Journal: Cancer discovery

Article Title: PTEN Methylation by NSD2 Controls Cellular Sensitivity to DNA Damage

doi: 10.1158/2159-8290.CD-18-0083

Figure Lengend Snippet: (A) Methylation of PTEN was detected using the Di-Methyl Lysine motif antibody. IB analysis of anti-PTEN IPs and WCL derived from U2OS cells treated with 30 μM etoposide as indicated time points before harvesting.

Article Snippet: Anti-phospho-ATM/ATR Substrate (S*Q) (9607), anti-phospho-ATM/ATR Substrate (6966), anti-pS15-p53 (9284), anti-pT68-Chk2 (2661), anti-Chk2 antibody (3440), anti-Di-Methyl Lysine Motif (14117), anti-Tri-Methyl Lysine Motif (14680), anti-His tag (2366), anti-γH2AX (9718), anti-pS473-Akt (4060), anti-Akt1 antibody (2938), anti-PTEN (9188), anti-Cleaved caspase3 (9661), anti-Mek1/2 (8727), anti-pS25/29–53BP1 (2674) and anti-H2AX (7631) antibodies were purchased from Cell Signaling Technology.

Techniques: Methylation, Derivative Assay

Journal: Nucleic Acids Research

Article Title: A multi-parametric flow cytometric assay to analyze DNA–protein interactions

doi: 10.1093/nar/gks1034

Figure Lengend Snippet: MagPIE allows simultaneous monitoring of protein–DNA binding and epigenetic DNA and histone methylation. ( A ) Comparative flow cytometric plots showing bead immunofluorescence intensity for methyl-CpG ( X axis) for beads coated with 88 bp DNA containing 40 bp randomized sequences flanking two CG dinucleotides and incubated without lysate (black), with lysate from mES cells (red) or with lysate from mES cells and RG108 (blue). ( B ) Graph showing mean bead fluorescence for H3K4Me1 after incubation with mES lysate for a set of DNA regions with (left) or without (right) ChIP-Seq H3K4Me1 marking (sequences in Supplementary Table S1 ). Flow cytometric plots showing bead immunofluorescence intensity for Sox2 ( Y axis) vs. bead immunofluorescence intensity for histone 3 lysine 4 monomethyl ( X axis) for beads coated with a 200 bp DNA sequence that does ( C ) or a 226 bp sequence that does not ( D ) show Sox2 binding and H3K4Me1 marking in mES cells in vivo . ( E ) Comparative flow cytometric plots showing bead immunofluorescence intensity for Histone H3 total protein ( X axis) for beads coated with DNA from a H3K4Me1 + mES region (black) or from a H3K4Me1 - mES region (red) and incubated with mES lysate and compared with DNA-coated beads without lysate (blue). ( F ) Mutation series of a 40 bp enhancer fragment with a strong SoxOct binding site (Sox binding site underlined, Oct binding site italicized with JASPAR motif overlaid above sequence) with mutations bolded. Amplified enhancer regions have a total DNA length of 88 bp. Flow cytometric plots showing bead immunofluorescence intensity for Sox2 ( Y axis) vs. bead immunofluorescence intensity for histone 3 lysine 4 monomethyl ( X axis) for beads coated with 48 bp primer DNA ( G ), 88 bp DNA sequences containing a 40 bp SoxOct wild-type binding site ( H ), 88 bp DNA sequences containing a 40 bp SoxOct Sox mutant binding site ( I ) or 88 bp DNA sequences containing a 40 bp SoxOct Oct mutant binding site ( J ) and incubated with lysate from mES cells. Flow cytometric plots showing bead immunofluorescence intensity for V5 tagged Cdx2 ( Y axis) vs. bead immunofluorescence intensity for histone 3 lysine 4 monomethyl ( X axis, K and L ) or FITC total protein ( X axis, M and O ) for beads coated with 88 bp DNA sequences containing a 40 bp Cdx2 binding site (K, M and N ) or 88 bp DNA sequences containing a 40 bp Cdx2 mutant binding site (L and O) and incubated with lysate from mES cells ectopically expressing Cdx2 (K, L, N and O) or without lysate (M).

Article Snippet: Antibodies used include mouse anti-V5 (R960-25, Invitrogen), mouse anti-Cdx2 (Biogenex), rabbit anti-Histone 3 Lysine 4 Monomethyl (Cell Signaling), sheep anti-Cytosine, 5-methyl (US Biological), sheep anti-Onecut1 (R&D Systems) and mouse anti-Sox2 (R&D Systems).

Techniques: Binding Assay, Methylation, Immunofluorescence, Incubation, Fluorescence, ChIP-sequencing, Sequencing, In Vivo, Mutagenesis, Amplification, Expressing

Journal: Nucleic Acids Research

Article Title: A multi-parametric flow cytometric assay to analyze DNA–protein interactions

doi: 10.1093/nar/gks1034

Figure Lengend Snippet: Mass spectrometric identification of histones in MagPIE samples

Article Snippet: Antibodies used include mouse anti-V5 (R960-25, Invitrogen), mouse anti-Cdx2 (Biogenex), rabbit anti-Histone 3 Lysine 4 Monomethyl (Cell Signaling), sheep anti-Cytosine, 5-methyl (US Biological), sheep anti-Onecut1 (R&D Systems) and mouse anti-Sox2 (R&D Systems).

Techniques: