Supplementary Material Online
Androgen receptor-driven chromatin looping in prostate cancer
Dayong Wu1*, Chunpeng Zhang1*, Yanping Shen1,2, Kenneth P. Nephew3, and Qianben
Wang1,2
1
Department of Molecular and Cellular Biochemistry and the Comprehensive Cancer
Center, The Ohio State University College of Medicine, Columbus, Ohio, 43210, USA,
2
Ohio State Biochemistry Graduate Program, The Ohio State University, Columbus,
Ohio, 43210, USA, 3Medical Sciences Program, Department of Cellular and Integrative
Physiology, Indiana University School of Medicine, Bloomington, IN 47405, USA
* These authors contributed equally to this work
Corresponding author: Wang, Q. (qianben.wang@osumc.edu)
Table S1. AR-regulated fusion genesa
Fusion genes
TMPRSS2ERG
TMPRSS2ETV1
AR binding sites
(distance from TSS)b
TMPRSS2 (uc010gor.1c):
47.3/39.4/34.8/29.6/27.7/
23.9/18.9/16.4/
3.5/1.7/1.1/0/-12.6/-13.
7/-18.8/-20.7/-22.7/
-28.4 (VCaP);
6.8/5.9/-12.8/-13.8/-18.5/20.7/-22.6 (LNCaP)
-0.77/-13.545
(LNCaP&LAPC4 [S1,
S2]);
10/-2.5 (LNCaP [S3])
ERG (uc002ywz.1):
32.6/0.9/-6.6/-9.2 (VCaP)
TMPRSS2 (uc010gor.1):
47.3/39.4/34.8/29.6/27.7/
23.9/18.9/16.4/
3.5/1.7/1.1/0/-12.6/-13.
7/-18.8/-20.7/-22.7/
-28.4 (VCaP);
6.8/5.9/-12.8/-13.8/-18.5/-
Androgen
regulation
Breakpoints
Methods
up
4 kb upstream
of TSS of
TMPRSS2, or
TMPRSS2
Exon 1(or 2
or 3): ERG
Exon 2
(NM_182918
d
)
RACE and
array CGH;
Exon-walk
PCR and
5’-RLMRACE
up
TMPRSS2
Exon 1(or 2):
ETV1 Exon 4
Exon-walk
PCR and
5’-RLMRACE
Reference
[S4-S6]
[S4, S7]
20.7/-22.6 (LNCaP);
-0.77/-13.545
(LNCaP&LAPC4 [S1,
S2]);
10/-2.5 (LNCaP [S3])
TMPRSS2ETV4
SLC45A3ETV1
HERV-KETV1
C15orf21ETV1
MIPOL1ETV1
ETV1 (uc003ssu.1):
22.2/-46 (LNCaP);
2 (LNCaP [S3])
TMPRSS2 (uc010gor.1):
47.3/39.4/34.8/29.6/27.7/
23.9/18.9/16.4/
3.5/1.7/1.1/0/-12.6/-13.
7/-18.8/-20.7/-22.7/
-28.4 (VCaP);
6.8/5.9/-12.8/-13.8/-18.5/20.7/-22.6 (LNCaP);
-0.77/-13.545
(LNCaP&LAPC4 [S1,
S2]);
10/-2.5 (LNCaP [S3])
ETV4 (uc002idy.1):
28.1/4.3 (VCaP);
4.1/0.7 (LNCaP)
SLC45A3 (uc001hda.1):
-18.6/-22.8 (VCaP);
47.1/41.9/15.7/3.1/0.4/18.6/-22.7/-30/-32.6
(LNCaP)
up
Exon-walk
PCR and
5’-RLMRACE
up
SLC45A3
Exon 1:
ETV1 Exons
5
5’-RLMRACE
up
HERV-K
Exon 2: ETV1
Exon 5
5’-RLMRACE
C15orf21
Exon2:
ETV1
Exon 6
5’-RLMRACE
ETV1 (uc003ssu.1):
22.2/-46 (LNCaP);
2(LNCaP [S3])
HERV-K (BC020811.1d):
11.2/ -37.1 (VCaP);
-0.6 /-37.1 (LNCaP)
ETV1 (uc003ssu.1):
22.2/-46 (LNCaP);
2(LNCaP [S3])
C15orf21 (uc010beg.1):
12.1/-49.3 (VCaP);
12.2/1.3/-0.2/-10.7 /-13.1/
(LNCaP)
ETV1 (uc003ssu.1):
22.2/-46 (LNCaP)
2 (LNCaP [S3])
MIPOL1 (uc001wuc.1):
50/48.7/2.7/0/-2.5
(LNCaP)
ETV1 (uc003ssu.1):
22.2/-46 (LNCaP);
[S8]
-8kb
upstream of
TSS of
TMPRSS2:19
bp upstream
of ETV4
Exon3
down
up
MIPOL1
Intron 13:
169.1kb
upstream of
TSS of ETV1
5’-RLMRACE
[S9]
[S9]
[S9]
[S9, S10]
TMPRSS2ETV5
SLC45A3ETV5
CANT1ETV4
KLK2-ETV4
FOXP1ETV1
2 (LNCaP [S3])
TMPRSS2 (uc010gor.1):
47.3/39.4/34.8/29.6/27.7/
23.9/18.9/16.4/
3.5/1.7/1.1/0/-12.6/-13.
