Transcript High resolution mapping of the X chromosome pseudoautosomal

High resolution mapping of the X
chromosome pseudoautosomal region in
two siblings with Hodgkin Lymphoma and
Leri-Weill Dyschondrosteosis
Kym Spencer
Liverpool Women’s Hospital
Reed-Sternberg cells & Hodgkin cells
Clinical Features
Incidence
Cancer Research UK figures for 2004:
1,519 new cases - 0.5% of all cancers
diagnosed.
Incidence of 2.4/100,000 individuals
2.7/100,000 males
2.1/100,000 females
Bimodal age of incidence
15-40 years
>55 years
A genetic cause of HL
 Several familial cases of HL reported.
Risk of HL higher in individuals with a family history of
the condition.
 Higher in siblings.
 Highest in gender concordant siblings.
 Combination of inherited susceptibility with shared
environment?
Male predominance of HL
 Horwitz & Weirnik (1999 & 2007) suggest pseudoautosomal
link due to recombination mechanism of pseudoautosomal
regions.
Family L
I
Leri-Weill
LWD
Dyschondrosteosis (LWD)
2 (GW)
Hodgkin
HL Lymphoma (HL)
II
1 (ML)
2 (PL)
3 (JW)
4 (GW)
1 (RL)
2 (GL)
3 (RW)
4 (NW)
III
LWD - Madelung Deformity
Pseudoautosomal Regions
p
PAR1
p
q
q
X
Y
PAR2
Map of PAR1
Not deleted (Shears et al 2003)
Deleted – (Shears et al.2003)
Not deleted – (present study)
Deleted – (present study)
END OF
PAR1
Gene
Deleted in IC - (present study)
*
LLNOYCO3’M’56G10
LLNOYCO3’M’34F5
LLNOYCO3’M’51D11
Direction of transcription
RP13-465B17
RP13-391G2
Microarray probes:
CXYorf2
Not deleted
Deleted
GTPBP6
(PGPL)
SLC25A6
(ANT3)
PLCXD1
Telomere
DXYS228
2726-L1588
MLPA probes
DXYS234
Distance from telomere (kb)
100
DXS6814
DXYS
Microsatellite markers
DXYS233
SHOX CA repeat
LLNOYCO3’M’2E2
FISH probe (approx. location)
100
CRLF2
SHOX
PPP2R3B
200
300
400
500
600
700
800
900
CSF2RA
1300
1000
IL3RA
1400
ZBED1
ASMTL
1500
CXYorf3
(XE7)
ASMT
P2RYB
1600
2500 1700
CD99 (MIC2)
2600 1800
XG
2700
Family L
I
Leri-Weill
LWD
Dyschondrosteosis (LWD)
2 (GW)
HL Lymphoma (HL)
Hodgkin
II
1 (ML)
2 (PL)
3 (JW)
4 (GW)
1 (RL)
2 (GL)
3 (RW)
4 (NW)
III
Methods
MLPA for SHOX copy number using
P018B MLPA kit from MRC Holland
Fluorescent microsatellite analysis
Addition of custom probes into existing
MLPA kit
SNP analysis
Microarray analysis
0.80
0.60
0.40
0.20
0.00
0.80
0.60
0.40
0.20
0.00
PPP2R3B
C10 10p14
C9 2p22
C8 13q12
C7 18q21
C6 8q24
C5 13q14
C4 9q34
C3 20q11
C2 16p13
SHOX Ex1
Xq25
DBY
SRY
SYBL1
ASMT
GPR143(ii)
GPR143
ARSF
PAR 5652-L5106
IL3RA
CSF2RA
PAR 5651-L5105
PAR 5650-L5104
PAR 5649-L5103
PAR 5648-L6218
PAR 6293-L6219
PAR 6292-L5801
