Myc Binding Sites Research Articles

High OGT activity is essential for MYC-driven proliferation of prostate cancer cells.

O-GlcNAc transferase (OGT) is overexpressed in aggressive prostate cancer. OGT modifies intra-cellular proteins via single sugar conjugation (O-GlcNAcylation) to alter their activity. We recently discovered the first fast-acting OGT inhibitor OSMI-2. Here, we probe the stability and function of the chromatin O-GlcNAc and identify transcription factors that coordinate with OGT to promote proliferation of prostate cancer cells.Methods: Chromatin immunoprecipitation (ChIP) coupled to sequencing (seq), formaldehyde-assisted isolation of regulatory elements, RNA-seq and reverse-phase protein arrays (RPPA) were used to study the importance of OGT for chromatin structure and transcription. Mass spectrometry, western blot, RT-qPCR, cell cycle analysis and viability assays were used to establish the role of OGT for MYC-related processes. Prostate cancer patient data profiled for both mRNA and protein levels were used to validate findings.Results: We show for the first time that OGT inhibition leads to a rapid loss of O-GlcNAc chromatin mark. O-GlcNAc ChIP-seq regions overlap with super-enhancers (SE) and MYC binding sites. OGT inhibition leads to down-regulation of SE-dependent genes. We establish the first O-GlcNAc chromatin consensus motif, which we use as a bait for mass spectrometry. By combining the proteomic data from oligonucleotide enrichment with O-GlcNAc and MYC ChIP-mass spectrometry, we identify host cell factor 1 (HCF-1) as an interaction partner of MYC. Inhibition of OGT disrupts this interaction and compromises MYC's ability to confer androgen-independent proliferation to prostate cancer cells. We show that OGT is required for MYC-mediated stabilization of mitotic proteins, including Cyclin B1, and/or the increased translation of their coding transcripts. This implies that increased expression of mRNA is not always required to achieve increased protein expression and confer aggressive phenotype. Indeed, high expression of Cyclin B1 protein has strong predictive value in prostate cancer patients (p=0.000014) while mRNA does not.Conclusions: OGT promotes SE-dependent gene expression. OGT activity is required for the interaction between MYC and HCF-1 and expression of MYC-regulated mitotic proteins. These features render OGT essential for the androgen-independent, MYC-driven proliferation of prostate cancer cells. Androgen-independency is the major mechanism of prostate cancer progression, and our study identifies OGT as an essential mediator in this process.

CREBBP/EP300 bromodomains are critical to sustain the GATA1/MYC regulatory axis in proliferation

BackgroundThe reported antitumor activity of the BET family bromodomain inhibitors has prompted the development of inhibitors against other bromodomains. However, the human genome encodes more than 60 different bromodomains and most of them remain unexplored.ResultsWe report that the bromodomains of the histone acetyltransferases CREBBP/EP300 are critical to sustain the proliferation of human leukemia and lymphoma cell lines. EP300 is very abundant at super-enhancers in K562 and is coincident with sites of GATA1 and MYC occupancy. In accordance, CREBBP/EP300 bromodomain inhibitors interfere with GATA1- and MYC-driven transcription, causing the accumulation of cells in the G0/G1 phase of the cell cycle. The CREBBP/CBP30 bromodomain inhibitor CBP30 displaces CREBBP and EP300 from GATA1 and MYC binding sites at enhancers, resulting in a decrease in the levels of histone acetylation at these regulatory regions and consequently reduced gene expression of critical genes controlled by these transcription factors.ConclusionsOur data shows that inhibition of CREBBP/EP300 bromodomains can interfere with oncogene-driven transcriptional programs in cancer cells and consequently hold therapeutic potential.

MiR-29 silencing modulates the expression of target genes related to proliferation, apoptosis and methylation in Burkitt lymphoma cells.

Burkitt lymphoma (BL) is a B-cell lymphoma frequently diagnosed in children. It is characterized by MYC translocations, which lead to the constitutive expression of the MYC oncogene. MYC contributes to miR-29 repression through an E-box MYC binding site on the miR-29b-1/miR-29a promoter region. We evaluated the role of miR-29a/b/c and their predicted targets in BL pathogenesis. Mature sequences of miR-29a/b/c were transfected to the BL cell lines BL41 and Raji, and evaluated for DNMT3B, MCL1, BIM, CDK6, AKT and TCL1 protein expression as well as for MCL-1 and CDK6 mRNA expression. BL cells were treated with 5-aza-2'-deoxycytidine (decitabine) and evaluated for miR29 expressions and methylation status. DNMT3B inhibition was performed by DNMT3B siRNA. Ectopic expression of miR-29s in BL cells decreased CDK6, DNMT3B, TCL1 and MCL-1 protein levels, but CDK6 and MCL-1 mRNA expression was unaffected by miR-29. Decitabine enhanced miR-29 expression levels and decreased CDK6 protein expression. Additionally, inhibition of DNMT3B by siRNA increased miR-29a/b expression. Notably, the miR-29a/b1 and miR-29b2/c promoter genes showed methylated CpG sequences that were demethylated after decitabine treatments. Furthermore, MYC-negative tumours had higher levels of miR-29 expression compared with MYC-translocated cases, suggesting that MYC regulates miR-29 in BL tumours. Our results suggest a significant role for miR-29s in BL pathogenesis in altering the expression of targets involved in critical cancer pathways, such as cell cycle control, apoptosis inhibition and DNA methylation. Moreover, methylation-mediated miR-29 epigenetic silencing may occur during BL development.

