Journal: Cell reports

Article Title: Overlapping Activities of Two Neuronal Splicing Factors Switch the GABA Effect from Excitatory to Inhibitory by Regulating REST

doi: 10.1016/j.celrep.2019.03.072

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Mouse anti-calbindin D-28K monoclonal antibody (clone CB-955) , Acris Antibodies , Cat# AM08219SU-N; RRID: AB_1954252.

Techniques: Expressing, Plasmid Preparation, Recombinant, SYBR Green Assay, Reporter Assay, Isolation, Staining, Microarray, Clone Assay, Software

Journal: Data in Brief

Article Title: Proteomic and microRNA data clarifying the effects of telomere shortening on cancer cells

doi: 10.1016/j.dib.2014.12.003

Figure Lengend Snippet:

Article Snippet: Microarray data were obtained by DNA microarrays hybridization (Affymetrix GeneChip ® Human Gene 1.0 ST arrays)..

Techniques: Mass Spectrometry, Microarray, Hybridization, Control, Multiplex sample analysis, Labeling, Agarose Gel Electrophoresis

Journal: The Journal of Biological Chemistry

Article Title: Mutation of the gene encoding the circadian clock component PERIOD2 in oncogenic cells confers chemoresistance by up-regulating the Aldh3a1 gene

doi: 10.1074/jbc.RA118.004942

Figure Lengend Snippet: Enhanced expression of Aldh3a1 gene in oncogene-transformed Per2m/m cells. A, microarray analysis of oncogene introduced WT and Per2m/m cells. Up-regulated or down-regulated genes in WT and Per2m/m cells with concomitant introduction of oncogenes H-rasV12 and SV40LT. The criteria for up-regulated genes were set at a z-score of 2.0 or more and a ratio of 3-fold or more; and the criteria for down-regulated genes were set at a z-score of −2.0 or less and a ratio of one-third or less. The numbers at the top left in the graphs indicate up-regulated genes, and those at the bottom right indicate down-regulated genes. B, differentially expressed genes between oncogene-introduced WT and Per2m/m cells in microarray analysis. The full transcriptome data have been deposited in NCBI GEO (accession number GSE113242). C, elevation of Aldh3a1 mRNA levels in oncogene-transformed Per2m/m cells. Values shown are means ± S.D. (error bars) (n = 3). **, p < 0.01, significantly different between two groups. D, elevation of ALDH3A1 protein levels in oncogene-transformed Per2m/m cells. The results shown are representative of three independent experiments. The band intensity was plotted by normalizing to actin, and the mean value of basal levels was set as 1.0. The values are plotted in the photographs of Western blotting. E, the expression levels of Klf4, Pou5f1, c-Myc, Sox2, and Nanog in WT and Per2m/m cells before and after oncogenic transformation. Data were normalized by actin mRNA levels. Values show the mean ± S.D. (n = 3–5). **, p < 0.01, significantly different between the two groups.

Article Snippet: To down-regulate ALDH3A1 expression, cells were infected with lentiviral vectors expressing shRNA against the mouse Aldh3a1 gene (pGFP-C-sh Aldh3a1 Lenti Vector; Origene Technologies, Inc., Rockville, MD).

Techniques: Expressing, Transformation Assay, Microarray, Western Blot

Journal: The Journal of Biological Chemistry

Article Title: Mutation of the gene encoding the circadian clock component PERIOD2 in oncogenic cells confers chemoresistance by up-regulating the Aldh3a1 gene