7/-18.8/-20.7/-22.7/
-28.4 (VCaP);
6.8/5.9/-12.8/-13.8/-18.5/20.7/-22.6 (LNCaP);
-0.77/-13.545
(LNCaP&LAPC4 [S1,
S2]);
10/-2.5 (LNCaP [S3])
ETV5 (uc003fpy.1):
-9.3 (VCaP);
10.7/-1.6/-9.3/-16
(LNCaP)
SLC45A3 (uc001hda.1):
-18.6/-22.8 (VCaP);
47.1/41.9/15.7/3.1/0.4/18.6/-22.7/-30/-32.6
(LNCaP)
ETV5 (uc003fpy.1):
-9.3 (VCaP);
10.7/-1.6/-9.3/-16
(LNCaP)
CANT1 (uc002jwj.1):
10.9/7.9/4.2/-15.8 /-23.5/33.9 (VCaP);
14/11/6.6/4.3/-23.5/32.7/-36.4 (LNCaP)
ETV4 (uc002idy.1):
28.1/4.3 (VCaP)
4.1/0.7 (LNCaP)
KLK2 (uc002ptu.1):
48.3/35.2/16.4/6.8/5.5/1.2
/0/-3.9/-22.5/-31.1/-37.3
(VCaP);
48.9/48.4/47.2/16.5/0.9/0.1/-3.8/-14.3/-18.6/21.4/-22.5/-31.1 (LNCaP)
[S11]
up
Exon-walk
PCR and
5’-RLMRACE
[S11]
up
SLC45A3
Exon 1: ETV5
Exon 8
Exon-walk
PCR and 5’RLM-RACE
5’-RLMRACE
up
CANT1
Intron 1(Exon
1a):
ETV4 Intron
5
up
KLK2 Exon
1:
ETV4 Exon
4a
up
FOXP1 Exon
11:
ETV1 Exon5
(or 6)
ETV4 (uc002idy.1):
28.1/4.3 (VCaP)
4.1/0.7 (LNCaP)
FOXP1 (uc003dos.1):
42.2/38.4/0.2/-27.4/-31.1
(LNCaP)
ETV1 (uc003ssu.1):
22.2/-46 (LNCaP);
2 (LNCaP [S3])
TMPRSS2
Exon 1(or 1a
or 3): ETV5
Exon 2
5’-RLMRACE
5’-RLMRACE
[S12,
S13]
[S13]
[S7]
ACSL3 (uc002vni.1):
24.3/17.4/-0.1 (LNCaP)
ACSL3ETV1
EST14ETV1
HERVK17ETV1
SLC45A3ERG
HERPUD1ERG
NDRG1ERG
5’-RLMRACE
[S14]
5’-RLMRACE
[S7]
up
ACSL3
Exon3: ETV1
Exon6
up
EST14
Exon1: ETV1
Exon5 (or 6)
up
ETV1 (uc003ssu.1):
22.2/-46 (LNCaP)
2 (LNCaP [S3])
SLC45A3 (uc001hda.1):
-18.6/-22.8 (VCaP);
47.1/41.9/15.7/3.1/0.4/18.6/-22.7/-30/-32.6
(LNCaP)
HERVK17
Exon1:
ETV1 Exon4
(or 5 or 6)
up
SLC45A3
Exon 1: ERG
Exon 4
5’-RLMRACE; RNAseq
ERG (uc002ywz.1):
32.6/0.9/-6.6/-9.2
(VCaP)
HERPUD1 (uc002eke.1):
-7.7 (VCaP);
36.1/0.2/-7.7/-14.4
(LNCaP)
up
HERPUD1
Exon1:
ERG Exon4
RNA-seq
[S15]
up
NDRG1 Exon
2 (or 3): ERG
Exon 4
RNA-seq
[S16]
up
SLC45A3
Exon 1:
BRAF Exon 8
RNA-seq
ETV1 (uc003ssu.1):
22.2/-46 (LNCaP);