MYC-Regulated Mevalonate Metabolism Maintains Brain Tumor-Initiating Cells.

Metabolic dysregulation drives tumor initiation in a subset of glioblastomas harboring isocitrate dehydrogenase (IDH) mutations, but metabolic alterations in glioblastomas with wild-type IDH are poorly understood. MYC promotes metabolic reprogramming in cancer, but targeting MYC has proven notoriously challenging. Here, we link metabolic dysregulation in patient-derived brain tumor-initiating cells (BTIC) to a nexus between MYC and mevalonate signaling, which can be inhibited by statin or 6-fluoromevalonate treatment. BTICs preferentially express mevalonate pathway enzymes, which we find regulated by novel MYC-binding sites, validating an additional transcriptional activation role of MYC in cancer metabolism. Targeting mevalonate activity attenuated RAS-ERK-dependent BTIC growth and self-renewal. In turn, mevalonate created a positive feed-forward loop to activate MYC signaling via induction of miR-33b. Collectively, our results argue that MYC mediates its oncogenic effects in part by altering mevalonate metabolism in glioma cells, suggesting a therapeutic strategy in this setting. Cancer Res; 77(18); 4947-60. ©2017 AACR.

Cooperative Targets of Combined mTOR/HDAC Inhibition Promote MYC Degradation.

Cancer treatments often require combinations of molecularly targeted agents to be effective. mTORi (rapamycin) and HDACi (MS-275/entinostat) inhibitors have been shown to be effective in limiting tumor growth, and here we define part of the cooperative action of this drug combination. More than 60 human cancer cell lines responded synergistically (CI<1) when treated with this drug combination compared with single agents. In addition, a breast cancer patient-derived xenograft, and a BCL-XL plasmacytoma mouse model both showed enhanced responses to the combination compared with single agents. Mice bearing plasma cell tumors lived an average of 70 days longer on combination treatment compared with single agents. A set of 37 genes cooperatively affected (34 downregulated; 3 upregulated) by the combination responded pharmacodynamically in human myeloma cell lines, xenografts, and a P493 model, and were both enriched in tumors, and correlated with prognostic markers in myeloma patient datasets. Genes downregulated by the combination were overexpressed in several untreated cancers (breast, lung, colon, sarcoma, head and neck, myeloma) compared with normal tissues. The MYC/E2F axis, identified by upstream regulator analyses and validated by immunoblots, was significantly inhibited by the drug combination in several myeloma cell lines. Furthermore, 88% of the 34 genes downregulated have MYC-binding sites in their promoters, and the drug combination cooperatively reduced MYC half-life by 55% and increased degradation. Cells with MYC mutations were refractory to the combination. Thus, integrative approaches to understand drug synergy identified a clinically actionable strategy to inhibit MYC/E2F activity and tumor cell growth in vivoMol Cancer Ther; 16(9); 2008-21. ©2017 AACR.

17β-Estradiol Increases Non-CpG Methylation in Exon 1 of the Rainbow Trout (Oncorhynchus mykiss) MyoD Gene.

MyoD is an important myogenic transcription factor necessary for the differentiation of myogenic precursor cells (MPC) to form mature myotubes, a process essential for muscle growth. Epigenetic markers such as CpH methylation are known gene regulators that are important for the differentiation process. In this study, we investigated whether DNA methylation is a potential mechanism associated with the ability of 17β-estradiol (E2) to reduce MyoD gene expression and muscle growth in rainbow trout. Rainbow trout received a single intraperitoneal injection of E2 or the injection vehicle (control). Skeletal muscle was collected 24h post injection and analyzed for DNA methylation within the MyoD gene and the expression of DNA methyltransferases. CpG islands of the MyoD gene were predicted using MethPrimer software, and these regions were PCR amplified and analyzed using bisulfite sequencing. The percent methylation of the targeted CpG did not differ between control and E2-treated fish. However, percent CpH methylation in the MyoD exon 1 region was elevated with E2 treatment. Two of the methylated CpH sites were located in conserved transcription factor binding motifs, estrogen response element (ERE), and Myc binding site. Quantitative real-time PCR analysis revealed a significant increase in expression of DNA methyltransferases, Dnmt3a and Dnmt3b, in E2-treated muscle, suggesting an increased genome methylation. Differential CpH methylation in MyoD gene of control and E2-treated fish suggests an epigenetic mechanism through which E2 decreases MyoD gene expression and contributes to reduced muscle growth.

