cervical hela s3  (DSMZ)

Journal: Scientific Reports

Article Title: The C16orf87 protein is a subunit of the MIER corepressor complex controlling embryonic development and cell migration

doi: 10.1038/s41598-026-50740-7

Figure Lengend Snippet: C16orf87 partially mediates HDAC1 and MIER1 protein interactions. ( A ) C16orf87 interacts with the HDAC and MIER proteins. Volcano plot of the IP-MS experiment showing identified proteins interacting with the Flag-C16orf87 protein in HeLa cells. An adjusted P -value cut-off of 0.05 and a log2 fold change cut-off of 2 were used. Data are shown from a biological triplicate experiment. ( B ) Lack of C16orf87 does not change HDAC and MIER protein accumulation. Soluble Panc-01 WT (WT) and Panc-01 KO (KO) whole-cell lysates were analyzed by WB with the indicated antibodies. ( C ) C16orf87 partially mediates HDAC1 and MIER1 interaction. Co-immunoprecipitation of Flag-HDAC1 from siRNA (siC16 and siScr) and pcDNA3-Flag-HDAC1-transfected HeLa cells. Isolated proteins were analyzed by WB with the indicated antibodies. An arrowhead indicates the migration of the MIER1 protein isoforms, whereas an asterisk indicates the migration of the C16orf87 isoforms. ( D ) HDAC1 interacts weakly with C16orf87 in vitro. GST (as a control) and GST-HDAC1 pull-down with bacterially purified 8 × His-tagged C16orf87(Wt, 5 × C > A, 1–130, and 5 × C > A/1–130) proteins. An asterisk indicates a degradation product/partially translated GST-HDAC1. Proteins were detected with the anti-His and anti-GST antibodies.

Article Snippet: Human pancreatic cancer cell lines Panc-01 (ATCC, CRL-1469) and MiaPaCa-2 (ATCC, CRL-1420), mouse skeletal muscle cell line C2C12 (ATCC, CRL-1772), and human cervical cancer cell line HeLa S3 (ATCC, CCL-2.2) were used in this study.

Techniques: Protein-Protein interactions, Immunoprecipitation, Transfection, Isolation, Migration, In Vitro, Control, Purification

Journal: bioRxiv

Article Title: Condensin and topoisomerases cooperate to relieve topological stress at stalled replication forks

doi: 10.1101/2025.08.06.668895

Figure Lengend Snippet: a Condensin binds nascent DNA. HeLa-S3 cells were labelled for 20 minutes with 10 μM EdU and chased for 60 minutes with thymidine. Proteins associated to nascent DNA before and after the thymidine chase were analyzed by iPOND-MS as described . b Condensin I and II are dispensable for normal fork progression. HeLa-S3 cells depleted for condensin I (siCAPG) or condensin II (siCAPG2) for 48 hours with siRNAs were sequentially labeled with IdU and CldU for 15 min before DNA fiber spreading. The length distribution of CldU tracks length is shown for four independent experiments. Box and whiskers indicate 25 th -75 th and 10 th -90 th percentiles, respectively. Median length is indicated. c The ATR-CHK1 pathway is functional in the absence of condensin II. HeLa-S3 cells were transfected with siCtrl, siCAPG and siCAPG2 for 48 hours. Cells were then treated with 4 mM HU for 2 hours and the activation of CHK1 was detected with an anti-pCHK1 (S345) antibody. CAPG and CAPG2 depletion was verified by Western blotting. Total CHK1 and tubulin were used as loading controls. d Condensin II promotes fork restart. HeLa-S3 cells were transfected with siCtrl or siCAPG2 for 48 hours and were treated with 4 mM HU for 3 hours after a 30 minutes IdU pulse. IdU and CldU tracks were analyzed by DNA fiber spreading 30 minutes after HU removal and CldU addition. Red and green signals are indicative of fork restart. Red only tracks correspond to stalled forks and green tracks to new origin firing (n = 3). e Condensin II is required for fork slowing after exposure to a low dose of HU. U2OS cells were transfected with siCtrl and siCAPG2 for 48 hours. Cells were first labelled for 30 minutes with IdU, and CldU was then added for 30 minutes in the presence of 50 μM HU. The length of IdU and CldU tracks was determined by DNA fiber spreading and was plotted as the ratio of CldU to IdU (n=3). Box and whiskers indicate median, 25th–75th and 10th–90th percentiles. f Condensin II promotes the resection of nascent DNA at HU-arrested forks. HeLa-S3 cells were transfected with siCtrl and siCAPG2 for 48 hours and were sequentially labeled for 15 minutes with IdU and CldU. Cells were either collected immediately or treated for 2 hours with 4 mM HU before DNA fiber analysis. The ratio of CldU to IdU track length was plotted for 4 independent experiments. Box and whiskers indicate median, 25th–75th and 10th–90th percentiles.

