Regulate Gene Expression Programs Research Articles

Structure of Liver Receptor Homolog-1 (NR5A2) with PIP3 hormone bound in the ligand binding pocket.

The nuclear receptor LRH-1 (Liver Receptor Homolog-1, NR5A2) is a transcription factor that regulates gene expression programs critical for many aspects of metabolism and reproduction. Although LRH-1 is able to bind phospholipids, it is still considered an orphan nuclear receptor (NR) with an unknown regulatory hormone. Our prior cellular and structural studies demonstrated that the signaling phosphatidylinositols PI(4,5)P2 (PIP2) and PI(3,4,5)P3 (PIP3) bind and regulate SF-1 (Steroidogenic Factor-1, NR5A1), a close homolog of LRH-1. Here, we describe the crystal structure of human LRH-1 ligand binding domain (LBD) bound by PIP3 - the first phospholipid with a head group endogenous to mammals. We show that the phospholipid hormone binds LRH-1 with high affinity, stabilizing the receptor LBD. While the hydrophobic PIP3 tails (C16/C16) are buried inside the LRH-1 ligand binding pocket, the negatively charged PIP3 head group is presented on the receptor surface, similar to the phosphatidylinositol binding mode observed in the PIP3-SF-1 structure. Thus, data presented in this work reinforce our earlier findings demonstrating that signaling phosphatidylinositols regulate the NR5A receptors LRH-1 and SF-1.

Chromosome folding: driver or passenger of epigenetic state?

Despite a growing understanding of how epigenetic marks such as histone modifications locally modify the activity of the chromatin with which they are associated, we know little about how marked regions on different parts of the genome are able to intercommunicate to effect regulation of gene expression programs. Recent advances in methods that systematically map pairwise chromatin interactions have uncovered important principles of chromosome folding, which are tightly linked to the epigenetic mark profiles and, hence, functional state of the underlying chromatin fiber.

Genome-wide analysis of H3.3 dissociation reveals high nucleosome turnover at distal regulatory regions of embryonic stem cells

BackgroundThe histone variant H3.3 plays a critical role in maintaining the pluripotency of embryonic stem cells (ESCs) by regulating gene expression programs important for lineage specification. H3.3 is deposited by various chaperones at regulatory sites, gene bodies, and certain heterochromatic sites such as telomeres and centromeres. Using Tet-inhibited expression of epitope-tagged H3.3 combined with ChIP-Seq we undertook genome-wide measurements of H3.3 dissociation rates across the ESC genome and examined the relationship between H3.3-nucleosome turnover and ESC-specific transcription factors, chromatin modifiers, and epigenetic marks.ResultsOur comprehensive analysis of H3.3 dissociation rates revealed distinct H3.3 dissociation dynamics at various functional chromatin domains. At transcription start sites, H3.3 dissociates rapidly with the highest rate at nucleosome-depleted regions (NDRs) just upstream of Pol II binding, followed by low H3.3 dissociation rates across gene bodies. H3.3 turnover at transcription start sites, gene bodies, and transcription end sites was positively correlated with transcriptional activity.H3.3 is found decorated with various histone modifications that regulate transcription and maintain chromatin integrity. We find greatly varying H3.3 dissociation rates across various histone modification domains: high dissociation rates at active histone marks and low dissociation rates at heterochromatic marks. Well- defined zones of high H3.3-nucleosome turnover were detected at binding sites of ESC-specific pluripotency factors and chromatin remodelers, suggesting an important role for H3.3 in facilitating protein binding. Among transcription factor binding sites we detected higher H3.3 turnover at distal cis-acting sites compared to proximal genic transcription factor binding sites.Our results imply that fast H3.3 dissociation is a hallmark of interactions between DNA and transcriptional regulators.ConclusionOur study demonstrates that H3.3 turnover and nucleosome stability vary greatly across the chromatin landscape of embryonic stem cells. The presence of high H3.3 turnover at RNA Pol II binding sites at extragenic regions as well as at transcription start and end sites of genes, suggests a specific role for H3.3 in transcriptional initiation and termination. On the other hand, the presence of well-defined zones of high H3.3 dissociation at transcription factor and chromatin remodeler binding sites point to a broader role in facilitating accessibility.Electronic supplementary materialThe online version of this article (doi:10.1186/1756-8935-7-38) contains supplementary material, which is available to authorized users.

