ATF site of human RB gene promoter is a responsive element of myogenic differentiation

Down-regulation of ATF1 leads to early neuroectoderm differentiation of human embryonic stem cells by increasing the expression level of SOX2

We reveal by high-throughput screening that activating transcription factor 1 (ATF1) is a novel pluripotent regulator in human embryonic stem cells (hESCs). The knockdown of ATF1 expression significantly up-regulated neuroectoderm (NE) genes but not mesoderm, endoderm, and trophectoderm genes. Of note, down-regulation or knockout of ATF1 with short hairpin RNA (shRNA), small interfering RNA (siRNA), or clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) was sufficient to up-regulate sex-determining region Y-box (SOX)2 and paired box 6 (PAX6) expression under the undifferentiated or differentiated conditions, whereas overexpression of ATF1 suppressed NE differentiation. Endogenous ATF1 was spontaneously down-regulated after d 1-3 of neural induction. By double-knockdown experiments, up-regulation of SOX2 was critical for the increase of PAX6 and SOX1 expression in shRNA targeting Atf1 hESCs. Using the luciferase reporter assay, we identified ATF1 as a negative transcriptional regulator of Sox2 gene expression. A novel function of ATF1 was discovered, and these findings contribute to a broader understanding of the very first steps in regulating NE differentiation in hESCs.-Yang, S.-C., Liu, J.-J., Wang, C.-K., Lin, Y.-T., Tsai, S.-Y., Chen, W.-J., Huang, W.-K., Tu, P.-W. A., Lin, Y.-C., Chang, C.-F., Cheng, C.-L., Lin, H., Lai, C.-Y., Lin, C.-Y., Lee, Y.-H., Chiu, Y.-C., Hsu, C.-C., Hsu, S.-C., Hsiao, M., Schuyler, S. C., Lu, F. L., Lu, J. Down-regulation of ATF1 leads to early neuroectoderm differentiation of human embryonic stem cells by increasing the expression level of SOX2.

Activating transcription factor 1 is a prognostic marker of colorectal cancer

OBJECTIVE

Identifying cancer-related genes or proteins is critical in preventing and controlling colorectal cancer (CRC). This study was to investigate the clinicopathological and prognostic value of activating transcription factor 1 (ATF1) in CRC.

METHODS

Protein expression of ATF1 was detected using immunohistochemistry in 66 CRC tissues. Clinicopathological association of ATF1 in CRC was analyzed with chi-square test or Fisher's exact test. The prognostic value of ATF1 in CRC is estimated using the Kaplan-Meier analysis and Cox regression models.

RESULTS

The ATF1 protein expression was significantly lower in tumor tissues than corresponding normal tissues (51.5% and 71.1%, respectively, P = 0.038). No correlation was found between ATF1 expression and the investigated clinicopathological parameters, including gender, age, depth of invasion, lymph node status, metastasis, pathological stage, vascular tumoral emboli, peritumoral deposits, chemotherapy and original tumor site (all with P > 0.05). Patients with higher ATF1 expression levels have a significantly higher survival rate than that with lower expression (P = 0.026 for overall survival, P = 0.008 for progress free survival). Multivariate Cox regression model revealed that ATF1 expression and depth of invasion were the predictors of the overall survival (P = 0.008 and P = 0.028) and progress free survival (P = 0.002 and P = 0.005) in CRC.

CONCLUSIONS

Higher ATF1 expression is a predictor of a favorable outcome for the overall survival and progress free survival in CRC.

Transcriptional regulation of ferritin and antioxidant genes by HIPK2 under genotoxic stress

ATF1 (activating transcription factor 1), a stimulus-induced CREB family transcription factor, plays important roles in cell survival and proliferation. Phosphorylation of ATF1 at Ser63 by PKA (cAMP-dependent protein kinase) and related kinases was the only known post-translational regulatory mechanism of ATF1. Here, we found that HIPK2 (homeodomain-interacting protein kinase 2), a DNA-damage-responsive nuclear kinase, is a new ATF1 kinase that phosphorylates Ser198 but not Ser63. ATF1 phosphorylation by HIPK2 activated ATF1 transcription function in the GAL4-reporter system. ATF1 is a transcriptional repressor of ferritin H, the major intracellular iron storage gene, through an ARE (antioxidant-responsive element). HIPK2 overrode the ATF1-mediated ARE repression in a kinase-activity-dependent manner in HepG2 cells. Furthermore, DNA-damage-inducing agents doxorubicin, etoposide and sodium arsenite induced ferritin H mRNA expression in HIPK2(+/+) MEF cells, whereas it was significantly impaired in HIPK2(-/-) MEF cells. Induction of other ARE-regulated detoxification genes such as NQO1 (NADPH quinone oxidoreductase 1), GST (glutathione S-transferase) and HO1 (heme oxygenase 1) by genotoxic stress was also decreased in HIPK2-deficient cells. Taken together, these results suggest that HIPK2 is a new ATF1 kinase involved in the regulation of ferritin H and other antioxidant detoxification genes in genotoxic stress conditions.

