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BBA - Gene Structure and Expression (v.1759, #8-9)

Editorial Board (pp. ii).

Influences along the path to maturity: Regulation of cellular levels of RNA by Michelle Craig Barton (pp. 385-387).

Initiation of RNA transcription may be a rate-limiting step in gene expression but it is only the first of many regulatory processes that impinge on nascent RNA along its path to maturity. Discontinuity between gene expression patterns within the nucleus and the cytoplasm suggests that multiple post-transcription regulatory points greatly influence the final RNA product, even to the extent of dramatically shifting the gene targets identified as a defined regulatory response.

Keywords: Microarray; Dioxin; RNA; Transcription; Processing

Genome-wide analyses show that nuclear and cytoplasmic RNA levels are differentially affected by dioxin by Jennifer A. Schwanekamp; Maureen A. Sartor; Saikumar Karyala; Danielle Halbleib; Mario Medvedovic; Craig R. Tomlinson (pp. 388-402).

The aryl hydrocarbon receptor (AHR) mounts the body's main molecular defense against environmental toxicants by inducing a battery of genes encoding xenobiotic metabolizing proteins. The AHR is activated by polycyclic aromatic hydrocarbon toxicants, including the pervasive teratogen and carcinogen 2,3,7,8-tetrachlorodibenzo- p-dioxin (TCDD or dioxin). The TCDD-activated AHR significantly changes the cytoplasmic mRNA levels of hundreds of genes, but little is known of the mechanism by which the activated AHR causes such a strong effect on global gene expression. We used high-density microarrays to compare nuclear and cytoplasmic RNA levels from untreated and TCDD-treated mouse embryonic fibroblasts (MEF) to test the hypotheses that (1) TCDD has a large impact on nuclear RNA levels and (2) that cytoplasmic RNA levels are dependent on nuclear RNA levels. We found that nuclear RNA levels are strongly affected by TCDD, and that nuclear and cytoplasmic RNA levels are only weakly correlated, indicating that other regulatory mechanisms are controlling cytoplasmic RNA levels. The nuclear RNAs most affected by TCDD encode proteins involved in nuclear RNA processing and transcription. We conclude that although the AHR regulates key xenobiotic metabolizing genes at the transcriptional level, a larger impact of the TCDD-activated AHR may be at post-transcriptional levels.

Keywords: Nuclear RNA; Aryl hydrocarbon receptor; Genomics; Gene regulation; Microarray; Dioxin

Cofactor CLIM2 promotes the repressive action of LIM homeodomain transcription factor Lhx2 in the expression of porcine pituitary glycoprotein hormone α subunit gene by Takao Susa; Takanobu Sato; Tetsuo Ono; Takako Kato; Yukio Kato (pp. 403-409).

We have cloned a porcine orthologue of cofactor CLIM2 (Ldb1/NLI) from the porcine pituitary cDNA library by protein–protein interaction with the Yeast Two-Hybrid System using porcine Lhx2 as a bait protein. Porcine CLIM2 shows a high identity (99%) in the dimerization domain, nuclear localization signal and LIM binding domain with those of man and mouse. The expression of CLIM2 gene in the anterior pituitary lobe was detected during the porcine fetal and postnatal period by RT-PCR analysis, suggesting that this protein is constitutively expressing and plays a basic role in the anterior pituitary. Transfection assay to the pituitary tumor derived LβT2 cells, and the Chinese hamster ovary cells demonstrated that CLIM2 acts as a corepressor of the porcine Lhx2 function. Interestingly, CLIM2 alone apparently repressed the high level of αGSU gene expression in LβT2 cells. These data suggest that CLIM2 is a basic factor in the pituitary development and function, and plays the role of repressor to modify the function of Lhx2 on the αGSU gene expression.

Keywords: Cofactor; CLIM2; Lhx2; Transcription factor; LIM; Pituitary; Gonadotropin

Targeted disruption of the genes, mlcR and ariB, which encode GAL4-type proteins in Penicillium citrinum by S. Baba; Y. Abe; C. Ono; M. Hosobuchi (pp. 410-416).

The role of two genes, mlcR and ariB, was investigated by gene disruption experiments. The mlcR gene in the ML-236B biosynthetic gene cluster of Penicillium citrinum encodes a putative 50.2-kDa protein with a Zn (II)₂Cys₆ DNA-binding domain, and has similarity to most of the GAL4-type regulatory proteins. The mlcR disruptant did not produce ML-236B or its intermediates, suggesting that mlcR is involved in ML-236B biosynthesis. Transcriptional analysis of the mlcR disruptant by Northern hybridization and RT-PCR indicated that MlcR activates the transcription of mlcA, B, C, D, F, G and H in a pathway-specific manner. On the other hand, MlcR did not affect the transcription of mlcE and the genes outside the ML-236B cluster. The ariB gene, next to mlcR, encodes another GAL4-type protein. Transcriptional analysis of the ariB disruptant indicated that it is a transcriptional activator of the genes outside the ML-236B cluster, and is not related to ML-236B biosynthesis.