Regulation of Fibulin-2 Gene Expression by Integrin α3β1 Contributes to the Invasive Phenotype of Transformed Keratinocytes

The laminin-binding integrin α3β1 is highly expressed in epidermal keratinocytes where it regulates both cell-autonomous and paracrine functions that promote wound healing and skin tumorigenesis. However, roles for α3β1 in regulating gene expression programs that control the behaviors of immortalized or transformed keratinocytes remain underexplored. In the current study, we used a microarray approach to identify genes that are regulated by α3β1 in immortalized keratinocytes. α3β1-responsive genes included several that are involved in extracellular matrix proteolysis or remodeling, including fibulin-2 and SPARC. However, α3β1-dependent induction of specific target genes was influenced by the genetic lesion that triggered immortalization, as α3β1-dependent fibulin-2 expression occurred in cells immortalized by either SV40 large T antigen or p53-null mutation, while α3β1-dependent SPARC expression occurred only in the former cells. Interestingly, qPCR arrays did not reveal strong patterns of α3β1-dependent gene expression in freshly isolated primary keratinocytes, suggesting that this regulation is acquired during immortalization. p53-null keratinocytes transformed with oncogenic RasV12 retained α3β1-dependent fibulin-2 expression, and RNAi-mediated knockdown of fibulin-2 in these cells reduced invasion, although not their tumorigenic potential. These findings demonstrate a prominent role for α3β1 in immortalized/transformed keratinocytes in regulating fibulin-2 and other genes that promote matrix remodeling and invasion.

Functions of SAGA in development and disease.

Precise regulation of gene expression programs during embryo development requires cooperation between transcriptional factors and histone-modifying enzymes, such as the Gcn5 histone acetyltransferase. Gcn5 functions within a multi-subunit complex, called SAGA, that is recruited to specific genes through interactions with sequence-specific DNA-binding proteins to aid in gene activation. Although the transcriptional programs regulated by SAGA in embryos are not well defined, deletion of either Gcn5 or USP22, the catalytic subunit of a deubiquitinase module in SAGA, leads to early embryonic lethality. Here, we review the known functions of Gcn5, USP22 and associated proteins during development and discuss how these functions might be related to human disease states, including cancer and neurodegenerative diseases.

Adapting in vitro embryonic stem cell differentiation to the study of locus control regions

Numerous locus control region (LCR) activities have been discovered in gene loci important to immune cell development and function. LCRs are a distinct class of cis-acting gene regulatory elements that appear to contain all the DNA sequence information required to establish an independently and predictably regulated gene expression program at any genomic site in native chromatin of a whole animal. As such, LCR-regulated transgenic reporter systems provide invaluable opportunities to investigate the mechanisms of gene regulatory DNA action during development. Furthermore the qualities of LCR-driven gene expression, including spatiotemporal specificity and “integration site-independence” would be highly desirable to incorporate into vectors used in therapeutic genetic engineering. Thus, advancement in the methods used to investigate LCRs is of considerable basic and translational significance. We study the LCR present in the mouse T cell receptor (TCR)-α gene locus. Until recently, transgenic mice provided the only experimental model capable of supporting the entire spectrum of LCR activities. We have recently reported complete manifestation of TCRα LCR function in T cells derived in vitro from mouse embryonic stem cells (ESC), thus validating a complete cell culture model for the full range of LCR activities seen in transgenic mice. Here we discuss the critical parameters involved in studying LCR-regulated gene expression during in vitro hematopoietic differentiation from ESCs. This advance provides an approach to speed progress in the LCR field, and facilitate the clinical application of its findings, particularly to the genetic engineering of T cells.

UTX and MLL4 Coordinately Regulate Transcriptional Programs for Cell Proliferation and Invasiveness in Breast Cancer Cells