doi: 10.1074/jbc.RA118.004942

Figure Lengend Snippet: Down-regulation of ALDH3A1 relieves the resistance of oncogene-transformed Per2m/m cells against chemotherapeutic drugs. A, the expression profiles of catalase, GSH peroxidase, and SOD3 in oncogene-transformed WT and Per2m/m cells. The results shown are representative of three independent experiments. B, effects of NAC, a GSH precursor, on the sensitivity of oncogene-transformed Per2m/m cells to chemotherapeutic drugs. Cells were treated with 1 μm MTX, 0.5 μm GEM, 50 μm VP-16, 5 μm VCR, or 50 μm L-OHP at the indicated concentrations in the presence or absence of NAC (2 mm). After treatment with each drug for 48 h, cell viability was determined by an ATP luminescent assay. Values are means ± S.D. (error bars) (n = 4). **, p < 0.01, significantly different from WT cells. C, effects of selective ALDH3A1 inhibitor CB29 on the sensitivity of oncogene-transformed Per2m/m cells to chemotherapeutic drugs. Cells were treated with chemotherapeutic drugs in the presence or absence of CB29 (30 μm). Cell viability was assessed 48 h after the initiation of drug treatment. Values are means ± S.D. (n = 4). **, p < 0.01, significantly different from WT cells. ##, p < 0.01, significantly different from Per2m/m cells without treatment with CB29. D, down-regulation of ALDH3A1 in oncogene-transformed Per2m/m cells by infection with shRNA-expressing vectors. E, effects of chemotherapeutic drugs on viability of Aldh3a1 down-regulated oncogene-transformed Per2m/m cells. Cell viability was assessed 48 h after the initiation of drug treatment. Values shown are means ± S.D. (n = 3–4). **, p < 0.01; *, p < 0.05, significantly different from WT cells. ##, p < 0.01; #, p < 0.05, significantly different from control shRNA-transfected oncogene-transformed Per2m/m cells (Per2m/m Control shRNA). F, influence of down-regulation of ALDH3A1 on the chemotherapeutic drug–induced production of ROS in oncogene-transformed Per2m/m cells. Values shown are means ± S.D. (n = 3). **, p < 0.01, significantly different between the two groups. ##, p < 0.01; #, p < 0.05, significantly different from the vehicle-treated group.

Article Snippet: To down-regulate ALDH3A1 expression, cells were infected with lentiviral vectors expressing shRNA against the mouse Aldh3a1 gene (pGFP-C-sh Aldh3a1 Lenti Vector; Origene Technologies, Inc., Rockville, MD).

Techniques: Transformation Assay, Expressing, Luminescence Assay, Infection, shRNA, Transfection

Journal: The Journal of Biological Chemistry

Article Title: Mutation of the gene encoding the circadian clock component PERIOD2 in oncogenic cells confers chemoresistance by up-regulating the Aldh3a1 gene

doi: 10.1074/jbc.RA118.004942

Figure Lengend Snippet: Epigenetic modifications of histone H3 on the mouse Aldh3a1 in oncogene-transformed Per2m/m cells. A, schematic representation of the mouse Aldh3a1 gene. The numbers indicate the distance (in bp) from the transcription start site (+1). Red rectangles, CCGG sites. The circled numbers (orange circles and blue circles) indicate the location on the gene where each of the different primer sets localize for analysis of DNA methylation and ChIP studies. B, methylation rate of DNA CCGG sites on Aldh3a1 in WT and Per2m/m cells. After digestion with isoschizomers, purified DNA was quantified by qPCR using primer sets that recognize the different regions indicated in the schematic in A (orange circles). Values shown are means ± S.D. (error bars) (n = 3). C, ChIP analysis for oncogene-induced changes in H3K9Ac and H3K27me3 enrichment across Aldh3a1 in WT and Per2m/m cells. Immunopurified DNA was quantified by qPCR using primer sets that recognize the different regions indicated in the schematic in A (blue circles). Values shown are means ± S.D. (n = 6). **, p < 0.01; *, p < 0.05, significantly different between the two groups. D, PER2 co-precipitated with HDAC1 and HDAC2. Cytosolic and nuclear extracts from oncogene-transformed WT and Per2m/m cells were immunoprecipitated with antibodies against PER2 or mouse IgG. Immune complexes generated by each antibody were subjected to Western blotting (WB). The results shown are representative of three independent experiments. E, ChIP analysis for oncogene-induced changes in recruitment of PCAF, HDCA1, and HDAC2 on Aldh3a1 in WT and Per2m/m cells. Immunopurified DNA was quantified by qPCR using primer sets that recognize the different regions indicated in the schematic in A (blue circles). Values shown are means ± S.D. (n = 4). **, p < 0.01; *, p < 0.05, significantly different between the two groups.

