Sp1 is essential and its position is important for p120 gene transcription: a 35 bp juxtaposed positive regulatory element enhances transcription 2.5 fold

Genome-wide identification of YABBY transcription factors in Brachypodium distachyon and functional characterization of Bd DROOPING LEAF

YABBY transcription factors (TFs) are plant-specific and are characterized by a C2-C2 zinc finger domain at the N-terminus and a YABBY domain at the C-terminus. In this study, eight YABBY genes were identified in the Brachypodium distachyon genome and were unevenly distributed across four chromosomes. Phylogenetic analysis classified BdYABBYs into FIL/YAB3, YAB2, CRC, and INO clades. Sixty-two putative cis-elements were identified in BdYABBY gene putative promoters, among them, CAAT-box, TATA-box, MYB, MYC, ARE, and Box_4 were shared by all. BdYABBY genes are highly expressed in inflorescences, and abiotic stresses regulate their expression. In addition, three transcripts of BdDL were identified. Over-expression in Arabidopsis has shown their different functions in reproductive development, as well as in response to cold stress. Our study lays the foundation for the functional elucidation of BdYABBY genes.

Genome-wide identification, expression analyses of Wuschel-related homeobox (WOX) genes in Brachypodium distachyon and functional characterization of BdWOX12

As one kind of plant-specific transcription factors (TFs), WOX (Wuschel-related homeobox) plays an essential role in plant growth and development. In this study, 21 WOX TFs were identified in Brachypodium distachyon. They were divided into ancient, intermediate, and WUS clades based on phylogenetic analysis. These 21 BdWOX genes are mapped on 5 chromosomes unevenly. In the promoters, the most abundant cis-elements are ABRE, TGACG-motif, and G-box. qRT-PCR results showed that most BdWOX genes are expressed in vegetative and reproductive organs. Meanwhile, the expression of 14, 12, and 15 BdWOX genes are up-regulated by exogenous 6-BA, NAA, and GA, respectively. These results indicated that BdWOX genes participate in hormone signaling and regulate plant growth and development. Overexpression of BdWOX12 in Arabidopsis improved the root system, further indicating the functions of BdWOX genes in growth and development. This study provided a basis for the functional elucidation of BdWOX genes.

Genome-wide identification and expression profiles of ERF subfamily transcription factors in Zea mays

The Ethylene-Response Factor (ERF) subfamily transcription factors (TFs) belong to the APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily and play a vital role in plant growth and development. However, identification and analysis of the ERF subfamily genes in maize have not yet been performed at genome-wide level. In this study, a total of 76 ERF subfamily TFs were identified and were found to be unevenly distributed on the maize chromosomes. These maize ERF (ZmERF) TFs were classified into six groups, namely groups B1 to B6, based on phylogenetic analysis. Synteny analysis showed that 50, 54, and 58 of the ZmERF genes were orthologous to those in rice, Brachypodium, and Sorghum, respectively. Cis-element analysis showed that elements related to plant growth and development, hormones, and abiotic stress were identified in the promoter region of ZmERF genes. Expression profiles suggested that ZmERF genes might participate in plant development and in response to salinity and drought stresses. Our findings lay a foundation and provide clues for understanding the biological functions of ERF TFs in maize.

Genome-wide identification of expansin genes in Brachypodium distachyon and functional characterization of BdEXPA27

Plant expansin belongs to a group of cell wall proteins and functions in plant growth and development. However, limited data are available on the contributions of expansins in Brachypodium distachyon. In the present study, a total of 38 expansins were identified in B. distachyon genome. Phylogenetic analysis divided the expansins into four groups, namely EXPA, EXPB, EXLA, and EXLB. Chromosomal distribution showed that they were unevenly distributed on 4 chromosomes. A total of six tandem duplication pairs and four segmental duplication pairs were detected, which contributed to the expansion of the B. distachyon expansin gene family. Expansins in the same group shared similar gene structure and motif composition. Three types of cis-elements, development-related, hormone-related, and abiotic stresses-related elements were found in the B. distachyon expansin gene promoters. Expression profiles indicated that most of B. distachyon expansin genes participate in plant development and abiotic stress responses. Overexpression of BdEXPA27 increased seed width and length, root length, root hair number and length in Arabidopsis and showed higher germination rate in transgenic lines. This study establishes a foundation for further investigation of B. distachyon expansin genes and provides novel insights into their biological functions.