PIAS3 interacts with ATF1 and regulates the human ferritin H gene through an antioxidant-responsive element

Gene transcription is coordinately regulated by the balance between activation and repression mechanisms in response to various external stimuli. Ferritin, composed of H and L subunits, is the major intracellular iron storage protein involved in iron homeostasis. We previously identified an enhancer, termed antioxidant-responsive element (ARE), in the human ferritin H gene and its respective transcriptional activators including Nrf2 and JunD. Here we found that ATF1 (activating transcription factor 1) is a transcriptional repressor of the ferritin H ARE. Subsequent yeast two-hybrid screening identified PIAS3 (protein inhibitor of activated STAT3) as an ATF1-binding protein. Further investigation of the human ferritin H ARE regulation showed that 1) PIAS3 reversed ATF1-mediated repression of the ferritin H ARE; 2) ATF1 was sumoylated, but PIAS3, a SUMO E3 ligase, did not appear to play a major role in SUMO1-mediated ATF1 sumoylation or ATF1 transcription activating function; 3) PIAS3 decreased ATF1 binding to the ARE; and 4) ATF1 knockdown with siRNA increased ferritin H expression, whereas PIAS3 knockdown decreased basal expression and oxidative stress-mediated induction of ferritin H. These results suggest that PIAS3 antagonizes the repressor function of ATF1, at least in part by blocking its DNA binding, and ultimately activates the ARE. Collectively our results suggest that PIAS3 is a new regulator of ATF1 that regulates the ARE-mediated transcription of the ferritin H gene.

Visualizing dynamic E2F-mediated repression in vivo

Although many E2F target genes have been identified recently, very little is known about how any single E2F site controls the expression of an E2F target gene in vivo. To test the requirement for a single E2F site in vivo and to learn how E2F-mediated repression is regulated during development and tumorigenesis, we have constructed a novel series of wild-type and mutant Rb promoter-LacZ transgenic reporter lines that allow us to visualize the activity of a crucial E2F target in vivo, the retinoblastoma tumor suppressor gene (Rb). Two mutant Rb promoter-LacZ constructs were used to evaluate the importance of a single E2F site or a nearby activator (Sp1/Ets) site that is found mutated in low-penetrance retinoblastomas. The activity of the wild-type Rb promoter is dynamic, varying spatially and temporally within the developing nervous system. While loss of the activator site silences the Rb promoter, loss of the E2F site stimulates its activity in the neocortex, retina, and trigeminal ganglion. Surprisingly, E2F-mediated repression of Rb does not act globally or in a static manner but, instead, is a highly dynamic process in vivo. Using neocortical extracts, we detected GA-binding protein alpha (GABPalpha, an Ets family member) bound to the activator site and both E2F1 and E2F4 bound to the repressor site of the Rb promoter in vitro. Additionally, we detected binding of both E2F1 and E2F4 to the Rb promoter in vivo using chromatin immunoprecipitation analysis on embryonic day 13.5 brain. Unexpectedly, we detect no evidence for Rb promoter autoregulation in neuroendocrine tumors from Rb+/-; RbP-LacZ mice that undergo loss of heterozygosity at the Rb locus, in contrast to the situation in human retinoblastomas where high RB mRNA levels are found. In summary, this study provides the first demonstration that loss of an E2F site is critical for target gene repression in vivo and underscores the complexity of the Rb and E2F family network in vivo.

Footprinting the 'essential regulatory region' of the retinoblastoma gene promoter in intact human cells

The retinoblastoma tumour suppressor protein is a key cell cycle regulator. Protein-DNA interactions at the retinoblastoma (RB1) promoter, including the 'essential regulatory region', were investigated using novel DNA-targeted nitrogen mustards in intact human cells. The footprinting experiments were carried out in two different environments: in intact HeLa and K562 cells where the access of DNA-targeted probes to chromatin is affected by cellular protein-DNA interactions associated with gene regulation; and in purified DNA where their access is unencumbered by protein-DNA interactions. Using the ligation-mediated PCR (LMPCR) technique, the sites of damage were determined at base pair resolution on DNA sequencing gels. Our results demonstrate that, in intact cells, footprints were observed at the E2F, ATF and RBF1/Sp1 DNA binding motifs in the RB1 promoter. In addition, a novel footprint was observed at a previously unidentified cycle homology region (CHR) and at four uncharacterised protein-DNA binding sites. In further experiments, nitrogen mustard-treated cells were FACS sorted into G1, S and G2/M phases of the cell cycle prior to LMPCR analysis. Expression of the RB1 gene is cell cycle-regulated and footprinting studies of the promoter in FACS-sorted cells indicated that transcription factor binding at the GC box, CHR binding motif and the 'essential regulatory region' are cell cycle dependent.