PAR 6291-L6222
PAR 5647-L5101
PAR 5646-L5100
PAR 5645-L5099
PAR 5644-L5098
PAR 5643-L5097
PAR 5642-L5096
SHOX Ex8
SHOX Ex7
SHOX Ex6
SHOX Ex5
SHOX Ex4
SHOX Ex3
SHOX Ex2
0.80
SMCY
0.00
LOC159015
0.20
C1 5q31
0.40
C1 5q31
C2 16p13
C3 20q11
C4 9q34
C5 13q14
C6 8q24
C7 18q21
C8 13q12
C9 2p22
C10 10p14
PPP2R3B
LOC159015
SHOX Ex1
SHOX Ex2
SHOX Ex3
SHOX Ex4
SHOX Ex5
SHOX Ex6
SHOX Ex7
SHOX Ex8
PAR 5642-L5096
PAR 5643-L5097
PAR 5644-L5098
PAR 5645-L5099
PAR 5646-L5100
PAR 5647-L5101
PAR 6291-L6222
PAR 6292-L5801
PAR 6293-L6219
PAR 5648-L6218
PAR 5649-L5103
PAR 5650-L5104
PAR 5651-L5105
CSF2RA
IL3RA
PAR 5652-L5106
ASMT
ARSF
GPR143
GPR143(ii)
Xq25
SYBL1
SMCY
SRY
DBY
RL
0.60
C1 5q31
C2 16p13
C3 20q11
C4 9q34
C5 13q14
C6 8q24
C7 18q21
C8 13q12
C9 2p22
C10 10p14
PPP2R3B
LOC159015
SHOX Ex1
SHOX Ex2
SHOX Ex3
SHOX Ex4
SHOX Ex5
SHOX Ex6
SHOX Ex7
SHOX Ex8
PAR 5642-L5096
PAR 5643-L5097
PAR 5644-L5098
PAR 5645-L5099
PAR 5646-L5100
PAR 5647-L5101
PAR 6291-L6222
PAR 6292-L5801
PAR 6293-L6219
PAR 5648-L6218
PAR 5649-L5103
PAR 5650-L5104
PAR 5651-L5105
CSF2RA
IL3RA
PAR 5652-L5106
ASMT
ARSF
GPR143
GPR143(ii)
Xq25
SYBL1
SMCY
SRY
DBY
ML
DEL
SHOX MLPA
1.20
1.00
1.40
1.20
1.00
1.40
1.20
1.00
SHOX MLPA
Key
Not deleted (Shears et al 2003)
Deleted – (Shears et al.2003)
Not deleted – (present study)
Deleted – (present study)
END OF
PAR1
Gene
Deleted in IC - (present study)
*
LLNOYCO3’M’56G10
LLNOYCO3’M’34F5
LLNOYCO3’M’51D11
Direction of transcription
RP13-465B17
RP13-391G2
Microarray probes:
CXYorf2
Not deleted
Deleted
SLC25A6
(ANT3)
GTPBP6
(PGPL)
PLCXD1
Telomere
DXYS228
2726-L1588
MLPA probes
DXYS234
Distance from telomere (kb)
100
DXS6814
DXYS
Microsatellite markers
DXYS233
SHOX CA repeat
LLNOYCO3’M’2E2
FISH probe (approx. location)
100
CRLF2
SHOX
PPP2R3B
200
300
400
500
600
700
800
1000
CSF2RA
1300
IL3RA
1400
ASMTL
1500
ASMT
P2RYB
2500
1600
CD99 (MIC2)
2600
1700
1153-L0712 (ASMT)
5652-L5106
1342-L0711 (IL3RA)
1170-L0710 (CSF2RA)
5651-L5105
5650-L5104
5649-L5103
5648-L6218
6293-L6219
6292-L5801
6291-L6222
5647-L5101
5646-L5100
5645-L5099
5644-L5098
5643-L5097
5642-L5096
1152-L0709 (SHOX exon 6b)
1151-L0708 (Between exon 6a & 6b)
1150-L0911 (SHOX exon 6a)
1149-L0910 (SHOX exon 5)
1148-L1331 (SHOX exon 4)
1147-L0802 (SHOX exon 3)
1146-L6220 (SHOX exon 2)
1145-L0702 (SHOX exon 1 – non-coding)
1341-L6221 (LOC159015)
2726-L1588 (PPP2R3B exon 5)
*
Putative SHOX
regulatory region
(Fukami et al. 2006)
900
CXYorf3
(XE7)
ZBED1
1800
XG
2700
PPP2R3B
 PPP2R3B encodes PR48.
 B subunit of the PP2A holoenzyme.
