Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Nucleosome mapping of human T47-MTVL breast cancer cells

ABSTRACT: Purification of Nucleosomal DNA

T47D-MTVL breast cancer cells carrying one stably integrated copy of the luciferase reporter gene driven by the MMTV promoter (Truss et al., 1995) were routinely grown in RPMI 1640 medium supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin, and 100 μg/mL streptomycin. For DNA preparation, cells were plated in RPMI medium without phenol red supplemented with 10% dextran-coated charcoal-treated FBS (DCC/FBS), and 48 hr later medium was replaced by fresh medium without serum. After 1 day in serum-free conditions, cells were treated for 5 minutes at 37ºC with 2mL of buffer A (150mM sucrose, 15mM Tris pH 7.5, 60mM KCl, 15mM NaCl, 2mM CaCl2) containing 0,5 mg/mL of lysolecithin. Micrococcal nuclease digestion was performed by adding 2mL of buffer A, supplemented with 720U of MNase (Worthington) for 3 minutes at 37ºC. The reaction was stopped with 40mM EDTA. Cells were scrapped and lysated with 1% SDS, 10mM EDTA and 50mM Tris pH 8.1 buffer, during 10 minutes on ice. Samples were then treated with 0,1mg/mL RNAse A for 30 minutes at 37ºC and 0,1 mg/mL of proteinase K for 1 hour at 45ºC. DNA was purified by phenol/chloroform extractions and ethanol precipitation. The digested DNA was run on 1% agarose gel, and band corresponding to mononucleosomes was gel-extracted.

Microarray hybridization

Labelling was done using Bioprime genomic labeling kit (Invitrogen, cat.no. 18095-011 and 18095-012) following manufacturers instructions. Briefly, 500 ng isolated nucleosomal DNA or total genomic DNA partially digested with MNase was labeled with either dUTP-Cy5 or dUTP-Cy3 fluorescent mononucleotides (Amersham GE PA55322), respectively. 2 mg of the obtained labeled sample were co-hybridized to the Agilent customized oligo microarray in the presence of 50 mg Human Cot-1 DNA and Agilent oligo aCGH hybridization kit (cat.no. 5188-5220) with includes blocking agents for unspecific hybridization following manufacturers instructions. Hybridization was performed in a rotating oven at 65ºC for 40 hours. Arrays were washed and fluorescent images were acquired using G2565BA Microarray Scanner System (Agilent) with 100% laser power and 100% PMT settings. 16-bit TIFF images, one for each channel, were quantified using GenePix Pro 6.0 microarray analysis software (Axon Instruments Inc.). Microarray data was normalized applying a global loess algorithm using a smoothing factor of 0.2 (Yang et al. 2002) obtaining normalized log2[intensity Cy5]/[Intensity Cy3] mean values for each spot on the array.

