Journal: Folia Biologica

Article Title: A Fraction of MCM 2 Proteins Remain Associated with Replication Foci During a Major Part of S Phase

doi: 10.14712/fb2011057010003

Figure Lengend Snippet: Fig. 1. Influence of extraction on nuclear architecture The organization of unextracted (first row) and extracted (second row) cell nucleus in a mid confocal optical section is documented by DNA (DAPI), euchromatin (H4Ac), MCM2 and DNA replication (EdU pulse) staining/labelling. Chro- matin condensation due to the extraction procedure is clearly visible, but the most striking effect is the removal of soluble MCMs. This allows us to analyse the localization of chromatin-bound MCMs. Bar: 10 μm.

Article Snippet: Sites of DNA replication were labelled by 5-ethynyl-2’-deoxyuridine (EdU, Invitrogen, Paisley, UK) that was added directly to the medium in a final concentration of 10 μM for 20 min. Then the cells were either briefly washed in PBS, fixed by 2% formaldehyde in PBS for 30 min and permeabilized by 0.2% Triton X-100 in PBS for 5 min or extracted before fixation.

Techniques: Extraction, Staining

Journal: Folia Biologica

Article Title: A Fraction of MCM 2 Proteins Remain Associated with Replication Foci During a Major Part of S Phase

doi: 10.14712/fb2011057010003

Figure Lengend Snippet: Fig. 4. Quantitative analysis of chromatin-bound MCM 2 with respect to DNA synthesis and chromatin CCF curves between MCM 2 and EdU/ DAPI/H4Ac sig- nals are shown in the corresponding graphs. White to black curves of different greyness represent specific periods of the cell cycle as described in the text and indicated in leg- ends next to the graphs. Most of the curves fit visual as- sessments from Fig. 3. However, two small “positive” peaks marked by white arrows are seen. These peaks testify for the existence of an MCM fraction that co-localizes with replication foci even in early S phase. Presented CCF curves were calculated as the average of five images for each group in Figs. 4 and 5.

Article Snippet: Sites of DNA replication were labelled by 5-ethynyl-2’-deoxyuridine (EdU, Invitrogen, Paisley, UK) that was added directly to the medium in a final concentration of 10 μM for 20 min. Then the cells were either briefly washed in PBS, fixed by 2% formaldehyde in PBS for 30 min and permeabilized by 0.2% Triton X-100 in PBS for 5 min or extracted before fixation.

Techniques: DNA Synthesis

Journal: Folia Biologica

Article Title: A Fraction of MCM 2 Proteins Remain Associated with Replication Foci During a Major Part of S Phase

doi: 10.14712/fb2011057010003

Figure Lengend Snippet: Fig. 5. Quantitative analysis of chromatin-bound MCM 2 with respect to DNA replication signal after chase The cells were, after 10 min incorporation of EdU, cultured for 90 min in medium free of EdU and processed for im- munocytochemistry as in Fig. 4 for EdU and MCM 2 sig- nals. In the graph, the CCF curve between MCM2 and EdU signals is shown for cells that incorporated EdU in the early S phase. With respect to Fig. 4, note that the small “posi- tive” peak has almost disappeared. This indicates that the remaining fraction of MCM proteins disassociated from former replication sites.

Article Snippet: Sites of DNA replication were labelled by 5-ethynyl-2’-deoxyuridine (EdU, Invitrogen, Paisley, UK) that was added directly to the medium in a final concentration of 10 μM for 20 min. Then the cells were either briefly washed in PBS, fixed by 2% formaldehyde in PBS for 30 min and permeabilized by 0.2% Triton X-100 in PBS for 5 min or extracted before fixation.

Techniques: Cell Culture

Journal: Cell reports

Article Title: Short Inverted Repeats Are Hot Spots For Genetic Instability: Relevance to Cancer Genomes

doi: 10.1016/j.celrep.2015.02.039

Figure Lengend Snippet: (A) Running average of IR motifs in the cancer (red) and control (black) datasets whose center loop positions are located at each base along the ±100 bp flanking cancer translocation breakpoints or the control sites. (B) Distribution of stem lengths for the IRs found in the cancer and control datasets. (C) Model of replication-related genetic instability where a cruciform impedes DNA replication (right), and replication-independent mechanisms of structure-specific cleavage (e.g. XPF) (left).