 Involved in cell cycle regulation - binds to Cdc6 in mammalian
cells and restricts DNA replication.
 PP2A is a cell cycle regulator and tumour suppressor.
 Consists of A, B and C subunits.
 B subunits confer substrate specificity.
B
PR55
α, β, γ or δ
B’
PR61
α, β, γ, δ or ε
B’’
PR72/PR130
or PR48
B’’’
PR93/SG2NA or
PR110/striatin
PR65
α or β
A
C
PP2A
α or β
Microsatellite Analysis
LWD
GW
HL
2
2
1
+
1
2
1
1
1
+
2
3
2
2
1
+
1
2
∆
-
ML
RL
PL
GL
2
2
1
+
1
1
∆
-
1
1
1
+
2
3
∆
-
2
2
1
+
1
1
3
3
1
+
2
4
DXYS10037
DXYS10038
DXYS10039
SHOX
DXYS10180
DXYS10181
Microsatellite Analysis
Key
Not deleted (Shears et al 2003)
Deleted – (Shears et al.2003)
Not deleted – (present study)
Deleted – (present study)
Gene
Deleted in IC - (present study)
*
LLNOYCO3’M’56G10
LLNOYCO3’M’34F5
LLNOYCO3’M’51D11
RP13-391G2
Microarray probes:
Not deleted
Deleted
GTPBP6
(PGPL)
PLCXD1
Telomere
DXYS10081
RP13-465B17
DXYS10080
2726-L1588
MLPA probes
DXYS233
Distance from telomere (kb)
100
DXYS10139
Microsatellite markers
DXYS10138
DXYS
DXYS10137
Direction of transcription
SHOX CA repeat
LLNOYCO3’M’2E2
FISH probe (approx. location)
100
SHOX
PPP2R3B
200
300
400
500
600
700
800
1000
5651-L5105
5650-L5104
5649-L5103
5648-L6218
6293-L6219
6292-L5801
6291-L6222
5647-L5101
5646-L5100
5645-L5099
5644-L5098
5643-L5097
5642-L5096
1152-L0709 (SHOX exon 6b)
1151-L0708 (Between exon 6a & 6b)
1150-L0911 (SHOX exon 6a)
1149-L0910 (SHOX exon 5)
1148-L1331 (SHOX exon 4)
1147-L0802 (SHOX exon 3)
1146-L6220 (SHOX exon 2)
1145-L0702 (SHOX exon 1 – non-coding)
1341-L6221 (LOC159015)
2726-L1588 (PPP2R3B exon 5)
*
Putative SHOX
regulatory region
(Fukami et al. 2006)
900
0.40
0.20
0.00
0.60
0.40
0.20
0.00
0.80
0.60
0.40
0.20
0.00
C1 5q31
C2 16p13
C3 20q11
C4 9q34
C5 13q14
C6 8q24
C7 18q21
C8 13q12
C9 2p22
C10 10p14
PPP2R3B Ex 5
PPP2R3B Ex 4
PPP2R3B Ex 1
LOC159015
SHOX Ex1
SHOX Ex2
SHOX Ex3
SHOX Ex4
SHOX Ex5
SHOX Ex6
SHOX Ex7
SHOX Ex8
PAR 5642-L5096
PAR 5643-L5097
PAR 5644-L5098
PAR 5645-L5099
PAR 5646-L5100
PAR 5647-L5101
PAR 6291-L6222
PAR 6292-L5801
PAR 6293-L6219
PAR 5648-L6218
PAR 5649-L5103
PAR 5650-L5104
PAR 5651-L5105
CSF2RA
IL3RA
PAR 5652-L5106
ASMT
ARSF
GPR143
GPR143(ii)
Xq25
SYBL1
SMCY
SRY
DBY
0.60
C1 5q31
C2 16p13
C3 20q11
C4 9q34
C5 13q14
C6 8q24
C7 18q21
C8 13q12
C9 2p22
C10 10p14
PPP2R3B Ex 5
PPP2R3B Ex 4
PPP2R3B Ex 1
LOC159015
SHOX Ex1
SHOX Ex2
SHOX Ex3
SHOX Ex4