Profiling and bioinformatic analysis of circular RNA expression regulated by c-Myc.

The c-Myc transcription factor is involved in cell proliferation, cell cycle and apoptosis by activating or repressing transcription of multiple genes. Circular RNAs (circRNAs) are widely expressed non-coding RNAs participating in the regulation of gene expression. Using a high-throughput microarray assay, we showed that Myc regulates the expression of certain circRNAs. A total of 309 up- and 252 down-regulated circRNAs were identified. Among them, randomly selected 8 circRNAs were confirmed by real-time PCR. Subsequently, Myc-binding sites were found to generally exist in the promoter regions of differentially expressed circRNAs. Based on miRNA sponge mechanism, we constructed circRNAs/miRNAs network regulated by Myc, suggesting that circRNAs may widely regulate protein expression through miRNA sponge mechanism. Lastly, we took advantage of Gene Ontology and KEGG analyses to point out that Myc-regulated circRNAs could impact cell proliferation through affecting Ras signaling pathway and pathways in cancer. Our study for the first time demonstrated that Myc transcription factor regulates the expression of circRNAs, adding a novel component of the Myc tumorigenic program and opening a window to investigate the function of certain circRNAs in tumorigenesis.

Transcriptional regulation of microsomal prostaglandin E synthase 1 by the proto-oncogene, c-myc, in the pathogenesis of inflammation and cancer

Pro-inflammatory molecules play a key role in the progression of various types of cancers highlighting the importance of studying the pathways that regulate the inflammatory cytokine production. To this end, prostaglandins have been reported to correlate with exacerbated cancer phenotypes that may be prevented by using anti-inflammatory drugs in humans. To understand how the prostaglandin E synthase 1 (mPGES1) may be regulated we analyzed its promoter sequence and identified myc-binding sites. Functional validation was performed by mutating the sites that led to attenuated promoter activation of mPGES1. The known c-myc inhibitor (10058-F4) also blocked PGE2 activity, indicating the importance of c-Myc in PGE2 synthesis. Isocoumarin analogs were able to reduce the expressions of both c-myc as well as mPGES1 and also inhibit the production of PGE2. Based on these data and the well-established role of c-myc in oncogenesis, we have demonstrated an additional role of c-myc in exacerbating cancers via PGE2 production, which may provide a therapeutic opportunity to treat these diseases.

Downregulation of miR-451 in Tunisian chronic myeloid leukemia patients: potential implication in imatinib resistance

ABSTRACTObjectives: Resistance to imatinib has been recognized as a major challenge for the treatment of chronic myeloid leukemia (CML). Aberrant expression of miR-451 has been reported to participate in anticancer drug resistance. However, the role of miR-451 in imatinib resistance has not been investigated. The present study was undertaken to determine the expression of miR-451 in order to find a possible association between the expression of this miRNA and imatinib resistance in Tunisian CML patients.Methods: First, real-time RT-PCR was performed to identify the expression of miR-451 in peripheral leukocytes of 59 CML patients treated with imatinib. Then, bioinformatics analysis was carried out to understand the regulatory roles of miR-451 in imatinib-resistant process.Results: Downregulated miR-451 was observed in imatinib-resistant CML cases. In silico analysis identified MYC as a potential target of miR-451. We further revealed the existence of an MYC-binding site in MiR-451 promoter region. On the other hand, increased level of MYC was detected in imatinib-resistant CML cases which may explain the causative role of MYC in CML cases and the downregulation of miR-451.Conclusion and discussion: Taken together, our findings suggest that miR-451 and MYC form together a regulatory loop which may act as a potential therapeutic target, and disruption of suggested regulatory loop could help to improve CML therapy.