Histone methyltransferases and demethylases reversibly modulate histone lysine methylation, which is considered a key epigenetic mark associated with gene regulation. Recently, aberrant regulation of gene expression by histone methylation modifiers has emerged as an important mechanism for tumorigenesis. However, it remains largely unknown how histone methyltransferases and demethylases coregulate transcriptional profiles for cancer cell characteristics. Here, we show that in breast cancer cells, the histone H3 lysine 27 (H3K27) demethylase UTX (also known as KDM6A) positively regulates gene expression programs associated with cell proliferation and invasion. The majority of UTX-controlled genes, including a cohort of oncogenes and prometastatic genes, are coregulated by the H3K4 methyltransferase mixed lineage leukemia 4 (MLL4, also called ALR, KMT2D, and MLL2). UTX interacted with a C-terminal region of MLL4. UTX knockdown resulted in significant decreases in the proliferation and invasiveness of breast cancer cells in vitro and in a mouse xenograft model. Such defective cellular characteristics of UTX-depleted cells were phenocopied by MLL4 knockdown cells. UTX-catalyzed demethylation of trimethylated H3K27 and MLL4-mediated trimethylation at H3K4 occurred interdependently at cotarget genes of UTX and MLL4. Clinically, high levels of UTX or MLL4 were associated with poor prognosis in patients with breast cancer. Taken together, these findings uncover that coordinated regulation of gene expression programs by a histone methyltransferase and a histone demethylase is coupled to the proliferation and invasion of breast cancer cells.

Expression of microRNA-21 in non-small cell lung cancer tissue increases with disease progression and is likely caused by growth conditional changes during malignant transformation

MicroRNAs can govern up to hundred different mRNAs and are important regulators of gene expression programs in development and disease. We analyzed the expression of microRNA-21, one of the most common oncomirs, in non-small cell lung cancer (NSCLC). Using northern blots the microRNA-21 expression levels of NSCLC-derived tissue and cell lines were measured. In line with earlier observations we show that mature microRNA-21 expression levels are highly increased in NSCLC-derived tissue compared to normal lung tissue. Additionally, we demonstrate that microRNA-21 levels correlate with malignancy since its expression in higher staged tumors is significantly more elevated compared to stage 1A. Interestingly, microRNA-21 levels in cultured NSCLC-derived cells are comparable to the expression detected in non-malignant lung tissue. Since microRNA-21 levels showed no fluctuation during the cell cycle, accelerated proliferation of tumor cells is not responsible for microRNA-21 upregulation in the tumor compartment. Similarly to NSCLC-derived cancer cells, the tumor-associated fibroblasts show low expression levels of microRNA-21. Together, these data indicate that rather microenviromental and growth conditional changes than intrinsic features of the cancer cells are responsible for the observed increase of microRNA-21 levels in tumor tissues. Subsequently culturing conditions were changed to assess the impact of co-cultivation with fibroblasts, hypoxia and anchorage-independent growth on microRNA-21 expression. While co-cultivation with tumor-associated fibroblasts had no effect on microRNA-21 expression, both hypoxia and anchorage-independent growth cause a microRNA-21 elevation. In summary, our data demonstrate that growth conditions especially expected in more malignant tumors result in microRNA-21 upregulation explaining the observed increase in higher staged lung cancer tissue, but not in lung cancer-derived cells.

PARP inhibitors: current status and implications for anticancer therapeutics

Poly(ADP-ribose) polymerases (PARPs) comprise of a large family of 17 proteins encoded by various genes which participate in genome maintenance, apoptosis, inflammatory responses and the regulation of gene expression programs. PARP inhibitors, as therapeutic agents, come into play acting on both PARP 1 and PARP 2. These drugs seem to target tumor cells in a moment of vulnerability when they are undergoing DNA repair. In the past few years this class of anti-cancer drug has been discovered to show a promising niche in the clinic.

Systematic identification of transcriptional regulatory modules from protein–protein interaction networks

Transcription factors (TFs) combine with co-factors to form transcriptional regulatory modules (TRMs) that regulate gene expression programs with spatiotemporal specificity. Here we present a novel and generic method (rTRM) for the reconstruction of TRMs that integrates genomic information from TF binding, cell type-specific gene expression and protein–protein interactions. rTRM was applied to reconstruct the TRMs specific for embryonic stem cells (ESC) and hematopoietic stem cells (HSC), neural progenitor cells, trophoblast stem cells and distinct types of terminally differentiated CD4+ T cells. The ESC and HSC TRM predictions were highly precise, yielding 77 and 96 proteins, of which ∼75% have been independently shown to be involved in the regulation of these cell types. Furthermore, rTRM successfully identified a large number of bridging proteins with known roles in ESCs and HSCs, which could not have been identified using genomic approaches alone, as they lack the ability to bind specific DNA sequences. This highlights the advantage of rTRM over other methods that ignore PPI information, as proteins need to interact with other proteins to form complexes and perform specific functions. The prediction and experimental validation of the co-factors that endow master regulatory TFs with the capacity to select specific genomic sites, modulate the local epigenetic profile and integrate multiple signals will provide important mechanistic insights not only into how such TFs operate, but also into abnormal transcriptional states leading to disease.