2 (LNCaP [S3])
EST14 (BF673302d):
2.9/24.4 (VCaP);
31.3/24.3/2.9/-16.9/36.5/-41.6/-46.3/
(LNCaP)
ETV1 (uc003ssu.1):
22.2/-46 (LNCaP)
2 (LNCaP [S3])
HERVK17 (uc002gjx.1):
11.4/10/-0.2 (VCaP);
11.3/9.9/4.4/3.5/2.2/-0.2/15.5/-22.5/-24.8(LNCaP)
ERG (uc002ywz.1):
32.6/0.9/-6.6/-9.2 (VCaP)
NDRG1 (uc003yug.1):
47.9/47.1/40.1/28/25/23.2
/21.4/19.4/17.2
/13/12.5/11.9/9.6/0.2/-1/25.3/-27.8/-29.5/
-30.3/-31.4 (VCaP);
49.7/47.2/25.1/23.3/8.9/0.
8/-0.2/-14.1/-25.2/-29.7/43.9 (LNCaP)
5’-RLMRACE
ERG (uc002ywz.1):
32.6/0.9/-6.6/-9.2
(VCaP)
SLC45A3BRAF
SLC45A3 (uc001hda.1):
-18.6/-22.8 (VCaP);
47.1/41.9/15.7/3.1/0.4/-
[S7, S12,
S15]
[S12,
S16]
18.6/-22.7/-30/-32.6
(LNCaP)
TMPRSS2FKBP5ERG
BRAF (uc003vwc.2):
14.8/-0.4 (VCaP)
14.8 /4.2 /-7. 3/-48.4
(LNCaP)
TMPRSS2 (uc010gor.1):
47.3/39.4/34.8/29.6/27.7/
23.9/18.9/16.4/
3.5/1.7/1.1/0/-12.6/-13. 7/
-18.8/-20.7/-22.7/
-28.4 (VCaP);
6.8/5.9/-12.8/-13.8/-18.5/20.7/-22.6 (LNCaP);
-0.77/-13.545
(LNCaP&LAPC4 [S1,
S2]);
10/-2.5 (LNCaP [S3])
[S17]
[S18]
up
TMPRSS2
Exon3 (or -99
bp upstream
of TMPRSS2
Exon1):
FKBP5 Exon
6 or (6 to 7):
ERG Exon 2
RNA-seq
up
KLK2 Exon 1
(or 2):
ETV1 Exon 9
RNA-seq
up
FKBP5 Exon
5: TMPRSS2
Exon 4
RNA-seq
FKBP5 (uc003okx.1):
25.7/-2.6/-31.6/-33.7/34.6/-36.9/-38/-39.2/
-40.2/-43.1 (VCaP)
48.7/25.6/-33.7/-34.7/37.5/-39 /-42.6/-43.1/
-45 /-49.2 (LNCaP)
KLK2-ETV1
FKBP5TMPRSS2
ERG (uc002ywz.1):
32.6/0.9/-6.6/-9.2 (VCaP)
KLK2 (uc002ptu.1):
48.3/35.2/16.4/6.8/5.5/1.2
/0/-3.9/-22.5/-31.1/-37.3
(VCaP);
48.9/48.4/47.2/16.5/0.9/0.1/-3.8/-14.3/-18.6/21.4/-22.5/-31.1 (LNCaP)
ETV1 (uc003ssu.1):
22.2/-46 (LNCaP);
2(LNCaP [S3])
FKBP5 (uc003okx.1):
25.7/-2.6/-31.6/-33.7/34.6/-36.9/
-38/-39.2/-40.2/-43.1
(VCaP);
48.7/25.6/-33.7/-34.7/37.5/-39 /-42.6/-43.1/-45
/-49.2(LNCaP)
TMPRSS2 (uc010gor.1):
47.3/39.4/34.8/29.6/27.7/
23.9/18.9/16.4/
3.5/1.7/1.1/0/-12.6/-13.
