Chromatin Remodeling Machinery Research Articles

Purine-Rich Element Binding Protein Alpha, a Nuclear Matrix Protein, Has a Role in Prostate Cancer Progression.

Solid tumors as well as leukemias and lymphomas show striking changes in nuclear structure including nuclear size and shape, the number and size of nucleoli, and chromatin texture. These alterations have been used in cancer diagnosis and might be related to the altered functional properties of cancer cells. The nuclear matrix (NM) represents the structural composition of the nucleus and consists of nuclear lamins and pore complexes, an internal ribonucleic protein network, and residual nucleoli. In the nuclear microenvironment, the NM is associated with multi-protein complexes, such as basal transcription factors, signaling proteins, histone-modifying factors, and chromatin remodeling machinery directly or indirectly through scaffolding proteins. Therefore, alterations in the composition of NM could result in altered DNA topology and changes in the interaction of various genes, which could then participate in a cascade of the cancer process. Using an androgen-sensitive prostate cancer cell line, LNCaP, and its androgen-independent derivative, LN96, conventional 2D-proteomic analysis of the NM proteins revealed that purine-rich element binding protein alpha (PURα) was detected in the NM proteins and differentially expressed between the cell lines. In this article, we will review the potential role of the molecule in prostate cancer.

Stress-Induced AMPK Interactome Analysis Reveals Novel Protein-Protein Interactions Associated with Chromatin Remodeling and Transcription Machinery in Acute Lymphoblastic Leukemia

Acute lymphoblastic leukemia (ALL) is a leading cause of cancer-related death among children, adolescents and young adults. Survival rates for relapsed/refractory ALL remain dismal. We have previously reported that ALL cells are vulnerable to energy/metabolic stress conditions following AMP-activated protein kinase (AMPK) activation, leading to cell death. AMPK is the master metabolic regulator, and our lab and others have reported it interacts with chromatin-associated proteins to epigenetically regulate gene expression in response to energy/metabolic stress. To identify genome-wide genes regulated by direct association of AMPK to chromatin in response to energy/metabolic stress, we previously used ChIP-seq and RNA-seq in Bp-ALL (KASUMI-2) and T-ALL (KE-37) cells treated with or without glucose or AICAR, a well-known AMPK activator, and found that (i) AMPK interacts with components of the transcription machinery including the TATA-Box Binding Protein Associated Factor (TAF) and RNA polymerase II, (ii) AMPKα2 was enriched for genes involved in histone H3-K4 methylation, protein localization, Notch signaling, and mRNA destabilization, (iii) AMPKa2 was recruited to promoter regions of the epigenetic regulators KMT2A and SETD1A, and (iv) the mRNA expression of KMT2A and SETD1A genes was upregulated in KASUMI-2 cells treated with AICAR. To further investigate AMPK's involvement in epigenetic mechanisms in response to energy/metabolic stress, we performed a comprehensive interactome analysis using TurboID-based proximity labeling proteomics. AMPK is a highly conserved heterotrimeric kinase complex composed of catalytic α-subunit (α1 or α2) and regulatory β (β1 or β2) and γ (γ1, γ2, or γ3) subunits. We generated HEK293T cells stably expressing TurboID fused to the AMPKα1, AMPKα2, AMPKβ1 or AMPKγ1 (which are the most abundant AMPK subunits expressed in ALL cells), and these stable cell lines were treated with the potent allosteric AMPK activator PF-06409577 for 1 hr, to mimic the cell's rapid response to energy/metabolic stress. Following characterization of these stable cell lines and small-scale optimization experiments, treated samples and controls were submitted to mass spectrometry analysis. Proteomics data analysis identified novel AMPK's protein-protein interactions (PPI) which were altered (enhanced or reduced) following PF-06409577 treatment. Among PPI altered by PF-06409577 treatment, 148 were enhanced and 144 reduced for AMPKα1, 169 enhanced and 172 reduced for AMPKα2, 250 enhanced and 188 reduced for AMPKβ1 and 289 enhanced and 153 reduced for AMPKγ1. For proteomics data visualization we used Cytoscape software. The GO analysis of proteins interacting with AMPKα1β1γ1 and/or AMPKα2β1γ1 heterotrimeric complexes in cells treated with PF-06409577 showed that energy/metabolic stress enhances their interaction with proteins involved in gene expression, cellular metabolic processes, chromatin organization, DNA repair, histone modifications, etc.. Using the STRING database, we performed MCL clustering analysis and uncovered a major cluster of known epigenetic regulators (e.g., histone modifiers such as KDM6A, HDAC2, SETD2, KMT2A and SETD1A etc.) and components of the transcription machinery (such as NELFE, POLR2A etc.) that interacted with AMPK under stress-induced conditions. These data support our previous findings uncovered by ChIP-seq and RNA-seq analysis. Consequently, our findings further validate an epigenetic role for AMPK via interactions with putative members of chromatin-associated and transcription machinery complexes and chromatin modifying enzymes that allow ALL cells to respond to conditions of energy/metabolic stress. To our knowledge, this is the first report describing the AMPK interactome in pediatric ALL. Further elucidation of the uncovered protein-protein interactions may lead to potential epigenetic-based targeted therapies to overcome therapeutic resistance in relapse/refractory ALL and other hematological malignancies.

