation of hybrid complexes (Chalkley, 2008).

These results and earlier studies (Moshkin, 2007) demonstrate the value of epistasis analysis combined with whole-genome expression profiling for the structure-function analysis of multisubunit regulatory complexes. Principal component analysis (PCA) of gene expression profiles after BAP- or PBAP-selective depletion revealed that BAP and PBAP regulate distinct but overlapping transcriptional circuitries, acting either together, independently, or antagonistically. Likewise, BAP and PBAP execute related but also distinct biological functions. Previously, it was found that BAP, but not PBAP, controls cell cycle progression (Moshkin, 2007). BAP mediates G2/M transition through direct regulation of the cell cycle regulator string/cdc25. BAP recruitment to the stg/cdc25 promoter was critically dependent on OSA. In contrast, PBAP neither bound nor activated the stg/cdc25 promoter. Deciphering the role of SWI/SNF in cell proliferation and differentiation is of particular interest because of the association between SWI/SNF malfunction and human cancer. For example, the loss of the human homologue of SNR1, hSNF5, causes a defective cell cycle and the loss of ploidy control in malignant rhabdoid tumor cells (Chalkley, 2008).

Previously, the genes encoding the BAP-signature subunit OSA and two core subunits, BRM and MOR, were identified as trxG members because they act as dominant suppressors of Pc. However, it remained unclear whether PBAP also antagonizes Pc silencing. This study found that mutations in the genes coding for the PBAP signature subunits suppress the leg transformations caused by Pc mutations. Thus, both BAP and PBAP can be classified as trxG transcriptional coactivator complexes (Chalkley, 2008).

This study has also implicated PBAP in additional developmental control pathways. Mutations in genes encoding PBAP-specific subunits were shown to cause characteristic leg malformations and microcephaly, which are reminiscent of phenotypes caused by defective ecdysone signaling. These observations suggest that PBAP might be involved in ecdysone-inducible gene regulation in vivo. Previous in vitro results suggested that human PBAF is selectively required for ligand-dependent transactivation by nuclear hormone receptors (Lemon, 2001). Therefore, it will be interesting to investigate the role of BAP and PBAP in nuclear hormone receptors signaling during development (Chalkley, 2008).

In summary, BAP and PBAP are essential chromatin remodeling factors that perform cooperative and unique functions during development. Because distinct subunits appear to be dedicated to specific regulatory pathways, a complete structure-function analysis is required to gain insight into the roles of SWI/SNF remodelers in development and disease. This study has identified the coactivator SAYP as novel PBAP subunit. It is concluded that SAYP is a novel signature subunit that is essential for the functional specificity of the PBAP holoenzyme. Furthermore, this analysis of SWI/SNF remodelers has suggested that they are dedicated to specific transcriptional pathways, rather than acting as true general factors. Future studies will aim at dissecting the gene-selective functions of remodelers during development and disease (Chalkley, 2008).

Evidence for chromatin-remodeling complex PBAP-controlled maintenance of the Drosophila ovarian germline stem cells

In the Drosophila oogenesis, germline stem cells (GSCs) continuously self-renew and differentiate into daughter cells for consecutive germline lineage commitment. This developmental process has become an in vivo working platform for studying adult stem cell fate regulation. An increasing number of studies have shown that while concerted actions of extrinsic signals from the niche and intrinsic regulatory machineries control GSC self-renewal and germline differentiation, epigenetic regulation is implicated in the process. This study reports that Brahma (Brm), the ATPase subunit of the Drosophila SWI/SNF chromatin-remodeling complexes, is required for maintaining GSC fate. Removal or knockdown of Brm function in either germline or niche cells causes a GSC loss, but does not disrupt normal germline differentiation within the germarium evidenced at the molecular and morphological levels. There are two Drosophila SWI/SNF complexes: the Brm-associated protein (BAP) complex and the polybromo-containing BAP (PBAP) complex. More genetic studies reveal that mutations in polybromo/bap180, rather than gene encoding Osa, the BAP complex-specific subunit, elicit a defect in GSC maintenance reminiscent of the brm mutant phenotype. Further genetic interaction test suggests a functional association between brm and polybromo in controlling GSC self-renewal. Taken together, studies in this paper provide the first demonstration that Brm in the form of the PBAP complex functions in the GSC fate regulation (He, 2014).

