Roberto Mantovani

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.

Complex Transcriptional Effects of p63 Isoforms: Identification of Novel Activation and Repression Domains†

ABSTRACT p63 is a transcription factor structurally related to the p53 tumor suppressor. The C-terminal region differs from p53s in that it contains a sterile alpha motif (SAM) domain and is subject to multiple alternative splicings. The N-terminal region is present in the transactivation (TA) and ΔN configurations, with the latter lacking the transcriptional activation domain 1. Single amino acid substitutions and frameshift mutations of p63 cause the human ankyloblepharon ectodermal dysplasia clefting (AEC) or ectrodactyly ectodermal dysplasia and facial clefting (EEC) syndromes. We have systematically compared the activities of the wild-type p63 isoforms and of the natural mutants in activation and repression assays on three promoters modulated by p53. We found that p63 proteins with an altered SAM domain or no SAM domain—the β isoforms, the EEC frameshift mutant, and the missense AEC mutations—all showed a distinctly higher level of activation of the MDM2 promoter and decreased repression on the HSP70 promoter. Fusion of SAM to the GAL4 DNA-binding domain repressed a heterologous promoter. A second activation domain, TA2, corresponding to exons 11 to 12, was uncovered by comparing the activation of ΔN isoforms on natural promoters and in GAL4 fusion systems. In colony formation assays, the AEC mutants, but not the EEC frameshift, were consistently less efficient in suppressing growth, in both the TA version and the ΔN version, with respect to their p63α counterparts. These data highlight the modularity of p63, identifying the SAM domain as a dominant transcriptional repression module and indicating that the AEC and EEC frameshift mutants are characterized by a subversion of the p63 transcriptional potential.

Direct p53 transcriptional repression: in vivo analysis of CCAAT-containing G2/M promoters.

ABSTRACT In response to DNA damage, p53 activates G1/S blocking and apoptotic genes through sequence-specific binding. p53 also represses genes with no target site, such as those for Cdc2 and cyclin B, key regulators of the G2/M transition. Like most G2/M promoters, they rely on multiple CCAAT boxes activated by NF-Y, whose binding to DNA is temporally regulated during the cell cycle. NF-Y associates with p53 in vitro and in vivo through the αC helix of NF-YC (a subunit of NF-Y) and a region close to the tetramerization domain of p53. Chromatin immunoprecipitation experiments indicated that p53 is associated with cyclin B2, CDC25C, and Cdc2 promoters in vivo before and after DNA damage, requiring DNA-bound NF-Y. Following DNA damage, p53 is rapidly acetylated at K320 and K373 to K382, histones are deacetylated, and the release of PCAF and p300 correlates with the recruitment of histone deacetylases (HDACs)—HDAC1 before HDAC4 and HDAC5—and promoter repression. HDAC recruitment requires intact NF-Y binding sites. In transfection assays, PCAF represses cyclin B2, and a nonacetylated p53 mutant shows a complete loss of repression potential, despite its abilities to bind NF-Y and to be recruited on G2/M promoters. These data (i) detail a strategy of direct p53 repression through associations with multiple NF-Y trimers that is independent of sequence-specific binding of p53 and that requires C-terminal acetylation, (ii) suggest that p53 is a DNA damage sentinel of the G2/M transition, and (iii) delineate a new role for PCAF in cell cycle control.

Monoclonal antibodies to NF-Y define its function in MHC class II and albumin gene transcription.

NF‐Y is a sequence‐specific DNA‐binding protein which, as a heterodimer, recognizes CCAAT motifs in a variety of transcriptional promoters. We have generated a panel of monoclonal and affinity‐purified polyclonal antibodies directed against various epitopes of NF‐Y. These reagents are highly specific for either of the A or B subunits; we have mapped the epitopes recognized by the monoclonal antibodies to the glutamine‐rich activation domain of NF‐YA. The antibodies inhibit in vitro transcription from the promoters of the albumin gene and of Ea, a class II gene of the major histocompatibility complex. These data definitively demonstrate the role of NF‐Y in regulating the transcription of two tissue‐specific genes whose expression patterns do not overlap. Interestingly, the antibodies cannot inhibit a formed pre‐initiation complex, but do block reinitiation of subsequent rounds of transcription from the same templates.