Abstract 18399: Loss of Myeloid Epigenetic-Metabolic Crosstalk by BAF60a Deficiency Aggravates Atherosclerosis

Introduction: Atherosclerosis is a primary medical concern, characterized by the involvement of immune cells within atherosclerotic plaques. Notably, the modulation of gene expression through chromatin remodeling and transcription machinery, known to be disrupted in disease conditions, is less studied in macrophages within atherosclerotic plaques. Hypothesis: We propose that BAF60a , a component of the SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex, might be instrumental in atherosclerosis by modulating disease-specific epigenetic-metabolic crosstalk, offering a potential therapeutic avenue. Methods: To evaluate our hypothesis, we assessed BAF60a expression in macrophages derived from advanced plaques. To decipher its role, myeloid Baf60a was deleted in mice with hypercholesterolemic ApoE deficient backgrounds. Subsequent changes in atherosclerotic lesion size, mitochondrial integrity, cellular adhesion, and apoptosis were characterized. ChIP-seq and ATAC-seq were employed to analyze the function of BAF60 a in maintaining key transcription factor activities. Results: Our results revealed a marked downregulation of BAF60a in macrophages from advanced plaques. Upon myeloid Baf60a deletion, we observed compromised mitochondrial integrity, increased cellular adhesion, enhanced apoptosis, and amplified plaque formation. Importantly, BAF60a was crucial in preserving mitochondrial energy homeostasis in the face of pro-atherogenic stimuli, as it sustained Nuclear Respiratory Factor 1 ( NRF1 ) access to critical genes. BAF60a overexpression rescued these defects in an NRF1-dependent manner. Conclusions: We conclude that the BAF60a-NRF1 axis is a key regulator of mitochondrial function in atherosclerosis. Our study underscores the potential of restoring the disrupted epigenetic-metabolic crosstalk as a promising therapeutic strategy in treating atherosclerosis.

Myeloid BAF60a deficiency alters metabolic homeostasis and exacerbates atherosclerosis

Atherosclerosis, a leading health concern, stems from the dynamic involvement of immune cells in vascular plaques. Despite its significance, the interplay between chromatin remodeling and transcriptional regulation in plaque macrophages is understudied. We discovered the reduced expression of Baf60a, a component of the switch/sucrose non-fermentable (SWI/SNF) chromatin remodeling complex, in macrophages from advanced plaques. Myeloid-specific Baf60a deletion compromised mitochondrial integrity and heightened adhesion, apoptosis, and plaque development. BAF60a preserves mitochondrial energy homeostasis under pro-atherogenic stimuli by retaining nuclear respiratory factor 1 (NRF1) accessibility at critical genes. Overexpression of BAF60a rescued mitochondrial dysfunction in an NRF1-dependent manner. This study illuminates the BAF60a-NRF1 axis as a mitochondrial function modulator in atherosclerosis, proposing the rejuvenation of perturbed chromatin remodeling machinery as a potential therapeutic target.

The Emerging Role of Chromatin Remodeling Complexes in Ovarian Cancer.