Differential targeting of two distinct SWI/SNF-related Drosophila chromatin-remodeling complexes

The SWI/SNF family of ATP-dependent chromatin-remodeling factors plays a central role in eukaryotic transcriptional regulation. In yeast and human cells, two subclasses have been recognized: one comprises yeast SWI/SNF and human BAF, and the other includes yeast RSC and human PBAF. Therefore, it was puzzling that Drosophila appeared to contain only a single SWI/SNF-type remodeler, the Brahma (BRM) complex. This study reports the identification of two novel BRM complex-associated proteins: Drosophila Polybromo and BAP170, a conserved protein not described previously. Biochemical analysis established that Drosophila contains two distinct BRM complexes: (1) the BAP complex, defined by the presence of Osa and the absence of Polybromo and BAP170, and (2) the PBAP complex, containing Polybromo and BAP170 but lacking Osa. Determination of the genome-wide distributions of Osa and Polybromo on larval salivary gland polytene chromosomes revealed that BAP and PBAP display overlapping but distinct distribution patterns. Both complexes associate predominantly with regions of open, hyperacetylated chromatin but are largely excluded from Polycomb-bound repressive chromatin. It is concluded that, like yeast and human cells, Drosophila cells express two distinct subclasses of the SWI/SNF family. These results support a close reciprocity of chromatin regulation by ATP-dependent remodelers and histone-modifying enzymes (Mohrmann, 2004).

Functions of Polybromo orthologs in other species

de Castro, R. O., Previato de Almeida, L., Carbajal, A., Gryniuk, I. and Pezza, R. J. (2022). PBAF chromatin remodeler complexes that mediate meiotic transitions in mouse. Development 149(18). PubMed ID: 36111709

Gametogenesis in mammals encompasses highly regulated developmental transitions. These are associated with changes in transcription that cause characteristic patterns of gene expression observed during distinct stages of gamete development, which include specific activities with critical meiotic functions. SWI/SNF chromatin remodelers are recognized regulators of gene transcription and DNA repair, but their composition and functions in meiosis are poorly understood. We have generated gamete-specific conditional knockout mice for ARID2, a specific regulatory subunit of PBAF, and have compared its phenotype with BRG1 knockouts, the catalytic subunit of PBAF/BAF complexes. While Brg1Delta/Delta knockout acts at an early stage of meiosis and causes cell arrest at pachynema, ARID2 activity is apparently required at the end of prophase I. Striking defects in spindle assembly and chromosome-spindle attachment observed in Arid2Delta/Delta knockouts are attributed to an increase in aurora B kinase, a master regulator of chromosome segregation, at centromeres. Further genetic and biochemical analyses suggest the formation of a canonical PBAF and a BRG1-independent complex containing ARID2 and PBRM1 as core components. The data support a model in which different PBAF complexes regulate different stages of meiosis and gametogenesis (de Castro, 2022).

PBRM1 Deficiency Confers Synthetic Lethality to DNA Repair Inhibitors in Cancer

Inactivation of Polybromo 1 (PBRM1), a specific subunit of the PBAF chromatin remodeling complex, occurs frequently in cancer, including 40% of clear cell renal cell carcinomas (ccRCC). To identify novel therapeutic approaches to targeting PBRM1-defective cancers, a series of orthogonal functional genomic screens was used that identified PARP and ATR inhibitors as being synthetic lethal with PBRM1 deficiency. The PBRM1/PARP inhibitor synthetic lethality was recapitulated using several clinical PARP inhibitors in a series of in vitro model systems and in vivo in a xenograft model of ccRCC. In the absence of exogenous DNA damage, PBRM1-defective cells exhibited elevated levels of replication stress, micronuclei, and R-loops. PARP inhibitor exposure exacerbated these phenotypes. Quantitative mass spectrometry revealed that multiple R-loop processing factors were downregulated in PBRM1-defective tumor cells. Exogenous expression of the R-loop resolution enzyme RNase H1 reversed the sensitivity of PBRM1-deficient cells to PARP inhibitors, suggesting that excessive levels of R-loops could be a cause of this synthetic lethality. PARP and ATR inhibitors also induced cyclic GMP-AMP synthase/stimulator of interferon genes (cGAS/STING) innate immune signaling in PBRM1-defective tumor cells. Overall, these findings provide the preclinical basis for using PARP inhibitors in PBRM1-defective cancers. This study demonstrates that PARP and ATR inhibitors are synthetic lethal with the loss of PBRM1, a PBAF-specific subunit, thus providing the rationale for assessing these inhibitors in patients with PBRM1-defective cancer (Chabanon, 2021).

CHD7 cooperates with PBAF to control multipotent neural crest formation

Heterozygous mutations in the gene encoding the CHD (chromodomain helicase DNA-binding domain) member CHD7, an ATP-dependent chromatin remodeller homologous to the Drosophila trithorax-group protein Kismet, result in a complex constellation of congenital anomalies called CHARGE syndrome, which is a sporadic, autosomal dominant disorder characterized by malformations of the craniofacial structures, peripheral nervous system, ears, eyes and heart. Although it was postulated 25 years ago that CHARGE syndrome results from the abnormal development of the neural crest, this hypothesis remained untested. This study shows that, in both humans and Xenopus, CHD7 is essential for the formation of multipotent migratory neural crest (NC), a transient cell population that is ectodermal in origin but undergoes a major transcriptional reprogramming event to acquire a remarkably broad differentiation potential and ability to migrate throughout the body, giving rise to craniofacial bones and cartilages, the peripheral nervous system, pigmentation and cardiac structures. CHD7 is essential for activation of the NC transcriptional circuitry, including Sox9, Twist and Slug. In Xenopus embryos, knockdown of Chd7 or overexpression of its catalytically inactive form recapitulates all major features of CHARGE syndrome. In human NC cells CHD7 associates with PBAF (polybromo- and BRG1-associated factor-containing complex) and both remodellers occupy a NC-specific distal SOX9 enhancer and a conserved genomic element located upstream of the TWIST1 gene. Consistently, during embryogenesis CHD7 and PBAF cooperate to promote NC gene expression and cell migration. This work identifies an evolutionarily conserved role for CHD7 in orchestrating NC gene expression programs, provides insights into the synergistic control of distal elements by chromatin remodellers, illuminates the patho-embryology of CHARGE syndrome, and suggests a broader function for CHD7 in the regulation of cell motility (Bajpai, 2010).