Axonal transcription factors: Novel regulators of growth cone‐to‐nucleus signaling

Developing axons contain transcripts that are locally translated to influence the axonal proteome. Recent studies have shown that axonal transcripts include mRNAs encoding transcription factors. These mRNAs are translated to produce transcription factors that can be retrogradely trafficked back to the nucleus, where they regulate gene expression programs. These findings point to a novel mechanism of growth cone-to-nucleus signaling that occurs when growth cones encounter extracellular signaling molecules that stimulate local translation of these transcription factors, thereby influencing gene transcription. Here we summarize recent findings on local translation of transcription factors in axons and their roles in different neuronal processes such as neuronal specification, survival, and axon regeneration. Comprehensive axonal transcriptome studies have revealed transcripts that encode many more transcription factors and cofactors, suggesting a potentially broad role for this type of signaling. We review the progress on the approaches and tools that have been developed to study local translation and retrograde trafficking of transcription factors. We also highlight the challenges in the field and discuss the potential routes to resolving them.

Estrogen response in luminal breast cancer

Estrogen receptor α (ERα) is the defining and driving transcription factor in luminal breast cancers and genes modulated by ERα can dictate cell growth and endocrine response. Nonetheless, genomic mechanisms which govern ERα-driven tumorigenesis, acquisition of chemoresistant phenotype and tumor metastases remain elusive. Recently, scientists have explored to shed light on ER regulated genomic events in primary breast cancer with divergent clinical outcome and in distant ERα+ metastases. Mapping of genome-wide ER binding events by chromatin immunoprecipitation followed by high-throughput sequencing revealed differential FoxA1-mediated ERα-chromatin binding programming that results in predictive gene signatures exclusive for ERα+ breast cancer clinical outcome, and is characterized by remarkable intensification of ERα binding signal in tumors that progress towards a poor prognosis [1,2]. Furthermore, ERα-chromatin interactions occur regardless of tumor endocrine therapy sensitivity. Nevertheless, there is differentially stronger ERα binding signal in tamoxifen resistant in comparison with tamoxifen sensitive lineages [1]. Although the mechanisms underlying ERα binding plasticity in breast cancer remain to be elucidated, the influence of specific stimuli, as those triggered by growth factors pathways [3,4], may result in differential ERα binding patterns that regulate gene expression programs, sensitivity to endocrine therapy and overall clinical outcome in ERα+ breast tumors. It is worthwhile to emphasize that the only DNA motif found enriched in the core of ER binding events is the estrogen response element (ERE) [1]. Of note, innovative model in ERα-driven tumorigenesis and cancer aggressiveness has emerged from the concept of the tag-team model of gene expression in luminal breast cancer, according to which amplified distant EREs (DEREs) coordinately and remotely modulates the transcription of distant genes through long-rage chromatin interactions [5]. The model hypothesis highlights DERE axes as hot spots for concomitant and aberrant genome amplification in luminal breast cancer; thus coordinately and persistently deregulating target transcriptome, including co-amplification of oncogenes and repression of tumor-suppressor loci for cancer development and endocrine therapy resistance. Using integrated next-generation sequencing approaches, two densely ERα-bound DERE regions, frequently amplified in ERα+ luminal breast cancers, were mapped on chromosomes 17q23 and 20q13 [5]; genomic amplification of which has been associated with endocrine therapy relapse and overall poor prognosis in breast cancer [6]. Moreover, integration of 3C dataset with published time-course study of gene expression revealed 95 loci remotely interacting with 20q13 DEREs, 38 genes with 17q23 DEREs, and 46 estrogen-responsive targets [5]. Interestingly, a strong body of evidences has demonstrated the novel role of the DEREs targeted genes THRAP1 and ZIM2 as tumor suppressors in luminal breast cancer. It is reasonable to speculate that the increased frequency of chromatin interactions might play a role to elicit epigenetic repression of DERE-regulated genes. The aforementioned phenomenon derives from genomic alterations induced by chronic estrogenic exposure of mammary cells that persist in breast progenitor cells [5], and progressively accumulate in malignant differentiating cells, in agreement with previous findings that points to the intensification of the ERα binding signal and ERE amplification during breast cancer worsening prognosis [1,2]. Precisely, these findings open new avenues to explore amplified DEREs in 17q23 and 20q13 as potential prognostic markers in luminal breast cancer, based on the rationale that the aberrant amplification of DEREs may enable functionality of residual estrogen/ERα regardless of the administration of selective ER blockers, such as tamoxifen [5]. This concept, at least partially, can explain the benefit of using aromatase inhibitors in post-menopausal women, which present the higher incidence of luminal breast cancer. The inhibition of the main source of estrogen production in these patients may prevent the E2/ERα-induced anomalous amplification of DEREs. On the other hand, the amplified DEREs axes and the tag-team model of gene expression modulation in luminal breast cancer currently challenges the investigators to determine the precise factors and mechanisms that trigger the malignant transformation of normal progenitor mammary cells. Amplified DNA regulatory elements may result from sustained amplification of DERE-DERE interactions that may intensify chromatin interaction within regions harboring clustered breakpoints, exquisitely prone to genomic rearrangements, as a result of genomic instability [5,7]. During neoplastic transformation, defects in double-strand break repair may destabilize these physical interactions, promoting insertions and self-duplication of 20q13 DERE clusters, for example, into regions of seven derivative chromosomes [5]. In contrast to this concept, it is puzzling that mammary cells sustain the benign phenotype in the majority of women regardless of the estrogenic milieu. At present, it is also important to evaluate the occurrence of aberrant DERE amplification and its peculiarities in controlling target genes expression in ovarian cancer, commonly lethal and tamoxifen resistant. Nonetheless, cumulative evidence hint the potential roles of the amplified distant DNA response elements axes and the tag-team model of gene expression modulation in hormone-driven carcinogenesis and cancer progression. More importantly, knowledge gained out of the study [5] should be instrumental for further understanding of cancer genomics and bringing of innovative interventions to control cancer.