Ovarian cancer (OC) is the fifth leading cause of women's death from cancers. The high mortality rate is attributed to the late presence of the disease and the lack of modern diagnostic tools, including molecular biomarkers. Moreover, OC is a highly heterogeneous disease, which contributes to early treatment failure. Thus, exploring OC molecular mechanisms could significantly enhance our understanding of the disease and provide new treatment options. Chromatin remodeling complexes (CRCs) are ATP-dependent molecular machines responsible for chromatin reorganization and involved in many DNA-related processes, including transcriptional regulation, replication, and reparation. Dysregulation of chromatin remodeling machinery may be related to cancer development and chemoresistance in OC. Some forms of OC and other gynecologic diseases have been associated with mutations in specific CRC genes. Most notably, ARID1A in endometriosis-related OC, SMARCA4, and SMARCB1 in hypercalcemic type small cell ovarian carcinoma (SCCOHT), ACTL6A, CHRAC1, RSF1 amplification in high-grade serous OC. Here we review the available literature on CRCs' involvement in OC to improve our understanding of its development and investigate CRCs as possible biomarkers and treatment targets for OC.

Transcriptional Factors and Epigenetic Mechanisms in Obesity and Related Metabolic Comorbidities

Recent advances in the study of chromatin remodeling and transcriptional machinery complex dysfunction, and how they drive metabolic-related gene expression have considerably increased our understanding of several molecular processes underlaying obesity and its complications [...].

Research advances in the plant TCP transcription factors

<p indent="0mm">Transcription factors (TFs) are a group of protein molecules that can bind to a specific gene with a specific sequence specificity, thus ensuring that the target gene is expressed at a specific time and in space at a specific intensity. The plant-specific TFs of the TCP family (for Teosinte branched 1 in corn, CYCLOIDEA (CYC) in snapdragon (<italic>Antirrhinum majus</italic>) and PROLIFERATING CELL FACTOR 1/2 in rice) are characterized by an N-terminal non-canonical beta helix-loop-helix (bHLH) domain known as the TCP domain, and regulate the spatiotemporal expression of genes by binding to specific promoter sequences. TCP TFs play important roles in regulating the development of roots, stems, leaves, flowers, fruits, and vascular tissues, and participate in physiological processes such as plant secondary metabolism, plant immunity, and the responses to biotic and abiotic stress. The TCP TF family is conserved and widespread in plants. Based on the TCP domain sequence, TCP TFs are categorized into Class I and Class II; based on the amino acid sequence of the basic region and bHLH domain, the Class II TCP TFs can be further divided into CINCINNATA (CIN)-like TCPs (CIN) and CYC-like TCPs (CYC-C). In recent years, increasing numbers of studies have shed light on how TCP TFs regulate plant growth and development, especially on the functions of upstream regulators and downstream target genes. Plants have evolved multiple ways to accurately regulate their downstream related factors, and their own gene expression is also strictly regulated. TCP genes have also been analyzed in various plants and found to take part in the regulation of circadian rhythms and the biosynthesis and signaling pathways of plant hormones, among other functions. Other studies have investigated the regulatory relationships between TCP TFs and microRNAs. Additionally, members of the TCP family are often functionally redundant, making it difficult to study their functions; therefore, gene-editing technology and high-throughput sequencing have opened up new avenues to study this TF family. Here, we summarize recent advances in our understanding of how TCP activity is translated to the dynamic spatiotemporal control of cell-fate determination, life-cycle transitions, dormancy release, seed germination, leaf development, outgrowth of shoot branches, growth-repressing microRNAs, and interactions with the chromatin remodeling machinery to modulate phytohormone responses. Furthermore, we discuss existing problems and future directions in TCP research, in particular the role of TCP-related protein modification in plant growth and development and stress responses. Finally, we provide perspectives on the future research that is needed to gain a deep understanding of the diverse regulatory networks of TCP TFs in plant growth and development.

