TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation

Wingender, Edgar; Kel, Alexander; Kel, O. V.; Karas, Holger; Heinemeyer, T.; Dietze, Peter; Knüppel, Rainer; Romaschenko, A. G.; Колчанов, Н. А.

doi:10.1093/nar/25.1.265

Cited by 143 publications

(90 citation statements)

References 12 publications

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“…That the hCMViep and the RSV LTR do not support nuclear import would imply that the putative transcription factor(s) do not bind to these promoters. Comparison of the transcription factor consensus binding sequences in these two promoters (20), and the sites identified experimentally (21), reveals that the binding sites for several transcription factors, including AP2 and AP3, are not present. To test the hypothesis that AP2 alone mediates the nuclear import of SV40 DNA, we tested the smooth muscle gamma actin promoter, which contains an AP2 site approximately 200 bp upstream of the transcriptional start site (22).…”

Section: Discussionmentioning

confidence: 99%

Sequence Requirements for Plasmid Nuclear Import

Dean

Müller³

et al. 1999

Experimental Cell Research

215

244

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SUMMARYThe nuclear envelope is a major barrier for nuclear uptake of plasmids and represents one of the most significant unsolved problems of non-viral gene delivery. We have previously shown that the nuclear entry of plasmid DNA is sequence-specific, requiring a 366 bp fragment containing the SV40 origin of replication and early promoter. In this report, we show that, although fragments throughout this region can support varying degrees of nuclear import, the 72 bp repeats of the SV40 enhancer facilitate maximal transport. The functions of the promoter and the origin of replication are not needed for nuclear localization of plasmid DNA. In contrast to the import activity of the SV40 enhancer, two other strong promoter and enhancer sequences, the human cytomegalovirus (CMV) immediate early promoter and the Rous sarcoma virus LTR, were unable to direct nuclear localization of plasmids. The inability of the CMV promoter to mediate plasmid nuclear import was confirmed by measurement of the CMV promoter-driven expression of green fluorescent protein (GFP) in microinjected cells. At times before cell division, as few as 3 to 10 copies per cell of cytoplasmically injected plasmids containing the SV40 enhancer gave significant GFP expression, while no expression was obtained with more than 1000 copies per cell of plasmids lacking the SV40 sequence. However, the levels of expression were the same for both plasmids after cell division in cytoplasmically injected cells and at all times in nuclear injected cells. Thus, the inclusion this SV40 sequence in non-viral vectors may greatly increase their ability to be transported into the nucleus, especially in non-dividing cells.

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Section: Discussionmentioning

confidence: 99%

Sequence Requirements for Plasmid Nuclear Import

Dean

Müller³

et al. 1999

Experimental Cell Research

215

244

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“…Computer analysis of the DNA sequences was performed using the GeneWorks sequence analysis system (Intelligenetics, San Diego, CA). A search of potential binding sites for transcription factors in the 5Ј-flanking region of the DBA/2-derived AOH1 gene was performed using the MatInspector algorithm and the TRANSFAC data base (23).…”

Section: Methodsmentioning

confidence: 99%

Regulation and Biochemistry of Mouse Molybdo-flavoenzymes

Vila¹,

Kurosaki²,

Barzago³

et al. 2004

Journal of Biological Chemistry

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Mouse molybdo-flavoenzymes consist of xanthine oxidoreductase, aldehyde oxidase (AOX1), and two recently identified proteins, AOH1 and AOH2 (aldehyde oxidase homologues 1 and 2). Here we demonstrate that CD-1, C57BL/6, 129/Sv, and other mouse strains synthesize high levels of AOH1 in the liver and AOH2 in the skin. By contrast, the DBA/2 and CBA strains are unique, having a selective deficit in the expression of the AOH1 and AOH2 genes. DBA/2 animals synthesize trace amounts of a catalytically active AOH1 protein. However, relative to CD-1 animals, an over 2 log reduction in the steady-state levels of liver AOH1 mRNA, protein, and enzymatic activity is observed in basal conditions and following administration of testosterone. The DBA/2 mouse represents a unique opportunity to purify AOX1 and compare its enzymatic characteristics to those of the AOH1 protein. The spectroscopy and biochemistry of AOX1 are very similar to those of AOH1 except for a differential sensitivity to the non-competitive inhibitory effect of norharmane. AOX1 and AOH1 oxidize an overlapping set of aldehydes and heterocycles. For most compounds, the substrate efficiency (V max /K m ) of AOX1 is superior to that of AOH1. Alkylic alcohols and acetaldehyde, the toxic metabolite of ethanol, are poor substrates of both enzymes. Consistent with this, the levels of acetaldehyde in the livers of ethanol administered CD-1 and DBA/2 mice are similar, indicating that neither enzyme is involved in the in vivo biotransformation of acetaldehyde.

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“…Searching for putative transcription-factor binding sites was performed by the MatInspector v2.2 program using TRANSFAC 4.0 matrices [7][8][9]. remove the RNA templates.…”

Section: Cloning Of the Myadm Promoter Regionmentioning

confidence: 99%