H2A.Z Acidic Patch Couples Chromatin Dynamics to Regulation of Gene Expression Programs during ESC Differentiation

The histone H2A variant H2A.Z is essential for embryonic development and for proper control of developmental gene expression programs in embryonic stem cells (ESCs). Divergent regions of amino acid sequence of H2A.Z likely determine its functional specialization compared to core histone H2A. For example, H2A.Z contains three divergent residues in the essential C-terminal acidic patch that reside on the surface of the histone octamer as an uninterrupted acidic patch domain; however, we know little about how these residues contribute to chromatin structure and function. Here, we show that the divergent amino acids Gly92, Asp97, and Ser98 in the H2A.Z C-terminal acidic patch (H2A.ZAP3) are critical for lineage commitment during ESC differentiation. H2A.Z is enriched at most H3K4me3 promoters in ESCs including poised, bivalent promoters that harbor both activating and repressive marks, H3K4me3 and H3K27me3 respectively. We found that while H2A.ZAP3 interacted with its deposition complex and displayed a highly similar distribution pattern compared to wild-type H2A.Z, its enrichment levels were reduced at target promoters. Further analysis revealed that H2A.ZAP3 was less tightly associated with chromatin, suggesting that the mutant is more dynamic. Notably, bivalent genes in H2A.ZAP3 ESCs displayed significant changes in expression compared to active genes. Moreover, bivalent genes in H2A.ZAP3 ESCs gained H3.3, a variant associated with higher nucleosome turnover, compared to wild-type H2A.Z. We next performed single cell imaging to measure H2A.Z dynamics. We found that H2A.ZAP3 displayed higher mobility in chromatin compared to wild-type H2A.Z by fluorescent recovery after photobleaching (FRAP). Moreover, ESCs treated with the transcriptional inhibitor flavopiridol resulted in a decrease in the H2A.ZAP3 mobile fraction and an increase in its occupancy at target genes indicating that the mutant can be properly incorporated into chromatin. Collectively, our work suggests that the divergent residues in the H2A.Z acidic patch comprise a unique domain that couples control of chromatin dynamics to the regulation of developmental gene expression patterns during lineage commitment.

