Figure S1. Representation of the junction sites of the MSMB-NCOA4 transcripts. The MSMB-NCOA4 fusions are colored, numbered and arrowed from the original reference sequences. Line graphs show the position and cDNA sequence of the fusion points. Bottom-left panel shows the sequencing result of the 5’RACE assay for MSMB-NCOA4 1 fusion transcript, including MSMB exon 1, MSMB exon 2, partial of NCOA4 exon 2 and 5’RACE primer sites.
Figure S2. Comparison of several concensus published androgen response elements (ARE) sequences and the four MSMB-NCO4 region ARE-like motifs.
Figure S3. BiblioSphere Pathway view network of the MSMB gene co-citated with the NCOA4 gene. A network of 21 genes was identified by analysis of MSMB-related genes with the BiblioSpherePathwayEdition software package based on co-citations with transcription factors, functional co-citations, and co-citations with other genes in the network.The nodes represent the genes. The BLACK edges indicate co-citation of two genes in the PubMed database; the GREEN edges indicate the presence of a significant TFBS on the promoter of the given gene for the specific interacting transcription factor.
Application / PrimerProbe / Sequence (5'-3') / Location
RT-PCR
Forward Primer / RT-MSMB-NCOA4 F1 / GTACCTGTCTATAAGGAGTCC / MSMB Exon 1
Reverse Primer / RT-MSMB-NCOA4 Rev1 / AAGGCTGCTCAACTCTTG / NCOA4 Exon 10
RT-MSMB-NCOA4 Rev2 / GGAATTTGAATGGTTTTGAGA / NCOA4 Exon 6-Exon 5
5'RACE
cDNA synthesis / MSMB-NCOA4 5RACE 2 / CCAATATTTGCTGAACTA / NCOA4 Exon 6
Reverse Primer (First) / MSMB-NCOA4 5RACE 1 / GCTGCTGAGCCTGCTGTTGAA / NCOA4 Exon 3
Reverse Primer (Second) / ME2NE2-5RACE-1 / TCATTCTCCTCACTGCTCTCCTGG / NCOA4 Exon 2-MSMB Exon 2
Reverse Primer (Second) / ME3NE2-5RACE-2 / ATTCTCCTTACTGCTCAGGGTGCA / NCOA4 Exon 2-MSMB Exon 3
Reverse Primer (Second) / RPL23-5RACE / TCCGCTAACCACTGAGTCACCAC / RPL23AP61
TaqmanqRT-PCR
Forward Primer / MSMBNCOA4 I-For / CGTTGTGATCTTTGCCACCTT / MSMB Exon 2
Reverse Primer / MSMBNCOA4 I-Rev / TTCATTCTCCTCACTGCTCTCC / NCOA Exon 2-MSMB Exon 2
MGB-Probe / MSMBNCOA4 I-Probe / TGCAATGCATCATGC / MSMB Exon 2
Forward Primer / MSMBNCOA4 II-For / CGTTGTGATCTTTGCCACCTT / MSMB Exon 2
Reverse Primer / MSMBNCOA4 II-Rev / CCTCACTGCTCTCCTGGTTGA / NCOA Exon 2-MSMB Exon 2
MGB-Probe / MSMBNCOA4 II-Probe / TGCAATGCATCATGC / MSMB Exon 2
Hs00738230_m1 (ABI) / MSMB I / MSMB Exon 1-Exon 2
Hs00159303_ml (ABI) / MSMB II / MSMB Exon 2-Exon 3
Forward Primer / PSP94-For / TCCAGGAGATTCAACCAGGAA / MSMB Exon 2
Reverse Primer / PSP94-Rev / CTCCGAGTTTATTGGGTGTTTGT / MSMB Exon 3-Exon 2
MGB-Probe / PSP94-Probe / TGCATGGATCTCAAAGG / MSMB Exon 2