Article Snippet: To down-regulate ALDH3A1 expression, cells were infected with lentiviral vectors expressing shRNA against the mouse Aldh3a1 gene (pGFP-C-sh Aldh3a1 Lenti Vector; Origene Technologies, Inc., Rockville, MD).

Techniques: Transformation Assay, DNA Methylation Assay, Methylation, Purification, Immunoprecipitation, Generated, Western Blot

Journal: The Journal of Biological Chemistry

Article Title: Mutation of the gene encoding the circadian clock component PERIOD2 in oncogenic cells confers chemoresistance by up-regulating the Aldh3a1 gene

doi: 10.1074/jbc.RA118.004942

Figure Lengend Snippet: Possible mechanism underlying the resistance of oncogene-transformed Per2m/m cells against chemotherapeutic drugs. Oncogenic stimuli induce the expression of Aldh3a1 in both WT and Per2m/m cells accompanied by histone H3 modifications. In oncogene-transformed Per2m/m cells, PER2 (mutated PER2 protein) fails to recruit HDACs on Aldh3a1, resulting in its enhanced expression. Elevated levels of ALDH3A1 contribute to the resistance against chemotherapeutic drugs through the enhancement of ROS degradation.

Article Snippet: To down-regulate ALDH3A1 expression, cells were infected with lentiviral vectors expressing shRNA against the mouse Aldh3a1 gene (pGFP-C-sh Aldh3a1 Lenti Vector; Origene Technologies, Inc., Rockville, MD).

Techniques: Transformation Assay, Expressing

Journal: The Journal of Biological Chemistry

Article Title: Mutation of the gene encoding the circadian clock component PERIOD2 in oncogenic cells confers chemoresistance by up-regulating the Aldh3a1 gene

doi: 10.1074/jbc.RA118.004942

Figure Lengend Snippet: Primer sets for PCR analysis of gene expression

Article Snippet: To down-regulate ALDH3A1 expression, cells were infected with lentiviral vectors expressing shRNA against the mouse Aldh3a1 gene (pGFP-C-sh Aldh3a1 Lenti Vector; Origene Technologies, Inc., Rockville, MD).

Techniques:

Journal: The Journal of Biological Chemistry

Article Title: Mutation of the gene encoding the circadian clock component PERIOD2 in oncogenic cells confers chemoresistance by up-regulating the Aldh3a1 gene

doi: 10.1074/jbc.RA118.004942

Figure Lengend Snippet: Primer sets for PCR analysis of DNA methylation The numbers indicate the distance from the putative transcription start site (+1).

Article Snippet: To down-regulate ALDH3A1 expression, cells were infected with lentiviral vectors expressing shRNA against the mouse Aldh3a1 gene (pGFP-C-sh Aldh3a1 Lenti Vector; Origene Technologies, Inc., Rockville, MD).

Techniques: DNA Methylation Assay

Journal: The Journal of Biological Chemistry

Article Title: Mutation of the gene encoding the circadian clock component PERIOD2 in oncogenic cells confers chemoresistance by up-regulating the Aldh3a1 gene

doi: 10.1074/jbc.RA118.004942

Figure Lengend Snippet: Primer sets for PCR analysis of chromatin immunoprecipitation The numbers indicate the distance from the putative transcription start site (+1).

Article Snippet: To down-regulate ALDH3A1 expression, cells were infected with lentiviral vectors expressing shRNA against the mouse Aldh3a1 gene (pGFP-C-sh Aldh3a1 Lenti Vector; Origene Technologies, Inc., Rockville, MD).

Techniques: Chromatin Immunoprecipitation