Characteristics and Expression Pattern of MYC Genes in Triticum aestivum, Oryza sativa, and Brachypodium distachyon

Myelocytomatosis oncogenes (MYC) transcription factors (TFs) belong to basic helix-loop-helix (bHLH) TF family and have a special bHLH_MYC_N domain in the N-terminal region. Presently, there is no detailed and systematic analysis of MYC TFs in wheat, rice, and Brachypodium distachyon. In this study, 26 TaMYC, 7 OsMYC, and 7 BdMYC TFs were identified and their features were characterized. Firstly, they contain a JAZ interaction domain (JID) and a putative transcriptional activation domain (TAD) in the bHLH_MYC_N region and a BhlH region in the C-terminal region. In some cases, the bHLH region is followed by a leucine zipper region; secondly, they display tissue-specific expression patterns: wheat MYC genes are mainly expressed in leaves, rice MYC genes are highly expressed in stems, and B. distachyon MYC genes are mainly expressed in inflorescences. In addition, three types of cis-elements, including plant development/growth-related, hormone-related, and abiotic stresses-related were identified in different MYC gene promoters. In combination with the previous studies, these results indicate that MYC TFs mainly function in growth and development, as well as in response to stresses. This study laid a foundation for the further functional elucidation of MYC genes.

p120 nucleolar-proliferating antigen is a direct target of G-CSF signaling during myeloid differentiation

Granulocyte-colony stimulating factor (G-CSF) is an essential cytokine, which contributes to proliferation and differentiation of granulocyte precursor cells in the bone marrow. Despite recent progress in understanding G-CSF signaling events, the mechanisms that underlie the distinct spectrum of biological functions attributed to G-CSF-mediated gene expression remain unclear. Previous studies have identified a number of genes, which are up-regulated in G-CSF-stimulated myeloid precursor cells. In this study, we sought to identify additional target genes of G-CSF-mediated proliferation and/or differentiation. cDNA representational difference analysis was used with the 32Dcl3 cell line as a model system to isolate genes, which are up-regulated in an immediate-early manner upon G-CSF stimualtion. We isolated p120 nucleolar-proliferation antigen (NOL1), a highly conserved, nucleolar-specific, RNA-binding protein of unknown function, and confirmed its expression by Northern blot analysis in 4-h, G-CSF-induced 32Dcl3 cells. Isolation of a mouse p120 genomic clone revealed the presence of a signal tranducer and activator of transcription (STAT)-binding site in the first intron of the gene. We demonstrate the importance of STAT3 and STAT5 in mediating the G-CSF response with respect to p120 expression by transient transfection analysis, oligonucleotide pull-down assays, and the loss of p120 expression in the bone marrow of mice lacking normal STAT3 signaling. In addition, overexpression of p120 in G-CSF-induced 32D cells revealed normal, morphologic maturation and growth characteristics but loss of lactoferrin expression, a marker of normal neutrophil maturation, suggesting that inappropriate expression of the p120 gene can result in aberrant neutrophil maturation.

Expression of nucleolar protein p120 predicts poor prognosis in patients with stage I lung adenocarcinoma

BACKGROUND

P120 is a proliferation-associated nucleolar protein found in most human malignant tumors, but not in resting normal cells. In our previous studies, the expression of p120 was statistically correlated with the proliferation capacity in human lung cancer cells and could be a prognostic marker for resected lung adenocarcinoma.

PATIENTS AND METHODS

The expression levels of p120 in tumors were assessed by immunohistochemistry in 59 patients with stage I lung adenocarcinoma who underwent radical resection. Using clinical follow-up data, the prognostic significance of p120 calculated by labeling indices was evaluated using Cox's proportional hazard model.

RESULTS

A mean +/- SD of the labeling index of p120 was 35.3+/-14.4%. No significant correlation was found between the expression levels of p120 and clinicopathological factors. Using a cutoff value of 35% in the labeling index of p120, patients with high expression of p120 experienced early recurrence and shorter survival compared with those having low expression of p120 (P = 0.04). Multivariate analysis revealed that p120 served as an independent and strongest prognostic factor for resected lung adenocarcinoma (P = 0.033).

CONCLUSION

This article provides the first evidence that the expression levels of p120 in tumor tissues can be used as an independent and powerful prognostic marker for resected stage I lung adenocarcinoma.

Differential expression of lacZ in the liver and kidney of transgenic mice carrying chimeric lacZ-erythropoietin gene constructs with or without its 1.2 kb 3'-flanking sequence

Erythropoietin (EPO) plays a key role in erythropoiesis and is expressed predominantly in the fetal liver and in the adult kidney. The EPO gene is up-regulated at the transcriptional level under hypoxic/anemic conditions. We studied the role of the 5'- and 3'-flanking sequences of the mouse EPO gene in its tissue-specific and hypoxia-induced expression by developing transgenic mouse lines carrying chimeric EPO-lacZ gene constructs. Transgenic mice carrying a 6.5 kb segment of the 5'-sequence and most of the EPO gene in which lacZ was substituted for exon 1 (5'-lacZ-EPO) demonstrated induction of lacZ expression following hypoxia/ anemia induction in both the liver and kidney of adult mice. However, transgenic mice carrying the above construct along with the 1.2 kb 3'-flanking sequence (5'-lacZ-EPO-3') showed a high level of lacZ expression following hypoxia/anemia induction in adult kidney but not in adult liver. With the aim of further understanding the role of the 3'-flanking sequence in tissue-specific expression of the EPO gene, we studied the interactions of protein factors with this 1.2 kb 3' region and demonstrated that multiple sets of protein factors interact tissue specifically with a 10 bp sequence, TCAAAGATGG, located downstream of the previously characterized 3' hypoxia-responsive enhancer element.