Abstract 2962: The oncogenic role of epigenetic factor, SNF2L in PCa

Abstract Prostate cancer (PCa) is the second-leading cause of cancer mortality in the United States and is the most commonly diagnosed malignancy in African American men. Epigenetic regulation including chromatin remodeling plays a crucial role in the development and progression of many human diseases such as cancers. Epigenetic alterations contribute to the development and progression of PCa. These alterations may cause drug resistance to readily available treatment options for human cancers including PCa. Nucleosome-remodeling factor (NURF) consists of bromodomain-PHD finger transcription factor (BPTF), sucrose non-fermenting-2-like (SNF2L), and pRBAP46/48, controls the chromatin remodeling machinery. One of NURF’s major function is to regulate histone modifications and gene expression. Epigenetic factor, SNF2L, serves as the energy transducing subunit in NURF and is encoded by the SMARCA1 gene. SNF2L is a ubiquitously expressed transcription activator and its elevation is associated with cancer development. However, the role of SNF2L on PCa progression is still elusive. Therefore, there are unmet needs to understand the role of SNF2L in PCa in order to develop effective therapeutic approaches of controlling this malignancy. The objective of this project is to assess the impact of SNF2L loss on PCa progression. We hypothesized that SNF2L knockout (KO) will inhibit the proliferation of androgen-sensitive and castration-resistant PCa cells and targeting SNF2L or SMARCA-1 gene may be beneficial for controlling cancer progression. We have generated SNF2L KO PCa cells with CRISPR-Cas9 technology and inhibited SMARCA-1 gene via transient transfection application. Our results showed that SNF2L loss resulted in a reduced proliferation and altered morphology of PCa cells. SNF2L KO destabilizes the NURF complex and impairs chromatin remodeling and histone modifications for cell growth and survival. Thereby, targeting SNF2L may serve as a novel therapeutic regime in PCa control. Citation Format: LaKendria K. Brown, Guoliang Li, Thanigaivelan Kanagasabai, Zhenbang Chen. The oncogenic role of epigenetic factor, SNF2L in PCa [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2962.

Deciphering Molecular Mechanisms Involved in Salinity Tolerance in Guar (Cyamopsis tetragonoloba (L.) Taub.) Using Transcriptome Analyses.

Guar is a commercially important legume crop known for guar gum. Guar is tolerant to various abiotic stresses, but the mechanisms involved in its salinity tolerance are not well established. This study aimed to understand molecular mechanisms of salinity tolerance in guar. RNA sequencing (RNA-Seq) was employed to study the leaf and root transcriptomes of salt-tolerant (Matador) and salt-sensitive (PI 340261) guar genotypes under control and salinity. Our analyses identified a total of 296,114 unigenes assembled from 527 million clean reads. Transcriptome analysis revealed that the gene expression differences were more pronounced between salinity treatments than between genotypes. Differentially expressed genes associated with stress-signaling pathways, transporters, chromatin remodeling, microRNA biogenesis, and translational machinery play critical roles in guar salinity tolerance. Genes associated with several transporter families that were differentially expressed during salinity included ABC, MFS, GPH, and P-ATPase. Furthermore, genes encoding transcription factors/regulators belonging to several families, including SNF2, C2H2, bHLH, C3H, and MYB were differentially expressed in response to salinity. This study revealed the importance of various biological pathways during salinity stress and identified several candidate genes that may be used to develop salt-tolerant guar genotypes that might be suitable for cultivation in marginal soils with moderate to high salinity or using degraded water.

Steroid receptor-coregulator transcriptional complexes: new insights from CryoEM.

Steroid receptors activate gene transcription through recruitment of a number of coregulators to facilitate histone modification, chromatin remodeling, and general transcription machinery stabilization. Understanding the structures of full-length steroid receptor and coregulatory complexes has been difficult due to their large molecular sizes and dynamic structural conformations. Recent developments in cryo-electron microscopy (cryoEM) technology and proteomics have advanced the structural studies of steroid receptor complexes. Here, we will review the insights we learned from cryoEM studies of the estrogen and androgen receptor transcriptional complexes. Despite similar domain organizations, the two receptors have different coregulator interaction modes. The cryoEM structures now have revealed the fundamental differences between the two receptors and their functional mechanisms.

Damage-induced chromatome dynamics link Ubiquitin ligase and proteasome recruitment to histone loss and efficient DNA repair

Eukaryotic cells package their genomes around histone octamers. In response to DNA damage, checkpoint activation in yeast induces core histone degradation resulting in 20%-40% reduction in nucleosome occupancy. To gain insight into this process, we developed a new approach to analyze the chromatin-associated proteome comprehensively before and after damage. This revealed extensive changes in protein composition after Zeocin-induced damage. First, core histones and the H1 homolog Hho1 were partially lost from chromatin along with replication, transcription, and chromatin remodeling machineries, while ubiquitin ligases and the proteasome were recruited. We found that the checkpoint- and INO80C-dependent recruitment of five ubiquitin-conjugating factors (Rad6, Bre1, Pep5, Ufd4, and Rsp5) contributes to core and linker histone depletion, reducing chromatin compaction and enhancing DNA locus mobility. Importantly, loss of Rad6/Bre1, Ufd4/TRIP12, and Pep5/VPS11 compromise DNA strand invasion kinetics during homology-driven repair. Thus we provide a comprehensive overview of a functionally relevant genome-wide chromatin response to DNA damage.

