Journal: Molecular cell

Article Title: Replication stress shapes a protective chromatin environment across fragile genomic regions

doi: 10.1016/j.molcel.2017.11.021

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Secondary antibodies were goat anti-mouse IgG-HRP (Santa Cruz sc-2005, Invitrogen 31430) and goat anti-rabbit IgG-HRP (Santa Cruz sc-2004, Invitrogen 31460, CST 7074).

Techniques: Recombinant, Staining, Protease Inhibitor, Imaging, shRNA, CRISPR, Software

Journal: eLife

Article Title: LSD1 defines the fiber type-selective responsiveness to environmental stress in skeletal muscle

doi: 10.7554/eLife.84618

Figure Lengend Snippet: ( A ) Chromatin immunoprecipitation (ChIP)-qPCR analyses of H3K4me3 at Sln , Gadd45a , and Ddit4 gene promoters in LSD1-mKO gastrocnemius (Gas) muscles after dexamethasone (Dex) treatment. The data are from three independent experiments. The enrichment levels of H3K4me3 were normalized to the input DNA and presented as fold differences in the LSD1-mKO against that of wild type (WT). ( B ) Motif analyses of the promoter regions of genes that were upregulated in Dex-treated LSD1-mKO Gas muscles. Analysis of the atrophy-associated genes identified Foxk1 and PITX1 motifs, while significant enrichment of NFATc1 motif was found when all the upregulated genes were scanned. ( C ) Expression of genes encoding the transcription factors (TFs) identified by the motif analyses. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) values (n=4) are shown as the fold differences, compared with those of the Gas muscles. ( D ) Effects of treatment with Dex and LSD1 inhibitor (T-3775440) on the expression of Foxk1 in C2C12 myotubes. Foxk1 and 5,6-diamidino-2-phenylindole (DAPI) co-staining revealed Foxk1-positive nuclei, which are indicated by arrowheads (scale bars, 20 μm). The graph shows the percentage of Foxk1-positive nuclei (n=3). ( E ) Co-immunoprecipitation of LSD1 and Foxk1. C2C12 myotubes were treated with insulin for 6 hr before harvest to enhance the nuclear retention of Foxk1. Input lane contains 10% amount of the whole-cell extract. ( F ) Effects of Foxk1-KO on the expression of atrophy- and slow fiber-associated genes in C2C12 myotubes (n=6). qRT-PCR values are shown as the fold differences, compared with those in the control-transfected cells (n=6). ( G ) ChIP-qPCR analyses of LSD1 and Foxk1 at Ddit4, Gadd45a, Padi2 (negative control) gene promoters in control and Foxk1-KO C2C12 myotubes. The enrichment levels of normal rabbit IgG, LSD1, and Foxk1 were normalized to the input DNA. Values are mean ± SD. *p<0.05, **p<0.01. Figure 3—source data 1. Original blots for .

Article Snippet: The secondary antibodies used were as follows: anti-mouse IgG-horseradish peroxidase (GE Healthcare, NA931V), anti-rabbit IgG-horseradish peroxidase (GE Healthcare, NA934V or CST, #7074), Alexa Fluor 488 anti-Mouse IgG1 (Thermo Fisher, A21121), Alexa Fluor 350 anti-Mouse IgG2b (Thermo Fisher, A21140), and Cy3 anti-Rabbit IgG (Jackson ImmunoResearch, 711-165-152).

Techniques: Chromatin Immunoprecipitation, Expressing, Reverse Transcription Polymerase Chain Reaction, Quantitative RT-PCR, Staining, Immunoprecipitation, Transfection, Negative Control