Cell cycle- and age-dependent transcriptional regulation of human thymidine kinase gene: the role of NF-Y in the CBP/tk binding complex

A New Signature of Sarcoma Based on the Tumor Microenvironment Benefits Prognostic Prediction

Sarcomas are a group of malignant tumors derived from mesenchymal tissues that display complex and variable pathological types. The impact of the immune properties of the tumor microenvironment (TME) on the prognosis, treatment, and management of sarcomas has attracted attention, requiring the exploration of sensitive and accurate signatures. In this study, The Cancer Genome Atlas (TCGA) database was searched to screen for an RNA sequencing dataset, retrieving 263 sarcoma and 2 normal samples with survival data. Genes associated with immune regulation in sarcomas were retrieved from the Tumor Immune Estimation Resource database to estimate tumor purity and immune cell infiltration levels. The samples were then divided into the immune-high and immune-low groups. Then, we screened for differentially expressed genes (DEGs) between the two groups. The intersection between immune-related genes and DEGs was then determined. Univariate Cox and least absolute shrinkage and selection operator analyses were used to select ideal genes for prognostic prediction and subsequent construction of a risk signature. A survival analysis was performed to reveal the dissimilarity in survival between the high- and low-score groups. Finally, a nomogram was generated to verify the accuracy and reliability of the signature. Through Estimation of STromal and Immune cells in MAlignant Tumour tissues using Expression (ESTIMATE) analysis, high ESTIMATE, and low tumor purity were significantly associated with a favorable prognosis. Moreover, a total of 5259 DEGs were retrieved, the majority of which were downregulated. In total, 590 immune-associated genes overlapped with the DEGs, among which nine hub genes were identified. Finally, two candidate genes, ACVR2B and NFYA, were identified, based on which a risk signature was constructed. The risk signature constructed in this study is accurate and reliable for the prognostic prediction and phenotyping of sarcomas.

A balance between NF-Y and p53 governs the pro- and anti-apoptotic transcriptional response

The transcription factor NF-Y is a trimer with histone-like subunits that binds and activates CCAAT-containing promoters. NF-Y controls the expression of several key regulators of the cell cycle. In this study, we examined the functional and molecular effects of NF-YB knockdown. Cell cycle progression is affected with a G2/M-specific depletion. This is due to the inability of activation of G2/M-specific genes, as evidenced by expression profiling, RT-PCR and ChIP data. Surprisingly, apoptosis is also observed, with Caspase 3/7/8 cleavage. A role of p53 and Bcl-2 family members is important. NF-YB inactivation is sufficient to functionally activate p53, in the absence of DNA damage. Failure to maintain a physiologic level of CCAAT-dependent transcription of anti-apoptotic genes contributes to impairment of Bax/Bcl-2 and Bax/Bcl-X_L ratios. Our data highlight the importance of fine balancing the NF-Y-p53 duo for cell survival by (i) maintaining transcription of anti-apoptotic genes and (ii) preventing p53 activation that triggers the apoptotic cascade.

The CCAAT-binding factor CBF/NF-Y regulates the human acetylcholinesterase promoter activity during calcium ionophore A23187-induced cell apoptosis

We previously reported that the expression of acetylcholinesterase during A23187-induced apoptosis of HeLa cells is regulated by Ca(2+) mobilization through the modulation of mRNA stability and acetylcholinesterase promoter activity. Transactivation of the human acetylcholinesterase promoter by A23187 was partially mediated by the distal CCAAT motif within the -1270 to -1248 fragment of the human acetylcholinesterase promoter, which was bound by the CCAAT binding factor (CBF/NF-Y). In the present study, we investigated the molecular mechanisms by which CBF/NF-Y regulates A23187-induced activation of the human acetylcholinesterase promoter. The results indicate that CBF/NF-Y binding to the distal CCAAT motif suppresses the promoter activity. Electrophoretic mobility shift assays (EMSAs) demonstrated that binding of CBF/NF-Y to the distal CCAAT motif decreased after A23187 treatment. Our results suggest that acetylcholinesterase promoter activation during A23187-induced HeLa cell apoptosis may result partly from the dissociation of CBF/NF-Y from the distal CCAAT motif in the acetylcholinesterase promoter, reversing this suppression.