MP90-04 A ROLE FOR HISTONE DEMETHYALASE JMJD1A IN THE DNA DAMAGE RESPONSE OF PROSTATE CANCER CELLS

INTRODUCTION AND OBJECTIVES: The major therapies for prostate cancer (PCa) such as radio-, chemoor androgen deprivation therapy induce DNA damage. Thus the DNA damage response (DDR) and expression of DDR genes are key factors in determining outcome of PCa therapies. Histone demethylase JMJD1A regulates the gene expression by demethylating H3K9. Our previous work shows that JMJD1A is essential for the long-term proliferation and survival of PCa cells in vitro or in the xenograft prostate tumor model, partly via its effect on the activities of androgen receptor (AR) and c-Myc transcription factors. Here, we find a new role for JMJD1A in the expression of DDR genes and sensitivity of PCa cells to irradiation and androgen deprivation. METHODS: Real-time PCR was used to measure the mRNA levels of some DDR genes in the PCa cells (control or siRNA knockdown (KD) of JMJD1A, AR or c-Myc). Chromatin immunoprecipitation (ChIP) was used to evaluate the binding of JMJD1A to the AR or MYC binding sites on these DDR genes. JMJD1A-KD PCa cells were treated with or without ionizing radiation (IR), and analyzed by the r-H2AX staining (a widely used marker for the DNA double strand breaks (DSBs)), western blot analysis of DNA damage signaling proteins, flow cytometry analysis of cell cycle, and GFP reporter assays for the DSB repair via the homologous recombination (HR) or non-homologous end joining (NHEJ) pathways. The growth of these PCa cells was also measured under the IR and androgen deprivation conditions. RESULTS: JMJD1A was found to promote the expression of some DDR genes by co-activating AR and/or c-Myc. The DDR genes regulated by JMJD1A encode factors mediating the DSB repair by both HR and NHEJ pathways. JMJD1A KD led to increased r-H2AX foci in the non-irradiated cells, and the delayed clearance of r-H2AX foci in the irradiated cells. JMJD1A KD also increased the levels of phospho-DNAPK or phospho-CHEK2 in the western blot analysis and caused G2 cell cycle arrest. Consistently, JMJD1A KD reduced the percentage of GFPpositive cells that reflects the DSB repair by both HR and NHEJ pathways. JMJD1A-KD cells showed a reduced growth under IR and androgen deprivation conditions. CONCLUSIONS: JMJD1A promotes the DSB repair via regulation of DDR gene expression through AR and/or c-Myc. The role of JMJD1A in the DSB repair may contribute to the resistance of PCa cells to the radioand androgen deprivation therapies.

Abstract A25: Dysregulation of MYC via STAT1 promotes tumor progression in serous papillary endometrial cancer

Abstract Serous papillary endometrial cancers (SPEC) harboring several genetic alterations, such as TP53 mutation, are known highly progressive with worse prognosis compared with endometrioid counter-part, but it still remains unclear which molecular pathway is responsible for their unfavorable features. The IFN-γ; transcription factor signal transducer and activator of transcription 1 (STAT1) has been considered as a tumor suppressor with transcription-dependent and transcription-independent mechanisms, but recent studies showed STAT1 was associated with poor prognosis, and was involved in maintaining basal expression of tumor pro-survival STAT3 target genes, such as MYC, with unclear mechanism in some cancers. A previous report of the cancer genome atlas (TCGA) indicated MYC amplification in some SPECs; as MYC is known to be maintained also by STAT1, we investigate the role of STAT1-MYC axis in the malignant features of SPECs. Gene expression microarray was conducted for 63 endometrial cancer samples and SPEC cell line, SPAC-1L. Immunohistochemical staining were conducted using endometrial cancer samples under protocols approved by the Institutional Review Board to investigate SPEC-specific pathways (Kyoto cohort: n=91, Vancouver cohort: n=462). Using SPAC-1L cell line, several functional assay in vitro such as cellular proliferation, migration, invasion and apoptosis under treatment of cisplatin, doxorubicin, and paclitaxel were assessed with or without suppressing target genes. In vivo tumorigenesis was performed in mouse model and some computational analysis were done in silico. Gene expression microarray analysis revealed STAT1 pathway was commonly activated in SPECs both in our dataset and TCGA dataset as a key molecule of ‘SPEC signature’. In two independent cohorts, STAT1 expression was confirmed significantly higher in SPECs (p&amp;lt;0.001), and the disease specific survival of EC with high STAT1 expression was worse than those with low STAT1 expression (p&amp;lt;0.05). We found that STAT1 regulates MYC as well as ICAM1, PD-L1, and SMAD7, as well as the capacity for proliferation, adhesion, migration, invasion, and in vivo tumorigenecity in cells with a high SPEC signature. In contrast, suppression of STAT1 attenuated induction of these genes and inhibited xenograft tumor growth on NOD-SCID mice. Furthermore, suppressing STAT1 expression by shRNA sensitized SPEC cells to cisplatin. In STAT1 suppressed cells, apoptosis and cleaved caspase3 expression was confirmed even under low dose cisplatin treatment (p&amp;lt;0.05). Based on silico analysis using cBioPortal, we found amplification of MYC and up-regulated of MYC mRNA in 42% SPECs. The 227 up-regulated genes in the SPEC signature harbor the MYC binding site motif by GATHER analysis (p&amp;lt;0.001), and the predictive MYC activity signature score was statistically higher in SPECs than in other subtypes of endometrial cancers, while that in SPAC-1L cells was diminished with STAT1 knockdown. These results indicate that STAT1 pathway modulates the micro-environment of SPECs in deregulating MYC, as well as other target genes, to promote tumor progression. Furthermore, STAT1-MYC axis could be developed as a novel potential target for molecular targeting therapy in SPECs. Citation Format: Budiman Kharma, Tsukasa Baba, Noriomi Matsumura, Ryusuke Murakami, Ken Yamaguchi, Junzo Hamanishi, Masaki Mandai, Ikuo Konishi. Dysregulation of MYC via STAT1 promotes tumor progression in serous papillary endometrial cancer. [abstract]. In: Proceedings of the AACR Special Conference on Myc: From Biology to Therapy; Jan 7-10, 2015; La Jolla, CA. Philadelphia (PA): AACR; Mol Cancer Res 2015;13(10 Suppl):Abstract nr A25.