Sequence-specific transcriptional repression by an MBD2-interacting zinc finger protein MIZF

MBD2 is a member of the methyl-CpG-binding protein family that plays an important role in methylated DNA silencing. We have recently identified a novel zinc finger protein, MIZF, as an MBD2-binding partner. To understand the physiological function of MIZF in MBD2-mediated gene silencing, we investigated the DNA-binding properties of MIZF and its potential target genes. Using a cyclic amplification and selection of targets technique, the consensus sequence CGGACGTT, which contains a conserved CGGAC core, was determined as sufficient for MIZF binding. Deletion of individual zinc fingers revealed that five of the seven zinc fingers are required for DNA binding. Reporter assays demonstrated that MIZF represses transcription from the promoter including this DNA sequence. A database search indicated that a variety of human genes, including Rb, contain this sequence in their promoter region. MIZF actually bound to its recognition sequence within the Rb promoter and repressed Rb transcription. These results suggest that MIZF, through its DNA-binding activity, acts as a sequence-specific transcriptional repressor likely involved in MBD2-mediated epigenetic gene silencing.

MyoD stimulates RB promoter activity via the CREB/p300 nuclear transduction pathway

The induction of RB gene transcription by MyoD is a key event in the process of skeletal muscle differentiation, because elevated levels of the retinoblastoma protein are essential for myoblast cell cycle arrest as well as for the terminal differentiation and survival of postmitotic myocytes. We previously showed that MyoD stimulates transcription from the RB promoter independently of direct binding to promoter sequences. Here we demonstrate that stimulation by MyoD requires a cyclic AMP-responsive element (CRE) in the RB promoter, bound by the transcription factor CREB in differentiating myoblasts. We also show that both the CREB protein level and the level of phosphorylation of the CREB protein at Ser-133 rapidly increase at the onset of muscle differentiation and that both remain high throughout the myogenic process. Biochemical and functional evidence indicates that in differentiating myoblasts, MyoD becomes associated with CREB and is targeted to the RB promoter CRE in a complex also containing the p300 transcriptional coactivator. The resulting multiprotein complex stimulates transcription from the RB promoter. These and other observations strongly suggest that MyoD functions by promoting the efficient recruitment of p300 by promoter-bound, phosphorylated CREB.

Molecular mechanism of transcriptional repression of gelsolin in human breast cancer cells

Loss of gelsolin, a tumor suppressor, is one of the most frequently occurring molecular defects in breast cancers of diverse etiologies and across at least three animal species: human, mouse, and rat. Our previous analysis of breast cancer cells demonstrated that the deficiency is not due to mutation of the gelsolin gene, but instead to epigenetic factors, including decreased transcription of the gene. The study described herein provides the first functional characterization of the human gelsolin promoter and reveals a mechanistic basis for the reduced gelsolin transcription. In reporter gene assays, the gelsolin promoter was less active in low-gelsolin-expressing breast cancer cells. A cis-element mediating this reduced promoter activity was defined as a 27-bp sequence located approximately 135 bp upstream of the transcription start site. Gel shift and supershift assays and Southwestern blotting analysis indicated that activating transcription factor-1 (ATF-1) and a protein of approximately 100 kDa may have cancer cell-specific DNA-binding activity to the 27-bp gelsolin cis-element. Although the ATF-1 protein was highly expressed in both benign and tumorigenic breast cells, its DNA-binding activity was selectively abundant in the cancer cells and correlated inversely with the gelsolin mRNA level. Thus, our results suggest a role for ATF-1 in gelsolin promoter silencing in contrast to its transactivating effect on various other promoters.