Keywords: Penicillium citrinum; Transcriptional regulator; Zn (II); ₂; Cys; ₆; motif

Hyper-activated IRF-1 and STAT1 contribute to enhanced Interferon stimulated gene (ISG) expression by Interferon α and γ co-treatment in human hepatoma cells by Xiao-Nan Zhang; Jiang-Xia Liu; Yun-Wen Hu; Hui Chen; Zheng-Hong Yuan (pp. 417-425).

Previous reports suggest that type I and type II Interferon can co-operatively inhibit some virus replication, e.g. HCV, SARS-CoV, HSV-1. To find out the molecular mechanism underlying this phenomenon, we analyzed the transcription profile stimulated by IFN-α and IFN-γ in Huh-7 cells and found that the transcription of a subset of IFN stimulated genes (ISGs) including BclG, XAF1, TRAIL and TAP1 was enhanced when IFN-α and γ were both present. Promoter analysis of BclG revealed that IRF-1 and STAT1 were both required in this process. Enhanced IRF-1/DNA complex formation was observed in interferon co-treatment group by gel shift analysis. Furthermore, IRF-1 activation was found to be generally required in this cluster of ISGs. STAT1 tyrosine phosphorylation was elevated by IFN combination treatment, however, only the hyper-transactivation of GAS but not ISRE was observed. In conclusion, hyper-activation of IRF-1 and elevated STAT1 dimer formation may be two general switches which contribute to a much more robust antiviral symphony against virus replication when type I and type II IFNs are co-administered.

Keywords: Interferon regulatory factor-1; Interferon-α; Interferon-γ

HNF4α and NF-E2 are key transcriptional regulators of the murine Abcc6 gene expression by Vanessa Douet; Christopher M. VanWart; Matthew B. Heller; Sabrina Reinhard; Olivier Le Saux (pp. 426-436).

Mutations in an ABC transporter gene called ABCC6 are responsible for pseudoxanthoma elasticum (PXE), a rare heritable disease characterized by elastic fiber calcification in skin, ocular and vascular tissues. The presumed function of this ABC transporter is to export metabolites from polarized cells. However, the endogenous substrate(s) are unknown and the exact relationship with elastic fibers is unclear. As ABCC6 is only expressed at high level in liver and kidneys, tissues seemingly unrelated to the PXE phenotype, we explored the transcriptional regulation of the murine Abcc6 gene to define the transcriptional signal conferring tissue specificity and to gather clues on its possible biological function. We cloned 2.9kb of the mAbcc6 5′-flanking region and several deletion constructs linked to a luciferase reporter gene. We delineated a proximal promoter and a liver-specific enhancer region. We also demonstrated that the proximal region is a TATA-less promoter requiring an intact CCAAT-box and Sp1 binding for its basal activity. By using reporter assays and chromatin immunoprecipitations, we showed that HNF4α and surprisingly, NF-E2, enhanced the mAbcc6 promoter activity. The involvement of both HNF4α and NF-E2 in the mAbcc6 gene regulation suggests that Abcc6 might be involved in a detoxification processes related to hemoglobin or heme.

Keywords: Abcc6; ABC transporter; Pseudoxanthoma elasticum; Transcriptional regulation; Reporter gene analysis

New type of kdp region with a split sensor-kinase kdpD gene located within two divergent kdp operons from the thermoacidophilic bacterium Alicyclobacillus acidocaldarius by Erik Schleußinger; Roland Schmid; Evert P. Bakker (pp. 437-441).

The kdp region from the thermoacidophilic bacterium Alicyclobacillus acidocaldarius consists of two divergent operons: kdpZFABCN, which is tenfold induced at low K⁺ concentrations and encodes the K⁺-translocating P-type ATPase KdpZFABC as well as KdpN, a novel covalent homo-dimer of the cytoplasmic N-terminal part from sensor kinase KdpD; and secondly, the constitutively expressed kdpHE operon, encoding the remainder of KdpD and the response regulator KdpE.

Keywords: K; ⁺; transport; Genomic DNA; P-type ATPase; Two component system; Induction; Transcription

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BBA - Gene Structure and Expression (v.1759, #8-9)

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BBA - Gene Structure and Expression (v.1759, #8-9)