Epigenetic Targets for Oligonucleotide Therapies of Pulmonary Arterial Hypertension.

Arterial wall remodeling underlies increased pulmonary vascular resistance and right heart failure in pulmonary arterial hypertension (PAH). None of the established vasodilator drug therapies for PAH prevents or reverse established arterial wall thickening, stiffening, and hypercontractility. Therefore, new approaches are needed to achieve long-acting prevention and reversal of occlusive pulmonary vascular remodeling. Several promising new drug classes are emerging from a better understanding of pulmonary vascular gene expression programs. In this review, potential epigenetic targets for small molecules and oligonucleotides will be described. Most are in preclinical studies aimed at modifying the growth of vascular wall cells in vitro or normalizing vascular remodeling in PAH animal models. Initial success with lung-directed delivery of oligonucleotides targeting microRNAs suggests other epigenetic mechanisms might also be suitable drug targets. Those targets include DNA methylation, proteins of the chromatin remodeling machinery, and long noncoding RNAs, all of which act as epigenetic regulators of vascular wall structure and function. The progress in testing small molecules and oligonucleotide-based drugs in PAH models is summarized.

Toxoplasma gondii AP2XII-2 Contributes to Proper Progression through S-Phase of the Cell Cycle.

Toxoplasma gondii is a protozoan parasite that causes lifelong chronic infection that can reactivate in immunocompromised individuals. Upon infection, the replicative stage (tachyzoite) converts into a latent tissue cyst stage (bradyzoite). Like other apicomplexans, T. gondii possesses an extensive lineage of proteins called ApiAP2s that contain DNA-binding domains first characterized in plants. The function of most ApiAP2s is unknown. We previously found that AP2IX-4 is a cell cycle-regulated ApiAP2 expressed only in dividing parasites as a putative transcriptional repressor. In this study, we purified proteins interacting with AP2IX-4, finding it to be a component of the recently characterized microrchidia (MORC) transcriptional repressor complex. We further analyzed AP2XII-2, another cell cycle-regulated factor that associates with AP2IX-4. We monitored parallel expression of AP2IX-4 and AP2XII-2 proteins in tachyzoites, detecting peak expression during S/M phase. Unlike AP2IX-4, which is dispensable in tachyzoites, loss of AP2XII-2 resulted in a slowed tachyzoite growth due to a delay in S-phase progression. We also found that AP2XII-2 depletion increased the frequency of bradyzoite differentiation in vitro These results suggest that multiple AP2 factors collaborate to ensure proper cell cycle progression and tissue cyst formation in T. gondiiIMPORTANCEToxoplasma gondii is a single-celled parasite that persists in its host by converting into a latent cyst stage. This work describes a new transcriptional factor called AP2XII-2 that plays a role in properly maintaining the growth rate of replicating parasites, which contributes to signals required for development into its dormant stage. Without AP2XII-2, Toxoplasma parasites experience a delay in their cell cycle that increases the frequency of latent cyst formation. In addition, we found that AP2XII-2 operates in a multisubunit complex with other AP2 factors and chromatin remodeling machinery that represses gene expression. These findings add to our understanding of how Toxoplasma parasites balance replication and dormancy, revealing novel points of potential therapeutic intervention to disrupt this clinically relevant process.

ARID1a Associates with Lymphoid-Restricted Transcription Factors and Has an Essential Role in T Cell Development.

Maturation of lymphoid cells is controlled by the action of stage and lineage-restricted transcription factors working in concert with the general transcription and chromatin remodeling machinery to regulate gene expression. To better understand this functional interplay, we used Biotin Identification in human embryonic kidney cells to identify proximity interaction partners for GATA3, TCF7 (TCF1), SPI1, HLF, IKZF1, PAX5, ID1, and ID2. The proximity interaction partners shared among the lineage-restricted transcription factors included ARID1a, a BRG1-associated factor complex component. CUT&RUN analysis revealed that ARID1a shared binding with TCF7 and GATA3 at a substantial number of putative regulatory elements in mouse T cell progenitors. In support of an important function for ARID1a in lymphocyte development, deletion of Arid1a in early lymphoid progenitors in mice resulted in a pronounced developmental arrest in early T cell development with a reduction of CD4+CD8+ cells and a 20-fold reduction in thymic cellularity. Exploring gene expression patterns in DN3 cells from Wt and Arid1a-deficient mice suggested that the developmental block resided in the DN3a to DN3b transition, indicating a deficiency in β-selection. Our work highlights the critical importance of functional interactions between stage and lineage-restricted factors and the basic transcription machinery during lymphocyte differentiation.