[S18]
[S18]
7/-18.8/-20.7/-22.7/
-28.4 (VCaP);
6.8/5.9/-12.8/-13.8/-18.5/20.7/-22.6 (LNCaP)
-0.77/-13.545
(LNCaP&LAPC4 [S1,
S2]);
10/-2.5 (LNCaP [S3])
a
All the listed fusion genes have been validated by FISH. Gene fusions that only occur at RNA level are not
included.
b
AR binding sites within 50 kb downstream or upstream (-) of TSS. LNCaP and VCaP
AR ChIP-seq data from reference paper [S19] was visualized using UCSC hg18/NCBI 36.
c
UCSC hg18/NCBI 36 known Gene ID.
d
Genebank accession number
Supplementary References:
S1.
Wang, Q., et al. (2007) A hierarchical network of transcription factors governs
androgen receptor-dependent prostate cancer growth. Mol Cell 27, 380-392
S2.
Haffner, M.C., et al. (2010) Androgen-induced TOP2B-mediated double-strand
breaks and prostate cancer gene rearrangements. Nat Genet 42, 668-675
S3.
Lin, C., et al. (2009) Nuclear receptor-induced chromosomal proximity and DNA
breaks underlie specific translocations in cancer. Cell 139, 1069-1083
S4.
Tomlins, S.A., et al. (2005) Recurrent fusion of TMPRSS2 and ETS transcription
factor genes in prostate cancer. Science 310, 644-648
S5.
Hermans, K.G., et al. (2006) TMPRSS2:ERG fusion by translocation or
interstitial deletion is highly relevant in androgen-dependent prostate cancer, but is
bypassed in late-stage androgen receptor-negative prostate cancer. Cancer Res 66, 1065810663
S6.
Lapointe, J., et al. (2007) A variant TMPRSS2 isoform and ERG fusion product
in prostate cancer with implications for molecular diagnosis. Mod Pathol 20, 467-473
S7.
Hermans, K.G., et al. (2008) Truncated ETV1, fused to novel tissue-specific
genes, and full-length ETV1 in prostate cancer. Cancer Res 68, 7541-7549
S8.
Tomlins, S.A., et al. (2006) TMPRSS2:ETV4 gene fusions define a third
molecular subtype of prostate cancer. Cancer Res 66, 3396-3400
S9.
Tomlins, S.A., et al. (2007) Distinct classes of chromosomal rearrangements
create oncogenic ETS gene fusions in prostate cancer. Nature 448, 595-599
S10. Maher, C.A., et al. (2009) Transcriptome sequencing to detect gene fusions in
cancer. Nature 458, 97-101
S11. Helgeson, B.E., et al. (2008) Characterization of TMPRSS2:ETV5 and
SLC45A3:ETV5 gene fusions in prostate cancer. Cancer Res 68, 73-80
S12. Han, B., et al. (2008) A fluorescence in situ hybridization screen for E26
transformation-specific aberrations: identification of DDX5-ETV4 fusion protein in
prostate cancer. Cancer Res 68, 7629-7637
S13. Hermans, K.G., et al. (2008) Two unique novel prostate-specific and androgenregulated fusion partners of ETV4 in prostate cancer. Cancer Res 68, 3094-3098
S14. Attard, G., et al. (2008) Heterogeneity and clinical significance of ETV1
translocations in human prostate cancer. Br J Cancer 99, 314-320
S15. Maher, C.A., et al. (2009) Chimeric transcript discovery by paired-end
transcriptome sequencing. Proc Natl Acad Sci U S A 106, 12353-12358
S16. Pflueger, D., et al. (2009) N-myc downstream regulated gene 1 (NDRG1) is fused
to ERG in prostate cancer. Neoplasia 11, 804-811
S17. Palanisamy, N., et al. (2010) Rearrangements of the RAF kinase pathway in
prostate cancer, gastric cancer and melanoma. Nat Med 16, 793-798
S18. Pflueger, D., et al. (2011) Discovery of non-ETS gene fusions in human prostate
cancer using next-generation RNA sequencing. Genome Res 21, 56-67
S19. Yu, J., et al. (2010) An integrated network of androgen receptor, polycomb, and
TMPRSS2-ERG gene fusions in prostate cancer progression. Cancer Cell 17, 443-454