Abstract A46: Regulation of genomic Myc binding by Pin1 in serum-stimulated fibroblasts

Abstract The transcription factor Myc's induction of its pro-oncogenic target genes is regulated by Serine62 (S62) phosphorylation and the Pin1 prolyl-isomerase, where pS62-Myc is isomerized at Proline63 by Pin1 and this facilitates its recruitment to select target gene promoters. It is also known that Myc is an early serum response gene that controls cellular transition from quiescence to proliferation. In order to examine the global effects of Pin1 on Myc activity, we have performed unbiased genome-wide RNA-seq and ChIP-seq for Myc in primary murine embryo fibroblasts (MEFs) derived from Pin1 wild-type and knockout mice. The MEFs were serum starved for 72 hours and serum stimulated for 4 hours. Through RNA-seq we have observed a striking blunting of serum responsive genes in the Pin1 null cells. From our highly reproducible ChIP-seq data (6719 regions, IDR&amp;lt;0.1, Pin1 wild-type, stimulated), we found that both the number and magnitude of Myc DNA binding peaks were reduced in the null cells in genes showing blunted serum response. Using functional annotation analysis tools (DAVID and GSEA), we found opposing pathway-enrichments for Myc binding in null versus wild-type cells, with proliferation and migration genes enriched in wild-type cells. Furthermore, binding motif analysis of Myc-binding sites suggested a stronger enrichment of canonical E-box motif (CACGTG) in wild-type cells over null cells. In summary, our study suggested a key role that Pin1 plays in Myc global DNA binding activity. Citation Format: Yulong Su, Carl Pelz, Soren Impey, Rosalie Sears. Regulation of genomic Myc binding by Pin1 in serum-stimulated fibroblasts. [abstract]. In: Proceedings of the AACR Special Conference on Myc: From Biology to Therapy; Jan 7-10, 2015; La Jolla, CA. Philadelphia (PA): AACR; Mol Cancer Res 2015;13(10 Suppl):Abstract nr A46.

Abstract 1134: N-Myc promotes glutamine anaplerosis and aggressive tumor progression through direct GLS2 activation

Abstract Elevated glutamine metabolism is an essential feature for malignant transformation. Glutaminase-catalyzed deamidation of glutamine to glutamate is a key step in both glutaminolysis and synthesis of ROS-scavenging glutathione. Two predominant human isozymes of glutaminase, kidney-type GLS1 (also called GLS) and liver-type GLS2, are involved in regulation of glutaminolysis. It has been shown the Myc family member, c-Myc, specifically potentiates elevated expression of GLS1 and promotes the downstream utilization of glutamine carbon in anaplerosis in liver cancer, whereas p53 tumor suppressor specifically activates GLS2 to support cellular defense against oxidative stress, suggesting GLS1 promoted tumorigenesis whereas GLS2 may inhibited it. However, whether cancer cells of different origins use a common or unique signal pathways to regulate glutamine metabolism remains largely unexplored. Using MYCN-amplified neuroblastoma as a model system, we identified GLS2 expression dramatically increased while that of GLS1 substantially decreased in the tumorigenic process of N-Myc transformed neuroblastoma. GLS2 depletion profoundly inhibited glutaminolysis concomitant with a substantial decrease in cell proliferation and viability in vitro and inhibition of tumorigenesis in vivo. Mechanistically, N-Myc, but not p53, selectively activates GLS2 transcription by direct binding to a conserved Myc-binding site within GLS2 promoter. In support of this notion, we found significant elevation of GLS2 expression concomitant with considerable GLS1 down-regulation in primary tumors obtained from MYCN-amplified neuroblastoma patients (invariably with poor prognosis) in comparison with those from MYCN non-amplified patients. In aggregate, these studies suggest that the metabolic regulation of c-Myc induced liver tumors differs from that of N-Myc induced neuroblastoma tumors which is likely to depend on both the genotype and the tissues of origin and have implications regarding the design of selective therapies targeting tumor metabolism. Citation Format: Daibiao Xiao, Ping Ren, Hexiu Su, Ming Yue, Ruijuan Xiu, Lei Gan, Hudan Liu, Guoliang Qing. N-Myc promotes glutamine anaplerosis and aggressive tumor progression through direct GLS2 activation. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1134. doi:10.1158/1538-7445.AM2015-1134