Np95 Is a Histone-Binding Protein Endowed with Ubiquitin Ligase Activity

ABSTRACT Np95 is an important determinant in cell cycle progression. Its expression is tightly regulated and becomes detectable shortly before the entry of cells into S phase. Accordingly, Np95 is absolutely required for the G1/S transition. Its continued expression throughout the S/G2/M phases further suggests additional roles. Indeed, Np95 has been implicated in DNA damage response. Here, we show that Np95 is tightly bound to chromatin in vivo and that it binds to histones in vivo and in vitro. The binding to histones is direct and shows a remarkable preference for histone H3 and its N-terminal tail. A novel protein domain, the SRA-YDG domain, contained in Np95 is indispensable both for the interaction with histones and for chromatin binding in vivo. Np95 contains a RING finger. We show that this domain confers E3 ubiquitin ligase activity on Np95, which is specific for core histones, in vitro. Finally, Np95 shows specific E3 activity for histone H3 when the endogenous core octamer, coimmunoprecipitating with Np95, is used as a substrate. Histone ubiquitination is an important determinant in the regulation of chromatin structure and gene transcription. Thus, the demonstration that Np95 is a chromatin-associated ubiquitin ligase suggests possible molecular mechanisms for its action as a cell cycle regulator.

The Promiscuous Life of Plant NUCLEAR FACTOR Y Transcription Factors

The CCAAT box is one of the most common cis-elements present in eukaryotic promoters and is bound by the transcription factor NUCLEAR FACTOR Y (NF-Y). NF-Y is composed of three subunits, NF-YA, NF-YB, and NF-YC. Unlike animals and fungi, plants have significantly expanded the number of genes encoding NF-Y subunits. We provide a comprehensive classification of NF-Y genes, with a separation of closely related, but distinct, histone fold domain proteins. We additionally review recent experiments that have placed NF-Y at the center of many developmental stress-responsive processes in the plant lineage.

NF-Y and the transcriptional activation of CCAAT promoters

The CCAAT box promoter element and NF-Y, the transcription factor (TF) that binds to it, were among the first cis-elements and trans-acting factors identified; their interplay is required for transcriptional activation of a sizeable number of eukaryotic genes. NF-Y consists of three evolutionarily conserved subunits: a dimer of NF-YB and NF-YC which closely resembles a histone, and the “innovative” NF-YA. In this review, we will provide an update on the functional and biological features that make NF-Y a fundamental link between chromatin and transcription. The last 25 years have witnessed a spectacular increase in our knowledge of how genes are regulated: from the identification of cis-acting sequences in promoters and enhancers, and the biochemical characterization of the corresponding TFs, to the merging of chromatin studies with the investigation of enzymatic machines that regulate epigenetic states. Originally identified and studied in yeast and mammals, NF-Y – also termed CBF and CP1 – is composed of three subunits, NF-YA, NF-YB and NF-YC. The complex recognizes the CCAAT pentanucleotide and specific flanking nucleotides with high specificity (Dorn et al., 1997; ; ; ). A compelling set of bioinformatics studies clarified that the NF-Y preferred binding site is one of the most frequent promoter elements (; ; ; ; ; ; ; ; ; ; ). The same consensus, as determined by mutagenesis and SELEX studies (), was also retrieved in ChIP-on-chip analysis (; ; ; ). Additional structural features of the CCAAT box – position, orientation, presence of multiple Transcriptional Start Sites – were previously reviewed () and will not be considered in detail here.

