Journal: The Journal of Biological Chemistry

Article Title: Nuclear Receptors HNF4α and LRH-1 Cooperate in Regulating Cyp7a1 in Vivo *

doi: 10.1074/jbc.M112.421834

Figure Lengend Snippet: FGF19 reduces histone H3 acetylation and H3K4 trimethylation on the Cyp7a1 promoter. Histone H3 acetylation ( A ) and histone H3K4 trimethylation ( B ) on the Cyp7a1 promoter were tested by ChIP on liver samples ( n = 3) from the mouse experiments shown in and . Values are means ± S.E. Statistical significance was determined by two-tailed t tests. (*) refers to differences between wild-type or Ad-Con vehicle and FGF19 groups. (#) refers to differences between Ad-Cre vehicle and FGF19 groups. *, p < 0.05; **, p < 0.005; ***, p < 0.0005; #, p < 0.05; ##, p < 0.005; ###, p < 0.0005.

Article Snippet: Antibodies for the following proteins were purchased from indicated suppliers: HNF4α and LRH-1 (Perseus Proteomics), Histone H3K4 trimethyl and RNA Polymerase II-CTD (Abcam) and Acetyl-histone H3 (Millipore).

Techniques: Two Tailed Test

Journal: iScience

Article Title: The KRAS-G12D mutation induces metabolic vulnerability in B-cell acute lymphoblastic leukemia

doi: 10.1016/j.isci.2022.103881

Figure Lengend Snippet:

Article Snippet: Cells were harvested in lysis buffer and analyzed by SDS-PAGE with the following antibodies: phospho-AKT (S473), AKT, phospho-S6K (T389), S6K, phospho-S6 (S235/236), S6, phospho-GSK3 (S21), GSK3, phospho-Rb, mme-K, dme-K, tme-K, H3K4-me2, H3K4-me3, H3K9-me2, H3K27-me2, H3K27-me3, H3K36-me2, H3K79-me2 (purchased from Cell Signaling Technology, USA), phospho-PDK1 (S241), PDK1, RAS (bought from Abcam, UK), AMD1 (Proteintech, USA), and Actin (HuaBio, China).

Techniques: Recombinant, Plasmid Preparation, Software

Journal: PLoS ONE

Article Title: Xenopus Reduced Folate Carrier Regulates Neural Crest Development Epigenetically

doi: 10.1371/journal.pone.0027198

Figure Lengend Snippet: (A) Levels of different methylation forms of histone 3 in animal caps injected with XWnt7b and tBR with or without XRFC-MO. Knockdown of XRFC by injection XRFC-MO decreased both the mono- and trimethyl-H3-K4 levels but not dimethyl-H3-K4 level (left panel), which was restored by co-injection of XRFC mRNA (middle panel). Injection of 5-MTHF increased the mono- and trimethyl-H3-K4 levels but not dimethyl-H3-K4 level (right panel). (B–I) hMLL1 plasmid co-injection rescued the effect of XRFC-MO on the expression of Zic1 and FoxD3, and weakly on Snail2 and Twist1. (J-M) Overexpression of hMLL1 alone promoted the expression of Zic1 and FoxD3, but had no clear effects on Snail2 and Twist1. (N) Number of embryos showed reduced expression of Zic1 , FoxD3 , Snail2 and Twist1 injected with XRFC-MO with or without hMLL1 plasmid (50 pg/embryo).

Article Snippet: The antibodies used for monomethyl-, dimethyl- and trimethyl-H3-K4 were from Millipore.

Techniques: Methylation, Injection, Knockdown, Plasmid Preparation, Expressing, Over Expression

Journal: Molecular Cancer

Article Title: Epigenetic reactivation of estrogen receptor-α (ERα) by genistein enhances hormonal therapy sensitivity in ERα-negative breast cancer

doi: 10.1186/1476-4598-12-9

Figure Lengend Snippet: Epigenetic alterations in response to GE and/or TSA treatments. ( A ) Histone modification patterns in the ERα promoter were analyzed by ChIP assay. Representative photograph from an experiment was repeated in triplicate. ( B ) Histone modification enrichment in the ERα promoter was calculated from the corresponding DNA fragments amplified by ChIP-PCR as shown above. MDA-MB- 231 cells were treated as described previously and analyzed by ChIP assays using chromatin markers including acetyl-H3, acetyl-H3K9, acetyl-H4, dimethyl-H3K4 and mouse IgG control in the promoter region of ERα . Inputs came from the total DNA and served as the same ChIP-PCR conditions. DNA enrichment was calculated as the ratio of each bound sample divided by the input while the untreated MDA-MB-231 control sample is represented as 1. ( C ) HDACs enzymatic activity. ( D ) DNMTs enzymatic activity. Nuclear proteins of MDA-MB-231 cells were extracted after the treatment as described above. The HDACs and DNMTs activity assays were performed according to the manufacturer’s protocols. ( E ) Binding abilities of HDACs and DNMTs in the ERα promoter were determined by ChIP assay as described previously. The values of enzymatic activities of HDACs and DNMTs are the means of three independent experiments. Columns, mean; Bars, SD. *, P < 0.05, significantly different from control; £, P < 0.05, significantly different from GE; †, P < 0.05, significantly different from TSA. ( F ) The protein level changes of HDACs and DNMTs were determined by western-blot analysis. GAPDH antibody was used to ensure equal loading. Representative photograph from an experiment was repeated three times.

Article Snippet: The epigenetic antibodies used in the ChIP assays were ChIP-validated acetyl-histone H3 (Upstate Biotechnology), acetyl-histone H3-Lys9 (H3K9) (Upstate Biotechnology), acetyl-histone H4 (Upstate Biotechnology), dimethyl-histone H3-Lys4 (H3K4) (Upstate Biotechnology), histone deacetylase1 (HDAC1) (Santa Cruz Biotechnology) and DNMT1 (Abcam, Cambridge, MA).

Techniques: Modification, Amplification, Control, Activity Assay, Binding Assay, Western Blot