Beyond What Your Retina Can See: Similarities of Retinoblastoma Function between Plants and Animals, from Developmental Processes to Epigenetic Regulation.

The Retinoblastoma protein (pRb) is a key cell cycle regulator conserved in a wide variety of organisms. Experimental analysis of pRb’s functions in animals and plants has revealed that this protein participates in cell proliferation and differentiation processes. In addition, pRb in animals and its orthologs in plants (RBR), are part of highly conserved protein complexes which suggest the possibility that analogies exist not only between functions carried out by pRb orthologs themselves, but also in the structure and roles of the protein networks where these proteins are involved. Here, we present examples of pRb/RBR participation in cell cycle control, cell differentiation, and in the regulation of epigenetic changes and chromatin remodeling machinery, highlighting the similarities that exist between the composition of such networks in plants and animals.

MafK Mediates Chromatin Remodeling to Silence IRF8 Expression in Non-immune Cells in a Cell Type-SpecificManner

The regulation of gene expression is a result of a complex interplay between chromatin remodeling, transcription factors, and signaling molecules. Cell differentiation is accompanied by chromatin remodeling of specific loci to permanently silence genes that are not essential for the differentiated cell activity. The molecular cues that recruit the chromatin remodeling machinery are not well characterized. IRF8 is an immune-cell specific transcription factor and its expression is augmented by interferon-γ. Therefore, it serves as a model gene to elucidate the molecular mechanisms governing its silencing in non-immune cells. Ahigh-throughput shRNA library screen in IRF8 expression-restrictive cells enabled the identification of MafK as modulator of IRF8 silencing, affecting chromatin architecture. ChIP-Seq analysis revealed three MafK binding regions (−25 kb, −20 kb, and IRF8 6th intron) within the IRF8 locus. These MafK binding sites are sufficient to repress a reporter gene when cloned in genome-integrated lentiviral reporter constructs in only expression-restrictive cells. Conversely, plasmid-based constructs do not demonstrate such repressive effect. These results highlight the role of these MafK binding sites in mediating repressed chromatin assembly. Finally, a more thorough genomic analysis was performed, using CRISPR–Cas9 to delete MafK-int6 binding region in IRF8 expression-restrictive cells. Deleted clones exhibited an accessible chromatin conformation within the IRF8 locus that was accompanied by a significant increase in basal expression of IRF8 that was further induced by interferon-γ. Taken together, we identified and characterized several MafK binding elements within the IRF8 locus that mediate repressive chromatin conformation resulting in the silencing of IRF8 expression in a celltype-specific manner.

BAF60a deficiency uncouples chromatin accessibility and cold sensitivity from white fat browning

Brown and beige fat share a remarkably similar transcriptional program that supports fuel oxidation and thermogenesis. The chromatin-remodeling machinery that governs genome accessibility and renders adipocytes poised for thermogenic activation remains elusive. Here we show that BAF60a, a subunit of the SWI/SNF chromatin-remodeling complexes, serves an indispensable role in cold-induced thermogenesis in brown fat. BAF60a maintains chromatin accessibility at PPARγ and EBF2 binding sites for key thermogenic genes. Surprisingly, fat-specific BAF60a inactivation triggers more pronounced cold-induced browning of inguinal white adipose tissue that is linked to induction of MC2R, a receptor for the pituitary hormone ACTH. Elevated MC2R expression sensitizes adipocytes and BAF60a-deficient adipose tissue to thermogenic activation in response to ACTH stimulation. These observations reveal an unexpected dichotomous role of BAF60a-mediated chromatin remodeling in transcriptional control of brown and beige gene programs and illustrate a pituitary-adipose signaling axis in the control of thermogenesis.