Trabectedin (ET-743) promotes differentiation in myxoid liposarcoma tumors

Differentiation is a complex set of events that can be blocked by rearrangements of regulatory genes producing fusion proteins with altered properties. In the case of myxoid liposarcoma (MLS) tumors, the causative abnormality is a fusion between the CHOP transcription factor and the FUS or EWS genes. CHOP belongs to and is a negative regulator of the large CAAT/enhancer binding protein family whose α, β,and δ members are master genes of adipogenesis. Recent clinical data indicate a peculiar sensitivity of these tumors to the natural marine compound trabectedin. One hypothesis is that the activity of trabectedin is related to the inactivation of the FUS-CHOP oncogene. We find that trabectedin causes detachment of the FUS-CHOP chimera from targeted promoters. Reverse transcription-PCR and chromatin immunoprecipitation analysis in a MLS line and surgical specimens of MLS patients in vivo show activation of the CAAT/enhancer binding protein–mediated transcriptional program that leads to morphologic changes of terminal adipogenesis. The activity is observed in cells with type 1 but not type 8 fusions. Hence, the drug induces maturation of MLS lipoblasts in vivo by targeting the FUS-CHOP–mediated transcriptional block. These data provide a rationale for the specific activity of trabectedin and open the perspective of combinatorial treatments with drugs acting on lipogenic pathways. [Mol Cancer Ther 2009;8(2):449–57]

ΔNp63 regulates thymic development through enhanced expression of FgfR2 and Jag2

p63, a homologue of the tumor suppressor p53, is pivotal for epithelial development, because its loss causes severe epithelial dysgenesis, although no information is so far available on the role of p63 in the thymus. We identified the expression of all p63 isoforms in the developing thymus. The p63−/− thymi show severe abnormalities in size and cellularity, even though the organ expresses normal levels of keratins 5 and 8, indicating a p63-independent differentiation of thymic epithelial cells (TEC). TEC were sufficiently developed to allow a significant degree of education to produce CD4/CD8 single- and double-positive T cells. To study the selective contribution of transactivation-active p63 (TAp63) and amino-deleted p63 (ΔNp63) isoforms to the function of the TEC, we genetically complemented p63−/− mice by crossing p63+/− mice with transgenic mice expressing either TAp63α or ΔNp63α under the control of the keratin 5 promoter. Thymic morphology and cellularity were partially restored by complementation with ΔNp63, but not TAp63, one downstream effector being fibroblast growth factor receptor 2-IIIb (FgfR2-IIIb). Indeed, FgfR2-IIIb is regulated directly by p63, via its interaction with apobec-1-binding protein-1, and its knockout shows thymic defects similar to those observed in p63−/− thymi. In addition, expression of Jag2, a component of the Notch signaling pathway known to be required for thymic development, was enhanced by p63 in vivo genetic complementation. Like Jag2−/− thymi, p63−/− thymi also show reduced γδ cell formation. Therefore, p63, and particularly the ΔNp63 isoform, is essential for thymic development via enhanced expression of FgfR2 and Jag2. The action of ΔNp63 is not due to a direct regulation of TEC differentiation, but it is compatible with maintenance of their “stemness,” the thymic abnormalities resulting from epithelial failure due to loss of stem cells.

Regulation of the CCAAT-Binding NF-Y subunits in Arabidopsis thaliana

NF-Y is a CCAAT-specific binding factor composed of three distinct subunits. In vertebrates and fungi all three subunits are encoded by evolutionary conserved single copy genes. In this report we have cloned twenty-three NF-Y genes in A. thaliana, assessed their mRNA expression levels in a large number of tissues and confirmed that indeed multiple CCAAT-binding activities are present. Alignments of the genes coding for the three NF-Y subunits yield a considerable amount of information concerning the divergence/conservation of protein subdomains and of single residues within the conserved parts. Careful evaluation of mRNA expression levels by sensitive RT-PCR assays provide evidence that all three subunits have members that are ubiquitous and others that are tissue-specific and induced only after the switch to reproductive growth phase, in flowers and siliques.