Expression profiling of genes regulated by Fra-1/AP-1 transcription factor during bleomycin-induced pulmonary fibrosis

BackgroundThe Fra-1/AP-1 transcription factor regulates the expression of genes controlling various processes including migration, invasion, and survival as well as extracellular remodeling. We recently demonstrated that loss of Fra-1 leads to exacerbated bleomycin-induced pulmonary fibrosis, accompanied by enhanced expression of various inflammatory and fibrotic genes. To better understand the molecular mechanisms by which Fra-1 confers protection during bleomycin-induced lung injury, genome-wide mRNA expression profiling was performed.ResultsWe found that Fra-1 regulates gene expression programs that include: 1) several cytokines and chemokines involved in inflammation, 2) several genes involved in the extracellular remodeling and cell adhesion, and 3) several genes involved in programmed cell death.ConclusionLoss of Fra-1 leads to the enhanced expression of genes regulating inflammation and immune responses and decreased the expression of genes involved in apoptosis, suggesting that this transcription factor distinctly modulates early pro-fibrotic cellular responses.

Dicer1 Is Required to Repress Neuronal Fate During Endocrine Cell Maturation

MicroRNAs (miRNAs) are important regulators of gene expression programs in the pancreas; however, little is known about the role of miRNA pathways during endocrine cell specification and maturation during neonatal life. In this study, we deleted Dicer1, an essential RNase for active miRNAs biogenesis, specifically from NGN3+ endocrine progenitor cells. We found that deletion of Dicer1 in endocrine progenitors did not affect the specification of hormone-expressing endocrine cells. However, the islets in the mutant mice in the neonatal period exhibited morphological defects in organization and loss of hormone expression, and the mutant mice subsequently developed diabetes. Dicer1-deficient β-cells lost insulin expression while maintaining the expression of β-cell transcription factors such as Pdx1 and Nkx6.1 early in the postnatal period. Surprisingly, transcriptional profiling showed that that the Dicer1-deficient endocrine cells expressed neuronal genes before the onset of diabetes. The derepression of neuronal genes was associated with a loss in binding of the neuronal transcriptional repressor RE-1-silencing transcription factor to its targets in Dicer1-deficient β-cells. These studies suggest that miRNAs play a critical role in suppressing neuronal genes during the maturation of endocrine cells.

Abstract 3564: ARID1A promotes endocrine resistance in ER+ breast cancer cells.

Abstract We recently identified the ARID1A gene as a new candidate tumor suppressor gene (TSG), mutated in the T47D cells, an ER+ breast cancer cell line. We have shown previously that re-expression of ARID1A in T47D cells inhibits both proliferation and anchorage-independent growth and also that nuclear expression of ARID1A is progressively decreased during the later stages of breast tumor progression. ARID1A encodes a member of the SWI/SNF family of proteins, which function to ‘remodel’ chromatin and thereby regulate gene expression programs. Most breast cancers express the estrogen receptor (ER), and are thus responsive to the mitogenic effects of the estrogen hormone as well as to the anti-proliferative effects of anti-estrogen therapies. To uncover the potential role of ARID1A in the regulation of estrogen signaling in ER+ breast cancer cells, we tested if re-expression of ARID1A may also affect estrogen-dependent growth. Surprisingly, we found that re-expression of ARID1A in T47D cells results in a decrease in the proliferative response of these cells to estrogen but also to a decrease in the viability of the cells in hormone-depleted conditions. Then, to further investigate if the loss of ARID1A may promote estrogen-independent growth, we silenced ARID1A expression by shRNA in MCF-7 cells that express moderate levels of ARID1A protein. We found that ARID1A-silencing increases the survival of MCF-7 cells in the absence of hormones. In addition, we also observed that phosphorylation of FAK and Src, whose activities have been suggested to be important in endocrine resistance, is highly increased in the absence of ARID1A. All together, these results suggest that loss of ARID1A can promote endocrine-resistance in ER-positive breast cancer cells. Citation Format: Catherine Chabot, Mark Basik. ARID1A promotes endocrine resistance in ER+ breast cancer cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3564. doi:10.1158/1538-7445.AM2013-3564

Transcriptome Profiling Reveals Stage-Specific Production and Requirement of Flagella during Biofilm Development in Bordetella bronchiseptica

We have used microarray analysis to study the transcriptome of the bacterial pathogen Bordetella bronchiseptica over the course of five time points representing distinct stages of biofilm development. The results suggest that B. bronchiseptica undergoes a coordinately regulated gene expression program similar to a bacterial developmental process. Expression and subsequent production of the genes encoding flagella, a classical Bvg− phase phenotype, occurs and is under tight regulatory control during B. bronchiseptica biofilm development. Using mutational analysis, we demonstrate that flagella production at the appropriate stage of biofilm development, i.e. production early subsequently followed by repression, is required for robust biofilm formation and maturation. We also demonstrate that flagella are necessary and enhance the initial cell-surface interactions, thereby providing mechanistic information on the initial stages of biofilm development for B. bronchiseptica. Biofilm formation by B. bronchiseptica involves the production of both Bvg-activated and Bvg-repressed factors followed by the repression of factors that inhibit formation of mature biofilms.