Search PubMed for articles about Drosophila Polybromo

Aze, A., Fragkos, M., Bocquet, S., Cau, J. and Mechali, M. (2017). RNAs coordinate nuclear envelope assembly and DNA replication through ELYS recruitment to chromatin. Nat Commun 8(1): 2130. PubMed ID: 29242643

Bajpai, R., Chen, D. A., Rada-Iglesias, A., Zhang, J., Xiong, Y., Helms, J., Chang, C. P., Zhao, Y., Swigut, T. and Wysocka, J. (2010). CHD7 cooperates with PBAF to control multipotent neural crest formation. Nature 463(7283): 958-962. PubMed ID: 20130577

Chabanon, R. M., Morel, D., Eychenne, T., Colmet-Daage, L., Bajrami, I., Dorvault, N., Garrido, M., Meisenberg, C., Lamb, A., Ngo, C., Hopkins, S. R., Roumeliotis, T. I., Jouny, S., Henon, C., Kawai-Kawachi, A., Astier, C., Konde, A., Del Nery, E., Massard, C., Pettitt, S. J., Margueron, R., Choudhary, J. S., Almouzni, G., Soria, J. C., Deutsch, E., Downs, J. A., Lord, C. J. and Postel-Vinay, S. (2021). PBRM1 Deficiency Confers Synthetic Lethality to DNA Repair Inhibitors in Cancer. Cancer Res 81(11): 2888-2902. PubMed ID: 33888468

Chalkley, G. E., et al. (2008). The transcriptional coactivator SAYP is a trithorax group signature subunit of the PBAP chromatin remodeling complex. Mol Cell Biol. 28: 2920-2929. PubMed ID: 18299390

He, J., Xuan, T., Xin, T., An, H., Wang, J., Zhao, G. and Li, M. (2014). Evidence for chromatin-remodeling complex PBAP-controlled maintenance of the Drosophila ovarian germline stem cells. PLoS One 9(7): e103473. PubMed ID: 25068272

Kuhn, T. M., Pascual-Garcia, P., Gozalo, A., Little, S. C. and Capelson, M. (2019). Chromatin targeting of nuclear pore proteins induces chromatin decondensation. J Cell Biol. PubMed ID: 31366666

Mashtalir, N., D'Avino, A. R., Michel, B. C., Luo, J., Pan, J., Otto, J. E., Zullow, H. J., McKenzie, Z. M., Kubiak, R. L., St Pierre, R., Valencia, A. M., Poynter, S. J., Cassel, S. H., Ranish, J. A. and Kadoch, C. (2018). Modular organization and assembly of SWI/SNF family chromatin remodeling complexes. Cell 175(5): 1272-1288. PubMed ID: 30343899

McKowen, J. K., Avva, S., Maharjan, M., Duarte, F. M., Tome, J. M., Judd, J., Wood, J. L., Negedu, S., Dong, Y., Lis, J. T. and Hart, C. M. (2022), The Drosophila BEAF insulator protein interacts with the polybromo subunit of the PBAP chromatin remodeling complex. G3 (Bethesda) 12(11). PubMed ID: 36029240

Mohrmann, L., Langenberg, K., Krijgsveld, J., Kal, A. J., Heck, A. J. and Verrijzer, C. P. (2004). Differential targeting of two distinct SWI/SNF-related Drosophila chromatin-remodeling complexes. Mol Cell Biol 24(8): 3077-3088. PubMed ID: 15060132

Bajpai, R., Chen, D. A., Rada-Iglesias, A., Zhang, J., Xiong, Y., Helms, J., Chang, C. P., Zhao, Y., Swigut, T. and Wysocka, J. (2010). CHD7 cooperates with PBAF to control multipotent neural crest formation. Nature 463(7283): 958-962. PubMed ID: 20130577

Tian, Y. and Smith-Bolton, R. K. (2021). Regulation of growth and cell fate during tissue regeneration by the two SWI/SNF chromatin-remodeling complexes of Drosophila. Genetics 217(1): 1-16. PubMed ID: 33683366

Biological Overview

date revised: 20 April 2023

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