Isolation and characterization of chicken TaxREB107, a putative DNA binding protein abundantly expressed in muscle

Myogenic regulatory factors (MRFs) are vital transcription factors that act at multiple points during development to establish the skeletal muscle phenotype. This class of muscle-restricted, basic helix-loop-helix (bHLH) proteins acts in concert with additional transcriptional modulators to precisely control muscle gene expression. We have isolated the chicken homologue of Tax responsive element binding protein 107 (TaxREB107). The cDNA is 83% homologous at the amino acid level to human and mouse TaxREB107 and contains a centrally located leucine zipper motif. Northern analysis demonstrated that the gene is expressed in multiple tissues including skeletal muscle. Immunofluorescent staining revealed that the cTaxREB107 protein is located in both the nuclear and cytoplasmic compartments. Distinct localization to the nucleoli supports the evidence that TaxREB107 is a ribosomal protein. Because TaxREB proteins also are implicated in transcriptional regulation, we overexpressed cTaxREB107 in embryonic myoblasts. cTaxREB107 increased troponin I reporter gene activity as well as MRF-directed transcription from a multimerized skeletal muscle E-box reporter gene (4Rtk-luc). However, cotransfection of expression plasmids coding for MyoD and cTaxREB107 did not produce an increase in 4Rtk-luc suggesting that cTaxREB107 enhances myogenic gene transcription through a means independent of a physical association with MyoD. In conclusion, our results define a role for cTaxREB107 during avian myogenesis as a positive modulator of skeletal muscle gene expression.

p53 regulates myogenesis by triggering the differentiation activity of pRb

The p53 oncosuppressor protein regulates cell cycle checkpoints and apoptosis, but increasing evidence also indicates its involvement in differentiation and development. We had previously demonstrated that in the presence of differentiation-promoting stimuli, p53-defective myoblasts exit from the cell cycle but do not differentiate into myocytes and myotubes. To identify the pathways through which p53 contributes to skeletal muscle differentiation, we have analyzed the expression of a series of genes regulated during myogenesis in parental and dominant-negative p53 (dnp53)-expressing C2C12 myoblasts. We found that in dnp53-expressing C2C12 cells, as well as in p53(-/-) primary myoblasts, pRb is hypophosphorylated and proliferation stops. However, these cells do not upregulate pRb and have reduced MyoD activity. The transduction of exogenous TP53 or Rb genes in p53-defective myoblasts rescues MyoD activity and differentiation potential. Additionally, in vivo studies on the Rb promoter demonstrate that p53 regulates the Rb gene expression at transcriptional level through a p53-binding site. Therefore, here we show that p53 regulates myoblast differentiation by means of pRb without affecting its cell cycle-related functions.

Genomic organization and promoter analysis of the murine Id3 gene

Overexpression of the helix-loop-helix motif-containing transcription inhibitor Id3 has been shown to repress muscle-specific gene expression. Consistent with its putative negative regulatory role in the myogenic process, Id3 is highly expressed in proliferating myoblasts but down regulated when myoblasts are induced to differentiate. To investigate how Id3 expression may be transcriptionally regulated, we isolated a mouse Id3 genomic DNA fragment and characterized its organization and promoter activity. Comparison of the Id3 gene from human and mouse demonstrated a conserved exon-intron organization in which the first intron interrupts the C-terminal protein coding region and the second intron interrupts the 3' untranslated region at analogous positions in the two species. Sequence analysis of the 5'-flanking region revealed an unexpected mouse strain-specific genetic polymorphism due to a single base substitution. Deletion analysis revealed that as little as 180 base pairs of the mouse Id3 promoter upstream of the transcription start site is sufficient for a high level of gene expression in proliferating C2C12 myoblasts. In particular, the region between the nucleotide position -180 and -34 appeared to be crucial for maximal reporter gene activity and interacted specifically with C2C12 nuclear proteins. Finally, we showed that, despite the creation of a putative transcription factor-binding site, the genetic polymorphism observed did not affect Id3 promoter activity in proliferating C2C12 cells.

Differentiation-related changes in the cell cycle traverse

This review examines recent developments relating to the interface between cell proliferation and differentiation. It is suggested that the mechanism responsible for this transition is more akin to a "dimmer" than to a "switch," that it is more useful to refer to early and late stages of differentiation rather than to "terminal" differentiation, and examples of the reversibility of differentiation are provided. An outline of the established paradigm of cell cycle regulation is followed by summaries of recent studies that suggest that this paradigm is overly simplified and should be interpreted in the context of different cell types. The role of inhibitors of cyclin-dependent kinases in differentiation is discussed, but the data are still inconclusive. An increasing interest in the changes in G2/M transition during differentiation is illustrated by examples of polyploidization during differentiation, such as megakaryocyte maturation. Although the retinoblastoma protein is currently maintaining its prominent role in control of proliferation and differentiation, it is anticipated that equally important regulators will be discovered and provide an explanation at the molecular level for the gradual transition from proliferation to differentiation.