Forward Primer / NCOA4 II-For / GCAAATATTGGGCCCTTCCT / NCOA4 Exon 6
Reverse Primer / NCOA4 II-Rev / CAATACCGGATGCTGACTTCTG / NCOA4 Exon 7-Exon 6
MGB-Probe / NCOA4 II-Probe / AGAAGAGAGGCTGTATCT / NCOA4 Exon 6
Hs00428328_m1 (ABI) / NCOA4 / NCOA4 Exon 1-Exon 2
Hs00171172_m1 (ABI) / AR / AR Exon 4-Exon 5
Hs99999903_m1 (ABI) / Beta-actin / Beta-actin Exon 1
Table S2. Genes expression profiles in tissues and cancer cell lines
MSMB-NCOA4
MSMB-NCOA4 I / MSMB-NCOA4 II / MSMB / NCOA4 / AR / Tissue Type
PC3 / 0.69 / 0.23 / 1.48 / 1744.08 / 280.42 / Prostate
LNCaP / 1.60 / 9.95 / 893.70 / 7486.39 / 16727.05 / Prostate
DU145 / 0.00 / 0.98 / 0.60 / 7473.67 / 0.00 / Prostate
PCa2b / 112.94 / 190.50 / 12275.78 / 12721.09 / 11599.50 / Prostate
CAHPV10 / 0.00 / 0.72 / 3.49 / 1604.60 / 0.00 / Prostate
PZHPV7 / 0.00 / 0.45 / 8.76 / 1284.13 / 0.00 / Prostate
VCaP / 0.00 / 0.00 / 7.80 / 11431.88 / 98029.91 / Prostate
NCIH660 / 3.50 / 9.00 / 53.20 / 2329.83 / 1.70 / Prostate
RWPE1 / 4.01 / 3.15 / 4.77 / 2126.88 / 0.00 / Prostate
22RV1 / 0.00 / 0.00 / 6.60 / 4574.40 / 4376.20 / Prostate
SN12C / 0.00 / 0.00 / 0.00 / 559.78 / 0.42 / Renal
7860 / 33.99 / 22.30 / 0.00 / 1100.82 / 3.01 / Renal
TK10 / 12.36 / 12.68 / 0.00 / 1863.26 / 0.00 / Renal
ACHN / 0.00 / 0.00 / 0.12 / 2222.87 / 0.02 / Renal
MCF7 / 1.00 / 1.47 / 153.83 / 1213.03 / 254.50 / Breast
MCF10F / 0.61 / 0.62 / 1.56 / 894.71 / 5.48 / Breast
SUM229 / 0.82 / 1.71 / 1.14 / 1512.53 / 39.04 / Breast
SUM159 / 0.00 / 0.00 / 1.79 / 1613.42 / 128.22 / Breast
SUM149 / 0.00 / 0.00 / 0.30 / 2235.66 / 206.16 / Breast
T47D / 0.00 / 0.43 / 21.57 / 2375.30 / 410.21 / Breast
SKBR3 / 132.50 / 87.56 / 212.20 / 1128.78 / 11.68 / Breast
MB231 / 0.00 / 0.00 / 0.00 / 1040.56 / 0.08 / Breast
Hs578T / 0.03 / 0.00 / 0.23 / 397.01 / 38.36 / Breast
BT549 / 0.38 / 0.25 / 0.00 / 597.31 / 166.43 / Breast
AGS / 3.12 / 3.31 / 958.79 / 1272.57 / 0.00 / Stomatch
H.P.N.T.1 / 222.05 / 297.60 / 1182653.05 / 11966.00 / 8886.80 / Prostate normal tissue
H.P.N.T.2 / 50.81 / 135.48 / 845691.95 / 7208.69 / 11178.38 / Prostate normal tissue
H.P.N.T.3 / 52.60 / 114.63 / 540993.85 / 4192.61 / 7204.23 / Prostate normal tissue
H.P.T.T.1 / 65.50 / 71.02 / 143225.56 / 6484.11 / 4774.23 / Prostate tumor tissue
H.P.T.T.2 / 3.30 / 3.36 / 1272.13 / 4216.60 / 4038.47 / Prostate tumor tissue
H.T.N.T. / 22.75 / 37.98 / 205762.25 / 2677.42 / 804.47 / Trachea normal tissue
H.B.N.T. / 15.49 / 20.90 / 18.94 / 1657.52 / 738.76 / Breast normal tissue
H.B.T.T. / 14.65 / 10.55 / 20.61 / 1681.64 / 21.05 / Breast tumor tissue
Relative mRNA express =(Target gene/beta-actin)*105