Article Snippet: Human cervical adenocarcinoma HeLa S3 cells (ATCC, CCL2-2) and osteocarcinoma U2OS cells (ATCC, HTB-86) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) or McCoy’s 5a medium, respectively, supplemented with 10% fetal calf serum (FCS) and 100 U/mL penicillin/streptomycin (PS).

Techniques: Labeling, Functional Assay, Transfection, Activation Assay, Western Blot

Journal: bioRxiv

Article Title: Condensin and topoisomerases cooperate to relieve topological stress at stalled replication forks

doi: 10.1101/2025.08.06.668895

Figure Lengend Snippet: a Analysis of the frequency of reversed forks in control and condensin II-depleted cells by electron microscopy (EM). Control (shCtrl) or CAPG2-depleted (shCAPG2) HeLa-S3 cells were treated for 72 hours with 10 μM/ml doxycycline and then for 2 hours with 4 mM HU +/- 50 μM mirin before EM analysis. Electron micrographs of representative replication intermediates in shCAPG2 cells are shown. b The frequency of reversed forks in shCtrl and shCAPG2 cells is shown for the indicated conditions. Means and the number of analyzed forks are indicated (n=2). RI # indicates the number of analyzed replication intermediates. c Mechanism of fork reversal. See main text for details. d Reversed arms are shorter in the absence of condensin II. The length of reversed arms (in nt) was plotted for the indicated samples. Median values are indicated (n=2). RI # indicates the number of analyzed replication intermediates. P-values: Mann-Whitney rank sum test. e CAPG2 depletion restores fork restart in SMARCAL1-deficient cells. HeLa-S3 cells were transfected with siCtrl, siSMARCAL1, siCAPG2 or co-transfected with siSMARCAL1 and siCAPG2 for 48 hours. Cells were treated with 4 mM HU for 3 hours after a 30 minutes IdU pulse and fork restart was monitored 30 min after HU removal and CldU addition, as indicated in (n=3). f Defective fork slowdown in SMARCAL1-deficient cells is rescued by CAPG2 depletion. U2OS cells were transfected with siCtrl, siSMARCAL1, siCAPG2 or co-transfected with siSMARCAL1 and siCAPG2 for 48 hours. Cells were labeled for 30 minutes with IdU and 30 minutes with CldU in the presence of 50 μM HU and processed for DNA fiber spreading. The ratio of CldU to IdU track length is shown for 3 independent experiments. Box and whiskers correspond to 25th–75th and 10th–90th percentiles. Median ratio is indicated. g CAPG2 depletion restores fork resection in SMARCAL1-depleted cells. HeLa-S3 cells were transfected with siCtrl, siSMARCAL1, siCAPG2 or co-transfected with siSMARCAL1 and siCAPG2 for 48 hours. Cells were sequentially labeled for 15 minutes with IdU and CldU, and were either collected immediately or treated for 2 hours with 4 mM HU before DNA fiber analysis. The ratio of CldU to IdU track length was plotted for four independent experiments. Box and whiskers indicate median, 25th–75th and 10th–90th percentiles.

Article Snippet: Human cervical adenocarcinoma HeLa S3 cells (ATCC, CCL2-2) and osteocarcinoma U2OS cells (ATCC, HTB-86) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) or McCoy’s 5a medium, respectively, supplemented with 10% fetal calf serum (FCS) and 100 U/mL penicillin/streptomycin (PS).

Techniques: Control, Electron Microscopy, MANN-WHITNEY, Transfection, Labeling

Journal: bioRxiv

Article Title: Condensin and topoisomerases cooperate to relieve topological stress at stalled replication forks