ORGANISM(S): Homo sapiens

SUBMITTER: Pau Rué

PROVIDER: E-MEXP-1606 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Preparation of nuclear extracts D. melanogaster Schneider cells were prepared as previously described by Andrews and Faller (1991). Briefly, in a typical preparation, 8x106 cells (grown in Schneider medium plus 10% fetal calf serum; GIBCO-BRL) were pelleted and resuspended in 1,5 mL cold PBS1X; the cell suspension is then tranferred to a microfuge tube. Cells are pelleted for 10 seconds and resuspended in 400 M-5L cold Buffer A (10mM HEPES-KOH pH 7.9 at 4M-0C, 1.5mM MgCl2, 10mM KCl, 0.5mM duthiothreitol, 0.2mM PMSF, 0.2U/microL RNasin). The cells are allowed to swell on ice for 10 minutes, and then vortexed for 10 seconds. Samples are centrifuged for 10 seconds, and the supernatant fraction is discarded. The pellet is resuspended in 100 M-5L of cold Buffer C (20mM HEPES-KOH pH 7.9, 25% glycerol, 420mM NaCl, 1.5mM MgCl2, 0.2mM EDTA, 0.5mM dithiothreitol, 0.2mM PMSF) and incubated on ice for 20 min for high-salt extraction. Cellular debris is removed by centrifugation for 2 min at 4M-0C and the supernatant fraction is stored at M-^V70M-0C. All buffers were prepared from double-distilled autoclaved water that had been treated with 0.1% DEPC (Sigma). RNA immunoprecipitation and Reverse Transcription For RNA immunopreciptation, the nuclear extract was incubated whit 50M-5g of monoclonal C1A9 anti HP1 antibody and the mixture was kept at 4M-0C overnight under continuous gentle movement. One-hundred microliters ofprotein G-Sepharose (Sigma) suspension (50% packed Sepharose in Buffer C) was added and the incubation was continued overnight as described.The beads were pelleted by 2 min centrifugation at 240 g at 4M-0C; the pellet was washed briefly three times whit each 1mL of IP Wash Solution (150mM NaCl, 50mM Tris pH 7.5, 0.5% NP40) and the Sepharose was transferred for eluition into a fresh plastic tube , pelleted again and then the supernatant was removed completely. To elute the immunocomplexes for protein analysis, an aliquot of beads were suspended in 50M-5L SDS-PAGE sample buffer and incubated for 10 min at 90M-0C; following centrifugation the supernatant was removed and used for Western blot for testing the presence of HP1 protein. To elute the immunoprecipitated RNAs, the pelleted beads were boiled in 200M-5L of DEPC wather for 5 min, spun, and the supernatant recovered; 1mL of Trizol (Invitrogen) was added to 200 M-5L of supernatant and mixed well, followed by the addition of 200M-5L of chloroform. This mixture was incubated at 4M-0C for 5 min and then centrifuged at 12000 g for 15 min; the RNAs in the aqueous phase was precipitated whit half volume of isopropanol; after precipitation, the RNAs was resuspend in 10M-5L of DEPC wather. Contaminating DNA was digested whit RNase-free DNase I (Sigma). The RNA purified from the previous step is used as a template to synthesize cDNA using oligo dT , random hexamers and SuperScript reverse transcriptase III (Invitrogen) according to the manufacturer's protocol. cDNA amplification and labeling The cDNA was used as template for a two-step random PCR amplification; in Round A, Sequenase is used to extend randomly annealed primers (Primer A) to generate templates for subsequent PCR; during Round B, the specific primer B is used to aplify the templates previously generated and finally round C consist of additional PCR cycles to inorporate the amino allyl dUTP nucleotide. About 25 ng of each cDNA sample was used for two 8 min extension with 2,7 mM Round A primer (5M-^R-GTT TCC CAG TCA CGA TCN NNN NNN NN-3M-^R, N being a mixture of all four nucleotides with 60% A+T and 40% G+C) at 37M-0C with 267U/ml Sequenase version 2.0 (usb). DNA was denatured at 94M-0C for 2 min and cooled to 10M-0C , and Sequenase 2.0 was added between extensions. The resulting products were used as template for 25 cycles of PCR using 1U/100M-5l Taq polymerase (Platinum Taq Invitrogen) and 10mM Round B primer (5M-^R-GTT TCC CAG TCA CGA TC-3M-^R). Finally this DNA was used as template for 25 cycles PCR to inorporate the amino allyl dUTP nucleotides to which the fluorescent dye may then be attached. To remove Tris buffer which interferes with the indirect coupling, the aminoallyl-cDNA samples were desalted by filtering through a Microcon M-^V30 and then mixed with the succinimidyl esters of the Cy3 or Cy5 dyes (Amersham Biosciences) in 0,1M sodium bicarbonate buffer (pH 9); the coupling reaction was icubated overnight in the dark at room temperature. Each dye labeled sample was purified by AutoSeq MicroSpin G-50 columns (Amersham Biosciences) following the manufacterers directions. Microarrays Hybridization and washing The dried labeled cDNAs pellet were resuspended in 80M-5l of DIG Easy Hyb (Roche) hybridization buffer containg 0,5 mg/ml yeast tRNa and 0,5 mg/ml salmon sperm DNA. Finally the DNA probe was denaturated by incubation at 65M-0C for 10 min and, after a brief centrifugation to spin down the drops, the mixture was pipetted onto a microarray; a coverslip was applied and the slide was placed in a microarray hybridation chamber (BioRad) and incubated overnight at 37M-0C. After hybridization, the slide was submerged in 0,01% SDS, 1%SSC until the coverslip slipped off the surface; The slide was transferred to a solution of 1%SSC and shaken at 50M-0C for 10 min, then washed once more by shaking in 0,1%SSC. Slide was dried by centrifugation for 3 min at 550 rpm and scanned with an ScanArray Lite Microarray Scanner (Packard Bioscience) with laser intensities chosen to maximize signals while avoiding pixel saturation. ScanArray express softwere was used to quantify hybridation signals; bad spots were flagged automatically by softwere and subsequently each slide was inspected manually.

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Nucleosome mapping of human T47-MTVL breast cancer cells

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