Expression of the Op18 gene is maintained by the CCAAT-binding transcription factor NF-Y

Op18 (Oncoprotein 18, Stathmin) is a mitotic regulator that is highly expressed in many cancers. We have characterized four functional CCAAT boxes in the Op18 gene located at positions: -980, -745, -599 and -65, relative to the transcriptional start site. NF-Y is a ubiquitously expressed CCAAT-binding transcription factor that regulates a number of cell cycle controlled genes. We have used promoter-reporter assays and mobility shift assays to functionally examine these CCAAT boxes. All sites contribute to the basal expression of Op18, with the sites at -980 and -599 being repressive and the sites at -745 and -65 being stimulatory. Mobility shift assays indicate that all CCAAT box sites bind factors in nuclear extracts from Hek293. However, only the repressive site at -599 and the stimulatory site at -65 are competent to bind NF-Y, suggesting that NF-Y may play a role in promoting both activation and repression of Op18 expression. The NF-Y site at -65 accounts for greater than 60% of the Op18 gene expression. EMSA competition studies indicate that NF-Y binds with a much higher affinity to the -65 site than to the -599 site, suggesting that in asynchronously growing cells NF-Y functions only to stimulate expression through the -65 binding site. These data suggest that NF-Y is a major transcription factor promoting expression of Op18.

Recruitment of nuclear factor Y to the inverted CCAAT element (ICE) by c-Jun and E1A stimulates basal transcription of the bone sialoprotein gene in osteosarcoma cells

Bone sialoprotein (BSP), a major protein in the extracellular matrix of bone, is expressed almost exclusively by bone cells and by cancer cells that have a propensity to metastasize to bone. Previous studies have shown that v-src stimulates basal transcription of bsp in osteosarcoma (ROS 17/2.8) cells by targeting the inverted CCAAT element (ICE) in the proximal promoter. To identify possible downstream effectors of Src we studied the effects of the proto-oncogene c-jun, which functions downstream of Src, on basal transcription of bsp using transient transfection assays. Increased expression of endogenous c-Jun induced by the tumor promoter 12-O-tetradecanoyl-phorbol 13-acetate and ectopic expression of c-Jun increased basal transcription of chimeric reporter constructs encompassing the proximal promoter by 1.5-3-fold in ROS 17/2.8 osteosarcoma cells, with more modest effects in a normal bone cell line, RBMC-D8. The effects of c-Jun were abrogated by mutations in the ICE box and by co-expression of dominant negative nuclear factor Y, subunit A (NF-YA). The increase in bsp transcription did not require phosphorylation of c-Jun and was not altered by trichostatin treatment or by ectopic expression of p300/CREB-binding protein (CBP) or mutated forms lacking histone acetyltransferase (HAT) activity. Similarly, ectopic expression of p300/CBP-associated factor (P/CAF), which transduces p300/CBP effects, or of HAT-defective P/CAF did not influence the c-jun effects. Surprisingly, E1A, which competes with P/CAF binding to p300/CBP, also stimulated BSP transcription through NF-Y independently of c-jun, p300/CBP, and P/CAF. Collectively, these studies show that c-Jun and E1A regulate basal transcription of bsp in osteosarcoma cells by recruiting the NF-Y transcriptional complex to the ICE box in a mechanism that is independent of p300/CBP and P/CAF HAT activities.

p53 and its homologues, p63 and p73, induce a replicative senescence through inactivation of NF-Y transcription factor

Recent studies have identified two p53 homologues, p63 and p73. They activate p53-responsive promoters and induce apoptosis when overexpressed in certain human tumors. Here, we report that p63, like p53 and p73, induces replicative senescence when expressed in a tetracycline-regulated manner in EJ cells lacking a functional p53. In addition to transcription activation of p53-responsive genes, we found that p63 and p73 repress transcription of the cdk1 and cyclin B genes, both of which are irreversibly repressed in senescent human fibroblast. In transient transfection assay, p63 and p73 repress the cdk1 promoter regardless of the presence of a dominant negative mutant form of p53. Furthermore, we found that DNA binding activity of NF-Y transcription factor, which is essential for transcription of the cdk1 and cyclin B genes and inactivated in senescent fibroblast, is significantly decreased by expression of either of p53, p63, or p73. Since NF-Y binds to many promoters besides the cdk1 and cyclin B promoters, inactivation of NF-Y by p53 family genes may be a general mechanism for transcription repression in replicative senescence.