SHOX Ex5
SHOX Ex6
SHOX Ex7
SHOX Ex8
PAR 5642-L5096
PAR 5643-L5097
PAR 5644-L5098
PAR 5645-L5099
PAR 5646-L5100
PAR 5647-L5101
PAR 6291-L6222
PAR 6292-L5801
PAR 6293-L6219
PAR 5648-L6218
PAR 5649-L5103
PAR 5650-L5104
PAR 5651-L5105
CSF2RA
IL3RA
PAR 5652-L5106
ASMT
ARSF
GPR143
GPR143(ii)
Xq25
SYBL1
SMCY
SRY
DBY
RL
0.80
C1 5q31
C2 16p13
C3 20q11
C4 9q34
C5 13q14
C6 8q24
C7 18q21
C8 13q12
C9 2p22
C10 10p14
PPP2R3B Ex 5
PPP2R3B Ex 4
PPP2R3B Ex 1
LOC159015
SHOX Ex1
SHOX Ex2
SHOX Ex3
SHOX Ex4
SHOX Ex5
SHOX Ex6
SHOX Ex7
SHOX Ex8
PAR 5642-L5096
PAR 5643-L5097
PAR 5644-L5098
PAR 5645-L5099
PAR 5646-L5100
PAR 5647-L5101
PAR 6291-L6222
PAR 6292-L5801
PAR 6293-L6219
PAR 5648-L6218
PAR 5649-L5103
PAR 5650-L5104
PAR 5651-L5105
CSF2RA
IL3RA
PAR 5652-L5106
ASMT
ARSF
GPR143
GPR143(ii)
Xq25
SYBL1
SMCY
SRY
DBY
ML
DEL
Custom MLPA
1.40
1.20
1.00
1.20
1.00
0.80
1.40
1.20
1.00
5651-L5105
5650-L5104
5649-L5103
5648-L6218
6293-L6219
6292-L5801
6291-L6222
5647-L5101
5646-L5100
5645-L5099
5644-L5098
5643-L5097
5642-L5096
*
PPP2R3B exon 4 Custom
2726-L1588 (PPP2R3B exon 5)
PPP2R3B exon 1 Custom
1152-L0709 (SHOX exon 6b)
1151-L0708 (Between exon 6a & 6b)
1150-L0911 (SHOX exon 6a)
1149-L0910 (SHOX exon 5)
1148-L1331 (SHOX exon 4)
1147-L0802 (SHOX exon 3)
1146-L6220 (SHOX exon 2)
1145-L0702 (SHOX exon 1 – non-coding)
1341-L6221 (LOC159015)
Putative SHOX
regulatory region
(Fukami et al. 2006)
1000
900
800
700
DXYS10081
Distance from telomere (kb)
600
DXYS10080
DXYS233
SHOX CA repeat
Direction of transcription
500
400
300
200
DXYS10139
SHOX
PPP2R3B
PLCXD1
DXYS10138
Microarray probes:
2726-L1588
GTPBP6
(PGPL)
RP13-391G2
Not deleted
Deleted
RP13-465B17
DXYS10137
Microsatellite markers
DXYS
MLPA probes
100
LLNOYCO3’M’51D11
LLNOYCO3’M’2E2
FISH probe (approx. location)
LLNOYCO3’M’34F5
LLNOYCO3’M’56G10
Deleted in IC - (present study)
*
100
Telomere
Custom MLPA
Not deleted (Shears et al 2003)
Key
Deleted – (Shears et al.2003)
Deleted – (present study)
Not deleted – (present study)
Gene
SNP Analysis
PPP2R3B
+
+
rs4986484 G/T
rs28430679 C/T
G
G
A
C
G
C
A
G
A
A
G
T
C
G
T
C
C
A
C
C
G
G
A
C
G
C
A
G
A
G
A
C
C
T
C
C
C
G
G
C
SHOX
+
+
rs5991323 G/A
rs4986485 A/G
rs4986486 C/T
rs4131267 G/A
rs6645040 C/T
rs4986487 A/T
rs6645077 G/A
LWD
rs6644996 A/G
rs28715562 A/G
rs28418955 G/A
rs6644997 T/C
HL
rs6645078 C/T
rs28491143 G/T
rs28393142 T/C
GW
rs35933458 C/T
rs35741392 C/G