Nucleolar p120 is expressed as a delayed early response gene and is inducible by DNA-damaging agents

Regulation of the expression of the growth-related nucleolar p120 protein was examined in serum-deprived and stimulated nontransformed and SV40-transformed WI-38 human fibroblasts. In quiescent cells, transcriptional activity of the p120 gene was very low or undetectable, and the steady-state levels of the p120 mRNA and the p120 protein were also negligible. The transient expression of the p120 gene in the cell cycle was detected in middle G1-phase after the expression of the early response genes and before the expression of the DNA-synthesis genes. Protein synthesis was required for the induction of p120 expression in serum-stimulated cells. The increased level of p120 mRNA in middle G1-phase was attributed to an increased transcription rate of the p120 gene, and not to a change in p120 mRNA stability. The calculated half-life of p120 mRNA was unchanged (1.8 +/- 0.2 hr) in all four cell conditions tested; i.e., in middle G1- or S-phase cells and in exponentially growing normal or transformed cells. Transcription rate of the p120 gene was correlated with the steady-state levels of either p120 protein or p120 mRNA. A sharp increase in p120 mRNA level occurred in both normal and transformed cells treated with actinomycin D used to examine p120 mRNA stability. This induction of p120 mRNA expression was seen in early G1-phase, but not in quiescent cells, or in middle to late G1-phase when cells expressed the highest level of p120 mRNA. The same expression pattern was seen by treatment with chlorambucil, another DNA-damaging agent. The conclusions of these studies are that the expression of p120 (1) is serum inducible in a fashion characteristic of the delayed early response gene products, (2) requires the presence of newly synthesized proteins, (3) is regulated transcriptionally, and (4) can be induced by DNA-damaging agents.

Altered transcription control is responsible for the increased level of proliferation-associated P120 in rapidly growing breast carcinoma

Transcriptional and post-transcriptional regulation of proliferation-associated nucleolar P120 protein expression was examined in 1 normal and 5 malignant breast cell lines. The 6 breast cell lines could be placed into 3 categories on the basis of in vitro growth rate. BT549 and HBL100 grew rapidly; MCF-7/6, MCF-7/AZ and Hs578T grew at a moderate rate; and Hs578N normal epithelia grew slowly. There was a significant correlation between the growth rate, measured by percentage of S-phase fraction of cells or doubling time of cell numbers and the steady-state levels of either P120 protein or P120 mRNA. Next, the mechanisms responsible for the increased level of P120 expression, which is associated with rapidly growing breast carcinoma, were examined. The stability of P120 mRNA was measured by densitometry of quantitative Northern blots of mRNAs from cells treated with actinomycin D. Before the expected decay, a sharp increase in P120 mRNA level was detected shortly after inhibiting the overall RNA or protein synthesis. The calculated half-life of P120 mRNA was very similar (1.8 +/- 0.2 hr) in all 6 cell lines examined. The transcription rate of the P120 gene was determined by densitometric analysis of quantitative nuclear run-off assays. A significant positive correlation was found between the transcription rate of the P120 gene and the steady-state levels of either P120 protein or P120 mRNA. Our conclusion is that the expression of P120 protein is transcriptionally regulated in these breast cells. Therefore, the characteristically high level of P120 protein and mRNA found in most breast carcinomas is due to the altered transcription rate of the P120 gene in transformed cells.

Cis-acting elements in the promoter region of the human aldolase C gene

We investigated the cis-acting sequences involved in the expression of the human aldolase C gene by transient transfections into human neuroblastoma cells (SKNBE). We demonstrate that 420 bp of the 5'-flanking DNA direct at high efficiency the transcription of the CAT reporter gene. A deletion between -420 bp and -164 bp causes a 60% decrease of CAT activity. Gel shift and DNase I footprinting analyses revealed four protected elements: A, B, C and D. Competition analyses indicate that Sp1 or factors sharing a similar sequence specificity bind to elements A and B, but not to elements C and D. Sequence analysis shows a half palindromic ERE motif (GGTCA), in elements B and D. Region D binds a transactivating factor which appears also essential to stabilize the initiation complex.