Briefly, lysis was carried out in 0

Briefly, lysis was carried out in 0.7 M KCl, 20 mM Tris at pH 8.0, 0.1 mM EDTA, 2 mM PMSF, 0.4% NP40, 10% glycerol and PhosSTOP (Roche). enlargements of the co-localization foci TFR2 indicated by white arrows.(TIF) pgen.1003397.s002.tif (2.2M) GUID:?A5196DF8-7972-41E2-99AF-A3404E2D0855 Figure S3: In living cells, WSTF, SNF2h and NM1 transit through actively transcribing NORs. Cells were synchronized in prophase and subjected to a short FUrd pulse just before reaching telophase or early G1. Two times immunostaining was performed with antibodies to (A) FUrd and NM1, (B) FUrd and WSTF and (C) FUrd and SNF2h. Specimens were imaged by confocal microscopy (level pub 5 m).(TIF) pgen.1003397.s003.tif (3.0M) GUID:?7B343F74-E57C-4A3A-8641-AD32A8CA49D5 Figure S4: Distributions of NM1, SNF2h and WSTF in early mitotic HeLa cells. Localization was monitored by immunostaining (green) with the indicated antibodies and DAPI for DNA detection. Analysis was by confocal microscopy (level pub 5 m).(TIF) pgen.1003397.s004.tif (2.5M) GUID:?070EA4FC-84A2-44D8-95C8-DDE23B0028E4 Number S5: (A) Schematic representation of V5-tagged wt and mutated NM1 constructs stably expressed in HEK293T cell lines PD-1-IN-1 and used in the study. (B) Co-precipitations of actin from total lysates from HEK293T cells constitutively expressing wt and mutated V5-tagged NM1 constructs using anti-V5 antibodies. Bound proteins are recognized on immunoblots for V5 and actin. 5% of the input is demonstrated in Lane 1. IP, immunoprecipitation. PD-1-IN-1 (C) Schematic representation of the human being rDNA transcription unit and positions of PCR products. (D) ChIP assays performed on transfected HEK293T cells expressing V5-tagged wt NM1 or mutated NM1 constructs (as indicated) and HEK293T cells not expressing any of the NM1 constructs with antibodies against V5, histone H3 and non-specific rabbit immunoglobulins (IgG). Co-precipitated DNA was analyzed by PCR with primers for rDNA promoter, 18S rDNA PD-1-IN-1 and 28S rDNA. PCR products were resolved by 2% agarose gel electrophoresis (and exposed by ethidium bromide staining as seen above).(TIF) pgen.1003397.s005.tif (828K) GUID:?266577CA-BFBB-40F6-B454-5760891F67FF Number S6: rRNA gene occupancy of the HAT PCAF requires a functional NM1. (A) Schematic representation of the rDNA transcription unit. (BCC) ChIP assays on chromatin from HEK293T cells and HEK293T cells stably expressing V5-wtNM1, V5-RK605AA NM1, V5-C NM1 and V5-IQ NM1 mutants with antibodies against V5 and PCAF as indicated below the x-axis. qPCR analysis was performed with primers amplifying (B) promoter and (C) 18S rDNA. The ideals are offered as the percentage of the input signal for each pair. Error bars represent standard deviations.(TIF) pgen.1003397.s006.tif (531K) GUID:?A5E62AED-CC3C-4D6A-854F-123FE2DA6AD6 Number S7: FUrd incorporation assays performed on (A) HeLa cells subjected to NM1 gene silencing or control experiments with RNAi oligonucleotides with scrambled sequences (scrRNAi), and (B) HeLa cells incubated with BDM or DMSO. In all cases, detection of integrated FUrd was having a fluorochrome-conjugated anti-BrdU antibody. Detection was by confocal microscopy. Level bars, 10 m.(TIF) pgen.1003397.s007.tif (2.2M) GUID:?087BBE13-B820-433C-B0C1-C6E02043711D Number S8: (A) Schematic representation of V5-tagged wt and mutated NM1 constructs stably expressed in HEK293T cell lines and used in the study. (B) Chromatin profile from HEK293T cells stably expressing PD-1-IN-1 V5-wtNM1, V5-RK605AA NM1 and V5-C NM1 compared to V5-IQ NM1 shown as 2Ct of undigested and MNase digested cross-linked chromatin. The position of each primer pair is definitely indicated below the graph; 2c (coding), Position 2 in the coding region. Error bars symbolize standard deviations of three independent experiments.(TIF) pgen.1003397.s008.tif (1.0M) GUID:?52E4755A-5E49-44EA-9146-CD79F13C6481 Number S9: PCAF occupancy and H3K9 acetylation patterns about rRNA genes analyzed in growing HeLa cells and in cells arrested in S-phase. (A) FACS analysis on growing HeLa cells, HeLa cells caught in G1/S with aphidicolin, HeLa cells in S-phase 4 h after launch from your aphidicolin block and in S/G2 phase 6 h after launch from the.