Activation of telomerase rna gene promoter activity by NF-Y, Sp1, and the retinoblastoma protein and repression by Sp3

Expression of the human telomerase RNA component gene, hTERC is essential for telomerase activity. The hTERC gene is expressed during embryogenesis and then downregulated during normal development, leaving most adult somatic cells devoid of hTERC expression. During oncogenesis, however, hTERC is re-expressed consequently contributing to the unrestricted proliferative capacity of many human cancers. Thus the identification of the molecular basis for the regulation of the telomerase RNA component gene in normal cells and its deregulation in cancer cells is of immediate interest. We have previously cloned the hTERC promoter and in this study have identified several transcription factors that modulate the expression of hTERC. We demonstrate that NF-Y binding to the CCAAT region of the hTERC promoter is essential for promoter activity. Sp1 and the retinoblastoma protein (pRb) are activators of the hTERC promoter and Sp3 is a potent repressor. These factors appear to act in a species-specific manner. Whereas Sp1 and Sp3 act on the human, bovine, and mouse TERC promoters, pRb activates only the human and bovine promoter, and NF-Y is only essential for the human TERC gene.

In vivo structure of the cell cycle-regulated human cdc25C promoter

The cdc25C promoter is regulated during the cell cycle by the transcriptional repressor CDF-1 that inhibits the activation function of upstream transcriptional activators, most notably the nuclear factor Y/CAAT box binding factor (NF-Y/CBF). In this report a detailed analysis of the in vivo structure of the cdc25C promoter was made. Micrococcus nuclease and methidiumpropyl-EDTA footprinting strongly suggest that the proximal promoter encompassing the cell cycle-dependent element/cell cycle genes homology region and the upstream NF-Y sites is organized in a positioned nucleosome throughout the cell cycle. Furthermore, structural perturbations were detected by DNase I, phenanthroline copper, and KMnO(4) footprinting at the NF-Y binding sites in vivo, which is in agreement with the reported property of NF-Y to bend DNA in vitro. Similar results were obtained with the structurally and functionally related cyclin A promoter. The structural perturbations seen in DNase I and phenanthroline copper footprints were less pronounced in G(0) cells when compared with cycling cells. This presumably reflects a weakened in vivo interaction of NF-Y with its cognate DNA element in G(0). It is likely that these structural perturbations, together with the reported ability of NF-Y to recruit histone acetyl transferase activity, contribute to an opened chromatin structure as a prerequisite for optimal regulation through activation and repression.

Nuclear factor Y (NF-Y) and cellular senescence

NF-Y, also termed CBF, is a major CCAAT-binding transcription factor that specifically recognizes the consensus sequence 5'-CTGATTGGYYRR-3 or 5'-YYRRCCAATCAG-3' (Y = pyrimidines and R = purines) present in the promoter region of many constitutive, inducible, and cell-cycle-dependent eukaryotic genes. The functional NF-Y is a heterotrimeric protein, consisting of three different subunits, A, B, and C. Each of the three subunits contains two or three distinct protein-interacting domains for trimer formation and for interacting with other nuclear proteins. Only the trimeric NF-Y, and not the individual subunit, possess DNA-binding activity. The transcriptional activity of NF-Y can be regulated by differential expression, alternative splicing, protein-protein interactions, and cellular redox potential. The regulation of thymidine kinase (TK) and dihydrofolate reductase (DHFR) genes in human diploid fibroblasts serves as an example of how NF-Y may have a role in replicative senescence by regulating age-dependent G1/S genes.

