Cell culture
The Saos-2 and U2OS cells (The Culture Collection of the Chinese Academy of Sciences, China) were cultured in DMEM (Gibco, US) with 10% fetal bovine serum (Gibco, US),containing 1% penicillin-streptomycin Solution (Gibco, US), and placed in a 5% CO2 humidified incubator at room temperature.
Plasmid transfection and gene knockdown with siRNA
The RPL34 (GenBank accession NM. 000995.4) promoter sequence was cloned into pGL3-Basic Vector having the Mamhl/Xbal sites, while the c-myc (GenBank accession NM. 002467.4) CDS sequence was cloned into pcDNA3.1+ having the Kpml/Bglll sites. Successful cloning was then confirmed via sequencing alignment and restriction enzyme digestion, after which plasmids and siRNAs were separately transfected into cells with Lipofectamine 2000 (Invitrogen, USA). Cells were then grown for 6 h, after which media was exchanged for fresh complete media and cells were incubated for a further 24 h. Primers (Shanghai Tuo Ran Biological Technology , China) were as follows: c-Myc-si-1, 5’ -CGACGAGACCUUCAUCAAAdTdT-3’ and 5’-UUUGAUGAAGGUCUCG UCGdTdT-3’;c-Myc-si-2, 5’-CGAUGUUGUUUCU GUGGAAdTdT-3’ and 5’-UUCCACAGAAACAACAUCGdTdT-3’; c-Myc-si-3, 5’-GGAACUAUGACCUCGACUAdTdT-3’ and 5’-UAGUCGAGGUCAUAGUUC CdTdT-3’.
qRT-PCR assay
Cellular RNA was isolated using RNAiso Plus reagents (Takara, Japan), after which a 5x Prime Script RT Master Mix (Takara, Japan) was used to prepare cDNA using 500ng of RNA from each sample. qRT-PCR was then performed using 50ng of each cDNA sample with a real-time PCR machine (ABI, USA) using a SYBR GREEN kit (ABI, USA). The PCR cycle parameters were set as follows: 40 cycles of 50°C for 3min, 95°C for 3min, 95°C for 10 s and 60°C for 30s. GAPDH was used for normalization purposes, and relative gene expression was assessed via the △△Ct method [33]. Primers (Gene Wiz, China) were as follows: c-Myc, 5'-CCTG GTGCTCCATGAGGAGAC-3' and 5'-CAGACTCTGACCTTTTGCCAGG-3'; RPL34, 5’-GTTTGACATACCGACGTAGGC-3’, 5’-GCACACATGGAACCACC ATAG-3’; GAPDH, 5'-TGACAA CTTTGGTATCGTGGAAGG-3' and 5'-AGGCAG GGATGATGTTCTGGA GAG-3'.
Western blot
Western blot assays were performed as described previously [34] using the following antibody: anti-RPL34 (BBI; 1:1000); anti-c-Myc (CST; 1:1000); Goat anti-rabbit IgG secondary antibodies (Jackson ImmunoResearch; 1:5000); Goat anti-mouse IgG secondary antibodies (Jackson ImmunoResearch; 1:5000); GAPDH (Proteintech; 1:5000).
Chromatin immunoprecipitation
A Chromatin immunoprecipitation Kit (Millipore, USA) was used based on provided directions. Briefly, Saos-2 cells were added to 10 cm culture plates, then 1% formaldehyde was used to cross-link DNA and proteins within these cells for 10 minutes, after which glycine was added (0.125 M final concentration) to terminate this reaction. Cells were then collected, centrifuged, resuspended in a lysis buffer, and a 100 uL volume of each lysate underwent sonication to shear the DNA into fragments of approximately 500 bp. A total of 25 uL of each sample was then reserved as input, while the remaining fractions were mixed for 1 h with protein G agarose at 4°C. Samples were centrifuged and then incubated with 5 μg primary antibody (CST, USA) or normal IgG overnight with rotation at 4 °C. Then, supernatants were reicubated for 1 h using protein G agarose at 4 °C. Elution was then performed twice to collect purified protein-DNA complexes. Next, 5 M NaCl was added overnight to interfere with cross-linking between chromatin and proteins. RNase A and proteinase K treatments were then used to isolate DNA from input and immunoprecipitated samples, after which the following primers were used to analyze 1 uL of each sample via qRT-PCR: LEF1-chip: 5’-ATGATGAAGTCAAGCCACTGC-3’ and 5’-GCTTAT AACCCACCGAAAGGC-3’; RPL34-chip: 5’-AGGAA AGTTGAGTGGGTA-3’ and 5’-GACTTGAGTGTTGGCTTAT- 3’.
Dual-Luciferase assay
Using kits (Promega, USA), dual-luciferase reporter assays were performed thrice based on provided directions. Briefly, co-transfection into osteosarcoma cells was done with 500 ng of a pcDNA3.1 carrying c-Myc CDS sequence, 500 ng of a pGL3 reporter containing RPL34 promoter sequence and 500 ng of a pRL-TK (Promega, USA) having Renilla luciferase. Then the luciferase activity of the cells was measured after 24 h.
Identification of RPL34-interacting genes using bioinformatics
In order to identify Transcription factors (TFs) predicted to regulate RPL34 expression, human TF-gene pairs were identified using the UCSC ENCODE Genome Browser (http://genome.ucsc.edu). The STRING database was then used to construct a protein-protein interaction network for RPL34 [35], with an interaction pair threshold score of > 0.9, and with Cytoscape used for visualization purposes [36].This analysis revealed 11 TFs predicted to regulate RPL34 expression, including MYC and MAX[32], both of which can dimerize to regulate cellular proliferation, differentiation and apoptosis.
Statistical analysis
Data are presented as mean ± standard deviation, and experiments in this study were conducted in triplicate. Results were compared via one-way ANOVA, with GraphPad Prism 5.0 (CA, USA) or SPSS 20.0 (Chicago, US) used for all statistical testing. P < 0.05 was the significance threshold.