Article Snippet: In Vitro Mutagenesis Assays HeLa cell-free extracts from a CHIMERx DNA replication assay kit were used as a replication-incompetent system.

Techniques: Control, Translocation Assay

Journal:

Article Title: Gene-expression signature of benign monoclonal gammopathy evident in multiple myeloma is linked to good prognosis

doi: 10.1182/blood-2006-07-037077

Figure Lengend Snippet: Fifty-two SAM-defined genes are differentially expressed in NPC, MGUS, and MM

Article Snippet: 2.05 1.55 3.18 1.36 212038_s_at VDAC1 Ion channel for cytochrome c 2.62 1.56 3.17 1.42 208308_s_at GPI Energy metabolism 1.97 1.48 3.17 1.48 201013_s_at PA1CS DNA synthesis 2.81 1.43 3.17 1.45 202708_s_at HIST2H2BE Chromosome organization and biogenesis 2.35 1.71 3.14 2.11 215071_s_at HIST1H2AC Chromosome organization and biogenesis 3.47 3.62 3.13 1.97 225361_x_at LOC159090 Unknown 3.43 1.68 3.11 1.53 219366_at AVEN Antiapoptosis 2.63 1.76 3.10 1.47 209398_at H1ST1H1C Chromosome organization and biogenesis 5.39 5.53 3.09 2.02 221652_s_at C12orf11 Unknown; sarcoma antigen NY-SAR-95 2.07 1.37 3.06 1.57 225028_at LOC550643 Unknown 3.83 2.01 3.03 1.45 214214_s_at C1QBP Immunity 2.64 1.45 3.03 1.47 201577_at NME1 Nucleotide biosynthesis 3.57 1.62 2.99 1.58 218280_x_at H1ST2H2AA Chromosome organization and biogenesis 4.24 4.76 2.95 1.92 201479_at DKC1 Telomere maintenance 2.24 1.42 2.92 1.43 208864_s_at TXN Redox reactions 2.90 1.68 2.91 1.51 212297_at ATP13A3 Cation transport 2.64 1.42 2.88 1.54 222825_at OTUD6B Unknown 2.66 1.35 2.88 1.40 209267_s_at SLC39A8 Ion transport 3.41 1.86 2.88 1.56 217898_at C15orf24 Unknown 2.35 1.70 2.83 1.33 210275_s_at ZA20D2 Unknown 2.27 1.36 2.81 1.37 213485_s_at ABCC10 ATP-dependent efflux pump; multidrug resistance pump 3.17 1.51 2.76 1.34 200994_at IPO7 Nuclear trafficking 2.08 1.46 2.72 1.37 222428_s_at LARS Protein synthesis 3.64 1.68 2.71 1.32 202591_s_at SSBP1 Mitochondrial DNA replication 2.22 1.42 2.69 1.35 204244_s_at ASK Cell cycle 3.25 1.77 2.67 1.37 225916_at ZNF131 Gene transcription 2.47 1.39 2.63 1.36 202396_at TCERG1 Gene transcription 3.85 1.62 2.63 1.32 213340_s_at K1AA0495 Unknown −2.40 0.78 −2.52 0.75 206150_at TNFRSF7 Immune cell signaling −3.82 0.55 −2.56 0.75 228139_at RIPK3 Cell signaling −2.63 0.74 −2.59 0.77 220066_at CARD15 Antiapoptosis −4.02 0.50 −2.66 0.62 210347_s_at BCL11A Gene transcription 3.48 2.04 −2.67 0.64 232511_at RANBP2L1 Nuclear import 2.07 1.54 −2.71 0.64 214041_x_at RPL37A Ribosomal protein 2.22 1.80 −3.09 0.60 219371_s_at KLF2 Gene transcription 3.81 1.78 −3.11 0.66 202724_s_at FOXO1A Gene transcription 2.49 1.55 −3.27 0.64 215671_at PDE4B Drug metabolism 2.07 1.53 −3.30 0.59 219675_s_at UXS1 Glycosaminoglycan biosynthesis −2.33 0.76 2.97 1.35 Open in a separate window Genes are ordered based on the SAM score in the MM vs MGUS comparison.

Techniques: Binding Assay, DNA Synthesis