Long noncoding RNAs as a novel component of the Myc transcriptional network.

Myc is a well-known transcription factor with important roles in cell cycle, apoptosis, and cellular transformation. Long noncoding RNAs (lncRNAs) have recently emerged as an important class of regulatory RNAs. Here, we show that lncRNAs are a main component of the Myc-regulated transcriptional program using the P493-6 tetracycline-repressible myc model. We demonstrate that both Myc-induced mRNAs and lncRNAs are significantly enriched for Myc binding sites. In contrast to Myc-repressed mRNAs, Myc-repressed lncRNAs are significantly enriched for Myc binding sites. Subcellular localization analysis revealed that compared to mRNAs, lncRNAs more often have a specific subcellular localization with a markedly higher percentage of nuclear enrichment within the Myc-repressed lncRNA set. Parallel analysis of differentially expressed lncRNAs and mRNAs identified 105 juxtaposed lncRNA-mRNA pairs, indicative for regulation in cis. To support the potential relevance of the Myc-regulated lncRNAs in cellular transformation, we analyzed their expression in primary Myc-high and Myc-low B-cell lymphomas. In total, 54% of the lncRNAs differentially expressed between the lymphoma subsets were identified as Myc-regulated in P493-6 cells. This study is the first to show that lncRNAs are an important factor within the Myc-regulated transcriptional program and indicates a marked difference between Myc-repressed lncRNAs and mRNAs.

Myc and Max Genome-Wide Binding Sites Analysis Links the Myc Regulatory Network with the Polycomb and the Core Pluripotency Networks in Mouse Embryonic Stem Cells

Myc is a master transcription factor that has been demonstrated to be required for embryonic stem cell (ESC) pluripotency, self-renewal, and inhibition of differentiation. Although recent works have identified several Myc-targets in ESCs, the list of Myc binding sites is largely incomplete due to the low sensitivity and specificity of the antibodies available. To systematically identify Myc binding sites in mouse ESCs, we used a stringent streptavidin-based genome-wide chromatin immunoprecipitation (ChIP-Seq) approach with biotin-tagged Myc (Bio-Myc) as well as a ChIP-Seq of the Myc binding partner Max. This analysis identified 4325 Myc binding sites, of which 2885 were newly identified. The identified sites overlap with more than 85% of the Max binding sites and are enriched for H3K4me3-positive promoters and active enhancers. Remarkably, this analysis unveils that Myc/Max regulates chromatin modifiers and transcriptional regulators involved in stem cell self-renewal linking the Myc-centered network with the Polycomb and the Core networks. These results provide insights into the contribution of Myc and Max in maintaining stem cell self-renewal and keeping these cells in an undifferentiated state.

Epigenetic regulation of CD133/PROM1 expression in glioma stem cells by Sp1/myc and promoter methylation

Tumor stem cells, postulated to be the source cells for malignancies, have been identified in several cancers using cell-surface expression of markers including CD133, a pentaspan membrane protein. CD133+ve cells form neurospheres, exhibit self-renewal and differentiation, and are tumorigenic. However, despite its association with stem cells, a causal relationship of CD133 to tumorigenesis remains to be defined. Hypothesizing that specific epigenetic and transcription factors implicated in driving the stem cell state may concurrently regulate CD133 expression in stem cells, we analyzed the structure and regulation of CD133 promoter in glioma stem cells and glioma cell lines. Initially, a minimal promoter region was identified by analyzing the activity of CD133 promoter-driven luciferase-expressing 5'-and 3'-deletion-constructs upstream of the transcription start site. This region contained a CpG island that was hypermethylated in CD133-ve glioma stem cells (GSC) and glioma cells but unmethylated in CD133+ve ones. Of several predicted TF-binding sites in this region, the role of tandem Sp1 (-242 and -221) and two Myc (-541 and -25)-binding sites were examined. Overexpression of Sp1 or Myc increased CD133 minimal promoter-driven luciferase activity and CD133 levels in GSC and in glioma cell line. Mithramycin, a Sp1 inhibitor, decreased minimal promoter activity and downregulated CD133 levels in GSC. Gel-shift assays demonstrated direct binding of Sp1 to their predicted sites that was competitively inhibited by oligonucleotide-binding-site sequences and supershifted by anti-Sp1 confirming the interaction. Sp1 and Myc-antibody chromatin immunoprecipitation (ChIP) analysis in GSC showed enrichment of regions with Sp1 and Myc-binding sites. In CD133-ve cells, ChIP analysis showed binding of the methyl-DNA-binding proteins, MBD1, MBD2 and MeCP2 to the methylated CpG island and repression of transcription. These results demonstrate that Sp1 and Myc regulate CD133 transcription in GSC and that promoter methylation and methyl-DNA-binding proteins cause repression of CD133 by excluding transcription-factor binding.