Smarcad1 mediates microbiota-induced inflammation in mouse and coordinates gene expression in the intestinal epithelium

BackgroundHow intestinal epithelial cells interact with the microbiota and how this is regulated at the gene expression level are critical questions. Smarcad1 is a conserved chromatin remodeling factor with a poorly understood tissue function. As this factor is highly expressed in the stem and proliferative zones of the intestinal epithelium, we explore its role in this tissue.ResultsSpecific deletion of Smarcad1 in the mouse intestinal epithelium leads to colitis resistance and substantial changes in gene expression, including a striking increase of expression of several genes linked to innate immunity. Absence of Smarcad1 leads to changes in chromatin accessibility and significant changes in histone H3K9me3 over many sites, including genes that are differentially regulated upon Smarcad1 deletion. We identify candidate members of the gut microbiome that elicit a Smarcad1-dependent colitis response, including members of the poorly understood TM7 phylum.ConclusionsOur study sheds light onto the role of the chromatin remodeling machinery in intestinal epithelial cells in the colitis response and shows how a highly conserved chromatin remodeling factor has a distinct role in anti-microbial defense. This work highlights the importance of the intestinal epithelium in the colitis response and the potential of microbial species as pharmacological and probiotic targets in the context of inflammatory diseases.

Epstein-Barr Virus BART Long Non-coding RNAs Function as Epigenetic Modulators in Nasopharyngeal Carcinoma.

Epstein-Barr virus (EBV) establishes lifelong latent infection in humans and is associated with several lymphoid and epithelial cancers. In nasopharyngeal carcinoma (NPC), EBV expresses few viral proteins but elevated levels of Bam-HI A rightward transcripts (BARTs) RNA, which includes viral microRNAs and long non-coding RNAs (lncRNAs). BART lncRNAs localize within the nucleus of EBV-infected cells and knockdown of BART lncRNAs significantly affects the expression of genes associated with cell adhesion, oxidoreductase activity, inflammation, and immunity. Notably, downregulation of IKAROS family zinc finger 3 (IKZF3/Aiolos), which plays a role in lymphocyte development and cell attachment, occurred in NPC C666-1 cells following BART lncRNA-knockdown. Since Aiolos expression is normally restricted to lymphoid cells and rarely observed in epithelial cells, induction of Aiolos by BART lncRNA was confirmed by expressing the major BART lncRNA isoform, RPMS1, in EBV-positive and -negative cells. BART lncRNA associated with the CBP/p300 complex and RNA polymerase II (Pol II) in the nucleus, suggesting that BART lncRNAs may mediate epigenetic regulation of gene expression through interaction with the chromatin remodeling machinery. This contention is further supported by evidence that BART lncRNA appears to stall Pol II at the promoter region and may regulate IFNB1 and CXCL8 expression by inhibiting transcription by Pol II in NPC. We hypothesize that EBV BART lncRNA expression modulates host gene expression and maintains EBV latency by interfering with histone methylation and acetylation processes. Aberrant expression of affected host genes mediated by BART lncRNA may lead to immune evasion, progression, and metastasis of NPC.

Chromatin remodelling to facilitate treatment resistance in glioblastoma

Abstract Recent findings from our group, and the wider community, show that standard treatment does not impose an apparent bottleneck on the clonal evolution of adult glioblastoma (GBM), implying a lack of direct therapeutic opportunity. This does not negate the possibility that multiple treatment-resistance mechanisms co-exist in tumours, repeated across patients, making a combination of targeted therapies a potentially effective approach. We investigated whether treatment resistance may be driven by selection of cellular properties conferred above the level of the genome. Differential expression analysis was performed on 23 pairs of primary and recurrent tumours from patients who received standard treatment and had a local recurrence treated by surgery and second line chemotherapy. This revealed a treatment-induced shift in cell states linked to normal neurodevelopment. The latter is orchestrated by cascades of transcription factors. We, therefore, applied a bespoke gene set enrichment analysis to our paired expression data to investigate whether any factors were implicated in co-regulation of the genes that were altered through therapy. This identified a specific chromatin remodelling machinery, instrumental in normal neurogenesis. We validated our results in an independent cohort of 22 paired GBM samples. Our results suggest that the chromatin remodelling machinery is responsible for determining transcriptional hierarchies in GBM, shown elsewhere to have different treatment sensitivities such that their relative abundances are altered through treatment.