The p400/Brd8 Chromatin Remodeling Complex Promotes Adipogenesis by Incorporating Histone Variant H2A.Z at PPARγ Target Genes

Adipogenesis, the biological process by which preadipocytes differentiate into mature fat cells, is coordinated by a tightly regulated gene expression program. Indeed, it has been reported that a large number of genetic events, from fat cell-specific transcription factors expression, such as the master regulator of fat cell differentiation peroxisome proliferator-activated receptor (PPAR)γ2 to epigenetic modifications, govern the acquisition of a mature adipocyte phenotype. Here, we provide evidence that the E1A-binding protein p400 (p400) complex subunit bromo-containing protein 8 (Brd8) plays an important role in the regulation of PPARγ target genes during adipogenesis by targeting and incorporating the histone variant H2A.Z in transcriptional regulatory regions. The results reported here indicate that expression of both Brd8 and p400 increases during fat cell differentiation. In addition, small hairpin RNA-mediated knockdown of Brd8 or H2A.Z completely abrogated the ability of 3T3-L1 preadipocyte to differentiate into mature adipocyte, as evidenced by a lack of lipid accumulation. Chromatin immunoprecipitation experiments also revealed that the knockdown of Brd8 blocked the accumulation of PPARγ, p400, and RNA polymerase II and prevented the incorporation of H2A.Z at two PPARγ target genes. Taken together, these results indicate that the incorporation of the histone variant H2A.Z at the promoter regions of PPARγ target genes by p400/Brd8 is essential to allow fat cell differentiation.

PKB-mediated PHF20 phosphorylation on Ser291 is required for p53 function in DNA damage

PHD finger protein 20 (PHF20) is a transcription factor, which was originally identified in glioma patients. PHF20 appears to be a novel antigen in glioma, and has also termed glioma-expressed antigen 2. PHF20 is thought to contribute to the development of cancers, including glioblastoma, lung cancer, colon cancer and ovarian cancer. However, little is known about the function of PHF20 in various cancers. Here we report that PHF20 contains two consensus sites for protein kinase B (PKB) phosphorylation (RxRxxS/T). PKB can directly phosphorylate PHF20 on Ser291 in vitro and in vivo. It has been shown that PKB participates in the tumor suppressor p53 regulated gene expression program and has a direct effect on p21 regulation after DNA damage. UV‐induced DNA damage results in accumulation of p53 and PKB activation. Interestingly, PKB-mediated PHF20 phosphorylation led to an inhibition of p53 induction following UV treatment, leading to the reduction of p21 transcriptional activity. Using anti PHF20 and anti pPKB (S473) antibodies, these events were mapped in various human cancer tissues. Taken together, these data suggest that PHF20 is a novel substrate for PKB and its phosphorylation by PKB plays an important role in tumorigenesis via regulating of p53 mediated signaling.

The endoglycosidase heparanase enters the nucleus of T lymphocytes and modulates H3 methylation at actively transcribed genes via the interplay with key chromatin modifying enzymes

The methylation of histones is a fundamental epigenetic process regulating gene expression programs in mammalian cells. Dysregulated patterns of histone methylation are directly implicated in malignant transformation. Here, we report the unexpected finding that the invasive extracellular matrix degrading endoglycosidase heparanase enters the nucleus of activated human T lymphocytes and regulates the transcription of a cohort of inducible immune response genes by controlling histone H3 methylation patterns. It was found that nuclear heparanase preferentially associates with euchromatin. Genome-wide ChIP-on-chip analyses showed that heparanase is recruited to both the promoter and transcribed regions of a distinct cohort of transcriptionally active genes. Knockdown and overexpression of the heparanase gene also showed that chromatin-bound heparanase is a prerequisite for the transcription of a subset of inducible immune response genes in activated T cells. Furthermore, the actions of heparanase seem to influence gene transcription by associating with the demethylase LSD1, preventing recruitment of the methylase MLL and thereby modifying histone H3 methylation patterns. These data indicate that heparanase belongs to an emerging class of proteins that play an important role in regulating transcription in addition to their well-recognized extra-nuclear functions.