doi: 10.1101/2025.08.06.668895

Figure Lengend Snippet: a Condensin II acts with TOP2A to promote fork slowing. U2OS cells were transfected for 48 hours with siCtrl, siCAPG2, siTOP2A, or co-transfected with siTOP2A and siCAPG2. Cells were labeled for 30 minutes with IdU and 30 minutes with CldU in the presence of 50 μM HU and processed for DNA fiber spreading. The ratio of CldU to IdU track length is shown for three independent experiments. Box and whiskers correspond to median, 25th–75th and 10th–90th percentiles. b Condensin II acts with TOP2A to promote fork resection. HeLa-S3 cells were transfected with siCtrl, siCAPG2, siTOP2A, or co-transfected with siTOP2A and siCAPG2 for 48 hours. Cells were sequentially labeled for 15 minutes with IdU and CldU, and were either collected immediately or treated for 2 hours with 4 mM HU before DNA fiber analysis. The ratio of CldU to IdU track length was plotted for four independent experiments. Box and whiskers indicate median, 25th–75th and 10th–90th percentiles. c TOP1 depletion restores fork slowing in CAPG2-deficient cells. U2OS cells were transfected with siCtrl, siCAPG2, siTOP1, or co-transfected with siTOP1 and siCAPG2 for 48 hours. Cells were labeled and analyzed by DNA fiber spreading as indicated in panel a (n=4). d TOP1 depletion restores fork resection in CAPG2-deficient cells. HeLa-S3 cells were transfected with siCtrl, siCAPG2, siTOP1, or co-transfected with siTOP1 and siCAPG2 for 48 hours. Cells were labeled and analyzed by DNA fiber spreading as indicated in panel b (n=3). e TOP1 depletion restores fork resection in SMARCAL1-deficient cells. HeLa-S3 cells were transfected with siCtrl, siSMARCAL1, siTOP1, or co-transfected with siSMARCAL1 and siTOP1 for 48 h. Cells were labeled and analyzed by DNA fiber spreading as indicated in panel b (n=3). f Depletion of TOP2A does not restore fork resection in SMARCAL1-deficient cells. HeLa-S3 cells were transfected with siCtrl, siSMARCAL1, siTOP2A, or co-transfected with siSMARCAL1 and siTOP2A for 48 h. Cells were labeled and analyzed by DNA fiber spreading as indicated in panel b (n=3).

Article Snippet: Human cervical adenocarcinoma HeLa S3 cells (ATCC, CCL2-2) and osteocarcinoma U2OS cells (ATCC, HTB-86) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) or McCoy’s 5a medium, respectively, supplemented with 10% fetal calf serum (FCS) and 100 U/mL penicillin/streptomycin (PS).

Techniques: Transfection, Labeling

Journal: bioRxiv

Article Title: Condensin and topoisomerases cooperate to relieve topological stress at stalled replication forks

doi: 10.1101/2025.08.06.668895

Figure Lengend Snippet: a RPA-coated ssDNA accumulates at HU-arrested forks in yeast cells lacking condensin and Top1. WT, SMC4 -AID, top1D and top1D SMC4 -AID cells were arrested in G 1 with a-factor and SMC4 was depleted by addition of auxin for 60 minutes. Then, cells were released into S phase in the presence of 200 mM HU for another 60 minutes. RPA enrichment at indicated distances from ARS306 and ARS607 was determined by ChIP-qPCR after normalization to unreplicated regions. Mean and SD correspond to three independent experiments. b Levels of chromatin-bound RPA increase in the absence of both CAPG2 and TOP1. HeLa-S3 cells were transfected for 48 hours with siCtrl, siCAPG2, siTOP2A, siTOP1 or co-transfected as indicated. Cells were labeled with EdU and were treated with 4mM of HU for 2 hours. RPA70 (green) and EdU-labelled replication sites (red) were immunodetected. The mean fluorescence intensity (MFI) of RPA70 was quantified in 5 independent experiments using CellProfiler. Changes in median intensity relative to control cells are indicated in red.

Article Snippet: Human cervical adenocarcinoma HeLa S3 cells (ATCC, CCL2-2) and osteocarcinoma U2OS cells (ATCC, HTB-86) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) or McCoy’s 5a medium, respectively, supplemented with 10% fetal calf serum (FCS) and 100 U/mL penicillin/streptomycin (PS).

Techniques: ChIP-qPCR, Transfection, Labeling, Fluorescence, Control

Journal: Analytical and Bioanalytical Chemistry

Article Title: Comprehensive lipid structure annotation via photochemical epoxidation and mass spectrometry

doi: 10.1007/s00216-025-05953-6

Figure Lengend Snippet: Shotgun MS results for [PC 36:0;Ep + Na] + for A H9c2 and B HeLa cells revealing sn -isomer diagnostic fragment ions. C Comparison of the intensity ( I ) of diagnostic fragments of a sn -isomer divided by the sum of the intensities of both sn -isomers. Mean values and error bars are from three biological replicates, n.d. indicates not detected sn -isomers, dl indicates “detected-in-low-abundance,” and bars with only one sn -isomer identified do not have error bars

Article Snippet: The human cervical HeLa S3 (ACC 161, DSMZ, Germany) and rat H9c2 myoblast cells (Sigma Aldrich, Germany, RRID: CVCL_0286) were grown in Dulbecco’s Modified Eagle’s Medium (DMEM, PAN Biotech) with added 10% fetal bovine serum (Sigma Aldrich) as well as 1% 10,000 U/mL penicillin and streptomycin.

Techniques: Diagnostic Assay, Comparison