The molecular biology of the CCAAT-binding factor NF-Y

Protein coding genes are transcribed by Polymerase II, under the control of short discrete DNA elements in promoters and enhancers, recognized with high efficiency and specificity by trans-acting factors and by general transcription proteins (Tjian and Maniatis, 1994). The former regulate specific genes or set of genes, usually in a tissue-, developmental-, cell-cycle or stimuli-dependent way; the latter are involved in the activation of all promoters, as a whole multi-subunit holoenzyme (Parvis and Young, 1998). A limited set of elements, such as the GC and CCAAT-boxes, are present in a very high number of promoters. The whole process is further complicated by the need to operate in the context of higher order chromatin structures (Workman and Kingston, 1998). This review focuses on the CCAAT sequence and on the NF-Y protein, also known as CBF, which binds to it.

Transactivation of the human cdc2 promoter by adenovirus E1A. E1A induces the expression and assembly of a heteromeric complex consisting of the CCAAT box binding factor, CBF/NF-Y, and a 110-kDa DNA-binding protein

Cyclin-dependent kinases (CDKs) play an important role in the eukaryotic cell cycle progression. Cdc2 (CDK1) is expressed in late G(1)/S phase and required for G(2) to M phase transition in higher eukaryotes. The oncoproteins, SV40 large T antigen and adenovirus E1A, induce a 110-kDa protein which specifically recognizes the two inverted CCAAT motifs of the cdc2 promoter in cycling cells and plays an essential role in transactivation of the human cdc2 promoter. Since these CCAAT motifs also conform to the consensus binding sites for the ubiquitous heterotrimeric transcription factor, CBF/NF-Y, the role of CBF/NF-Y in the transactivation of the cdc2 promoter was examined in this study. Our results indicate that CBF/NF-Y and the 110-kDa protein interact with the CCAAT box motif to form a heteromeric complex. However, mutagenesis of the pentanucleotide CCAAT motif or in the presence of urea greater than 2.5 M, no heteromeric complex was formed. In contrast, the 110-kDa protein could still bind the mutant CCAAT motif or with the wild type motif in the presence of 2.5 M urea. Furthermore, E1A.12S induced the gene expression of all three subunits of CBF/NF-Y. Coexpression of E1A and a dominant negative mutant NF-YA subunit significantly reduced the E1A-mediated transactivation of the cdc2 promoter in a dose-dependent manner. These results support the conclusion that E1A protein mediates optimal transactivation of the human cdc2 promoter by inducing the expression and assembly of a heteromeric complex consisting of the 110-kDa protein and the CBF/NF-Y which interacts with the two CCAAT motifs of the cdc2 promoter.

The cyclin B2 promoter depends on NF-Y, a trimer whose CCAAT-binding activity is cell-cycle regulated

Cyclin B2 is a regulator of p34cdc2 kinase, involved in G2/M progression of the cell cycle, whose gene is strictly regulated at the transcriptional level in cycling cells. The mouse promoter was cloned and three conserved CCAAT boxes were found. In this study, we analysed the mechanisms leading to activation of the cyclin B2 CCAAT boxes: a combination of (i) genomic footprinting, (ii) transfections with single, double and triple mutants, (iii) EMSAs with nuclear extracts, antibodies and NF-Y recombinant proteins and (iv) transfections with an NF-YA dominant negative mutant established the positive role of the three CCAAT sequences and proved that NF-Y plays a crucial role in their activation. NF-Y, an ubiquitous trimer containing histone fold subunits, activates several other promoters regulated during the cell cycle. To analyse the levels of NF-Y subunits in the different phases of the cycle, we separated MEL cells by elutriation, obtaining fractions >80% pure. The mRNA and protein levels of the histone-fold containing NF-YB and NF-YC were invariant, whereas the NF-YA protein, but not its mRNA, was maximal in mid-S and decreased in G2/M. EMSA confirmed that the CCAAT-binding activity followed the amount of NF-YA, indicating that this subunit is limiting within the NF-Y complex, and suggesting that post-transcriptional mechanisms regulate NF-YA levels. Our results support a model whereby fine tuning of this activator is important for phase-specific transcription of CCAAT-containing promoters.