Journal: Communications Biology

Article Title: Repeat DNA methylation is modulated by adherens junction signaling

doi: 10.1038/s42003-024-05990-4

Figure Lengend Snippet: a – c Mean square displacement (MSD) of mVenus spots was measured in sparse and dense MCF10A-BiAD cultures. a Shown are representative trajectories integrated over a lag time of 3 s. N = 20. b Representative violin plot showing the distribution of mVenus spot movement (lag time of 1 s) in data collected from one biological repeat for sparse (blue) and dense (orange) seeded cells. N = 50–140, statistical testing was determined with a two-tailed unpaired t test, **** p < 0.0001. c Quantification of the MSD experiments representatively shown in ( b ). n = 3, N = 50–140. Statistical analysis was done with a two-tailed paired t test, * p < 0.05. d RT-qPCR analysis of α-satellite transcripts showing increased transcription in 5-aza-dC 24 h after drug treatment. n = 3. Statistical analysis was done with a two-tailed unpaired t test, ** p < 0.01. e RT-qPCR analysis of α-satellite transcripts was performed on RNA isolated from MCF10A cells grown for 24 h in either sparse or confluent conditions. n = 3. Statistical analysis was done with a two-tailed unpaired t test, ** p < 0.01. f RT-qPCR was used to analyze transcription from α-satellite DNA in MCF10A cells that had been treated for 24 h with the E-cadherin blocking antibody. n = 3. Statistical analysis was done with a two-tailed unpaired t test, ** p < 0.01. g Western blot analysis of cell lysates isolated from MCF10A, SK-BR-3 and SUM159 cells and probed for E-cadherin. GAPDH was used as loading control. h MSRE-qPCR analysis of the α-satellite locus on genomic DNA isolated from SK-BR-3 and SUM159 cells, which were cultured for 24 h under either sparse or dense conditions. n = 3. Statistical analysis was done with a two-tailed unpaired t test, ns not significant. i qPCR analysis of the α-satellite transcripts on RNA isolated from SK-BR-3 and SUM159 cells, which were cultured for 24 h under either sparse or dense conditions. n = 3. Statistical analysis was done with a two-tailed unpaired t test, ns: not significant. j Scheme of newly discovered pathway linking the methylation status and transcription state of satellite DNA to cell density, mediated by E-cadherin. The figure was generated using Biorender. c , d , e , f , h , i In the dot blots, each dot is the mean value obtained for one biological repeat, the line indicates the mean of all biological repeats, and error bars represent their standard deviation. Paired measurements are indicated with the color coding.

Article Snippet: SUM159 (provided by Dr. Thordur Oskarsson, DKFZ) and SK-BR-3 cells (CLS Cell Lines Service GmbH) were cultured in DMEM medium (Gibco) with 10% fetal calf serum (Gibco).

Techniques: Two Tailed Test, Quantitative RT-PCR, Isolation, Blocking Assay, Western Blot, Control, Cell Culture, Methylation, Generated, Standard Deviation

Journal: The Journal of Biological Chemistry

Article Title: The mucinous domain of pancreatic carboxyl-ester lipase (CEL) contains core 1/core 2 O- glycans that can be modified by ABO blood group determinants

doi: 10.1074/jbc.RA118.001934

Figure Lengend Snippet: The O-glycome of recombinant CEL is dramatically altered in cancer cell lines. A–D, the O-glycan pool of recombinant CEL expressed in HEK293 (A), pancreatic cancer (B, PANC-1; C, MIA PaCa-2), and breast cancer (D, SK-BR-3) cell lines were investigated by MALDI-TOF MS after alkaline β-elimination and permethylation. The O-glycan population varied with the cellular expression system employed. No ABO blood group antigens were detected in any cell line. See Fig. 8 legend for further information about the spectra.

Article Snippet: Human breast cancer cell line SK-BR-3 (ATCC) was grown and maintained in McCoy's 5A medium with 10% FBS and 100 units/ml penicillin/streptomycin.

Techniques: Recombinant, Expressing

Journal: EMBO Reports

Article Title: Repurposing an endogenous degradation domain for antibody-mediated disposal of cell-surface proteins

doi: 10.1038/s44319-024-00063-3

Figure Lengend Snippet: Reagents and tools.

Article Snippet: SK-BR-3 cells (C0006007, AddexBio/Caltag Medsystems) and HeLa cells (C0008001, AddexBio/Caltag Medsystems) were STR-profiled by the suppliers immediately prior to use and were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Merck) supplemented with 10% sterile-filtered foetal bovine serum (FBS; Merck) and penicillin (100 U/ml) plus streptomycin (100 μg/ml) (Merck).

Techniques: Recombinant, Plasmid Preparation, Modification, Saline, Software, Flow Cytometry, Microscopy