New Molecular Bridge between RelA/p65 and NF-κB Target Genes via Histone Acetyltransferase TIP60 Cofactor

The nuclear factor-κB (NF-κB) family is involved in the expressions of numerous genes, in development, apoptosis, inflammatory responses, and oncogenesis. In this study we identified four NF-κB target genes that are modulated by TIP60. We also found that TIP60 interacts with the NF-κB RelA/p65 subunit and increases its transcriptional activity through protein-protein interaction. Although TIP60 binds with RelA/p65 using its histone acetyltransferase domain, TIP60 does not directly acetylate RelA/p65. However, TIP60 maintained acetylated Lys-310 RelA/p65 levels in the TNF-α-dependent NF-κB signaling pathway. In chromatin immunoprecipitation assay, TIP60 was primarily recruited to the IL-6, IL-8, C-IAP1, and XIAP promoters in TNF-α stimulation followed by acetylation of histones H3 and H4. Chromatin remodeling by TIP60 involved the sequential recruitment of acetyl-Lys-310 RelA/p65 to its target gene promoters. Furthermore, we showed that up-regulated TIP60 expression was correlated with acetyl-Lys-310 RelA/p65 expressions in hepatocarcinoma tissues. Taken together these results suggest that TIP60 is involved in the NF-κB pathway through protein interaction with RelA/p65 and that it modulates the transcriptional activity of RelA/p65 in NF-κB-dependent gene expression.

欧美杨水分利用效率相关基因PdEPF1的克隆及表达

提高植物水分利用效率(WUE)是未来解决我国甚至世界干旱缺水的最重要手段之一。在对植物WUE的众多研究方法中,大多集中在生理手段,但通过分子生物学手段研究其表达调控机制的较少。欧美杨(<em>Populus deltoides</em>×<em>Populus nigra</em>)是中纬度地区最适合种植的短轮伐期工业用材集约经营树种之一。近年来我国引进了许多优良的欧美杨无性系用于营造大面积的速生丰产林并取得很好的经济和社会效益。但高耗水量的缺点限制了其进一步的推广。通过基因芯片技术从欧美杨中找到一个可能调控WUE的基因-<em>PdEPF1</em>. 荧光定量表达进一步验证了这一结果。荧光定量表达分析表明该基因受ABA、盐、冷、干旱等胁迫诱导表达。组织特异表达分析说明<em>PdEPF1</em>基因在顶端叶和根中有表达,成熟叶衰老叶中则无表达。克隆到启动子分析表明该启动子含有多种干旱响应元件(drought response elememt),赤霉素响应元件(GA response elememt),低温响应元件(cold response elememt),ABA响应元件(ABA response elememt)等逆境相关的作用元件。;Water-use efficiency (WUE) is crucial to plant survival, yield and vegetation dynamics. Many researches trended to reduce water use by more crop per drop. Althoughmuch progresses have been achieved in determining the physiological mechanisms of WUE, there is few report on the genetic controls of WUE. The first gene ERECTA, which t promotes WUE, was shown to decrease stomatal density and be involved in the positive regulation of photosynthetic capacity.<br> The EPIDERMAL PATTERNING FACTOR 1 (EPF1) gene identified in Arabidopsis is expressed specifically in stomatal cells and precursors. EPF1 controls stomatal patterning through the regulation of asymmetric cell division, its activity depends on the TOO MANY MOUTHS receptor-like protein and ERECTA family receptor kinases, suggesting that EPF1 provides a positional cue interpreted by these receptors. A mutation of EPF1 results in increased stomatal density and violation of the one-cell-spacing rule (clustering of stomata). However, there is no report on the relationship between AtEPF1 and WUE.<br> The cottonwood poplar, Populus deltoides×Populus nigra, is one of the most important species in large-scale forestation in China. However, its high water consumption is a key factor limiting its growth in arid and semiarid regions. Identifcation of genes increasing WUE in this species is important for understanding stress responses and improvement of this species.<br> In this study, microarray analysis between poplar genotypes NE-19 (<em>P. nigra</em>×(<em>P. deltoides</em>×<em>P. nigra</em>)) with the higher WUE and DN-2 (<em>P. deltoides×P. nigra</em>) with a lower WUE,was performed. PdEPF1 from NE-19,one of the WUE-related genes, was identified, strongly expressed in immature leaves and roots, but not in senescent leaves, functional leaves and the stem. This gene is strongly induced by drought, abscisic acid and high salt levels, and enhanced by gibberellic acid. To unvarel the mechanism responsible for the inducible expression of PdEPF1 by different stresses, a 1090-bp PdEPF1 promoter fragment was isolated by the adaptor PCR with reference to the transcriptional start site determined from the PdEPF1 cDNA sequence. The PdEPF1 promoter contains CAAT and TATA motifs located at nucleotides -204 and -35 relative to the transcriptional start site, respectively. Each of these motifs has characteristics of eukaryotic gene promoters. Interestingly,, the 1090-bp promoter region contained several motifs based on the computer prediction, such as a W-box (a GA-responsive element), an MYC binding site, an early response to dehydration binding site, and a controlling guard cell-specific gene expression binding site. This indicate, that the stress-inducible expression of PdEPF1 is regulated at the level of transcription.

Deep Sequencing of MYC DNA-Binding Sites in Burkitt Lymphoma

BackgroundMYC is a key transcription factor involved in central cellular processes such as regulation of the cell cycle, histone acetylation and ribosomal biogenesis. It is overexpressed in the majority of human tumors including aggressive B-cell lymphoma. Especially Burkitt lymphoma (BL) is a highlight example for MYC overexpression due to a chromosomal translocation involving the c-MYC gene. However, no genome-wide analysis of MYC-binding sites by chromatin immunoprecipitation (ChIP) followed by next generation sequencing (ChIP-Seq) has been conducted in BL so far.Methodology/Principal FindingsChIP-Seq was performed on 5 BL cell lines with a MYC-specific antibody giving rise to 7,054 MYC-binding sites after bioinformatics analysis of a total of approx. 19 million sequence reads. In line with previous findings, binding sites accumulate in gene sets known to be involved in the cell cycle, ribosomal biogenesis, histone acetyltransferase and methyltransferase complexes demonstrating a regulatory role of MYC in these processes. Unexpectedly, MYC-binding sites also accumulate in many B-cell relevant genes. To assess the functional consequences of MYC binding, the ChIP-Seq data were supplemented with siRNA- mediated knock-downs of MYC in BL cell lines followed by gene expression profiling. Interestingly, amongst others, genes involved in the B-cell function were up-regulated in response to MYC silencing.Conclusion/SignificanceThe 7,054 MYC-binding sites identified by our ChIP-Seq approach greatly extend the knowledge regarding MYC binding in BL and shed further light on the enormous complexity of the MYC regulatory network. Especially our observations that (i) many B-cell relevant genes are targeted by MYC and (ii) that MYC down-regulation leads to an up-regulation of B-cell genes highlight an interesting aspect of BL biology.

MYC Protein Inhibits Transcription of the MicroRNA Cluster MC-let-7a-1∼let-7d via Noncanonical E-box

The human microRNA cluster MC-let-7a-1∼let-7d, with three members let-7a-1, let-7f-1, and let-7d, is an important cluster of the let-7 family. These microRNAs play critical roles in regulating development and carcinogenesis. Therefore, precise control of MC-let-7a-1∼let-7d level is critical for cellular functions. In this study, we first showed that the expression of these three members was significantly reduced in human hepatocellular carcinoma HepG2 cells as compared with the immortalized human liver L02 cells. We demonstrated that the MC-let-7a-1∼let-7d cluster was encoded by a single polycistronic transcript driven by a 10-kb upstream promoter, with two MYC-binding sites. Importantly, MYC inhibited MC-let-7a-1∼let-7d promoter activity via binding to the noncanonical E-box 3 downstream of the transcription start sites, whereas it enhanced promoter activity by binding to the canonical E-box 2 upstream of the transcription start sites. We found that although the binding affinity of MYC to E-box 2 was stronger than E-box 3, the binding quantum of MYC to E-box 3 was significantly higher in cancerous HepG2 cells as compared with the noncancerous L02 cells. In addition, forced expression of let-7 could reverse the MYC-mediated cell proliferation. These findings suggested that in L02 cells with a low level of MYC, MYC binds mainly to E-box 2 to enhance MC-let-7a-1∼let-7d expression. However, in HepG2 cells with an elevated MYC, the extra MYC could bind to E-box 3 to suppress the transcription of MC-let-7a-1∼let-7d and thus enable HepG2 cells to maintain a high level of MYC and a low level of let-7 microRNAs simultaneously.