rs6645016 G/A
rs6645017 G/C
PPP2R3B
+
+
PPP2R3B
+
+
rs4986484 G/T
T
G
G
T
A
T
T
G
A
A
G
T
C
G
T
C
C
G
G
C
rs4986484 G/T
rs28430679 C/T
G
G
A
C
G
C
A
G
A
G
A
C
C
T
C
C
C
A
C
C
rs28430679 C/T
G
G
A
C
G
C
A
G
A
A
G
T
C
G
T
C
C
A
C
C
SHOX
+
+
SHOX
+
G
G
A
C
G
C
A
-
rs5991323 G/A
rs4986485 A/G
rs4986486 C/T
rs4131267 G/A
rs6645040 C/T
rs4986487 A/T
rs6645077 G/A
rs6644996 A/G
rs28715562 A/G
rs28418955 G/A
rs6644997 T/C
rs6645078 C/T
rs28491143 G/T
rs28393142 T/C
rs35933458 C/T
rs35741392 C/G
rs6645016 G/A
rs6645017 G/C
rs5991323 G/A
rs4986485 A/G
rs4986486 C/T
rs4131267 G/A
rs6645040 C/T
rs4986487 A/T
rs6645077 G/A
rs6644996 A/G
rs28715562 A/G
rs28418955 G/A
rs6644997 T/C
rs6645078 C/T
rs28491143 G/T
ML
PL
rs28393142 T/C
rs35933458 C/T
rs35741392 C/G
rs6645016 G/A
rs6645017 G/C
PPP2R3B
+
+
PPP2R3B
+
+
rs4986484 G/T
rs28430679 C/T
T
G
G
T
A
T
T
G
A
A
G
T
C
G
T
C
C
G
G
C
SHOX
+
G
G
A
C
G
C
A
-
rs4986484 G/T
rs28430679 C/T
G
G
A
C
G
C
A
G
A
G
A
C
C
T
C
C
C
A
C
C
SHOX
+
G
G
A
C
G
C
A
-
rs5991323 G/A
rs4986485 A/G
rs4986486 C/T
rs4131267 G/A
rs6645040 C/T
rs4986487 A/T
rs6645077 G/A
rs6644996 A/G
rs28715562 A/G
rs28418955 G/A
rs6644997 T/C
rs6645078 C/T
rs28491143 G/T
rs28393142 T/C
rs35933458 C/T
rs35741392 C/G
rs6645016 G/A
rs6645017 G/C
rs5991323 G/A
rs4986485 A/G
rs4986486 C/T
rs4131267 G/A
rs6645040 C/T
rs4986487 A/T
rs6645077 G/A
rs6644996 A/G
rs28715562 A/G
rs28418955 G/A
rs6644997 T/C
rs6645078 C/T
rs28491143 G/T
rs28393142 T/C
RL
GL
rs35933458 C/T
rs35741392 C/G
rs6645016 G/A
rs6645017 G/C
5651-L5105
5650-L5104
5649-L5103
5648-L6218
6293-L6219
6292-L5801
6291-L6222
5647-L5101
5646-L5100
5645-L5099
5644-L5098
5643-L5097
5642-L5096
*
PPP2R3B exon 4 Custom
2726-L1588 (PPP2R3B exon 5)
PPP2R3B exon 1 Custom
1152-L0709 (SHOX exon 6b)
1151-L0708 (Between exon 6a & 6b)
1150-L0911 (SHOX exon 6a)
1149-L0910 (SHOX exon 5)
1148-L1331 (SHOX exon 4)
1147-L0802 (SHOX exon 3)
1146-L6220 (SHOX exon 2)
1145-L0702 (SHOX exon 1 – non-coding)
1341-L6221 (LOC159015)
Putative SHOX
regulatory region
(Fukami et al. 2006)
1000
900
800
700
600
DXYS10081
Distance from telomere (kb)
500
DXYS10080
DXYS233
DXYS10139
SHOX CA repeat
DXYS10138
Direction of transcription
400
300
200
DXYS10137
445kb – 6 SNPs
SHOX
PPP2R3B
PLCXD1
355kb – 8 SNPs
Microarray probes:
2726-L1588
GTPBP6
(PGPL)
RP13-391G2
Not deleted
Deleted
RP13-465B17
282kb – 7 SNPs
Microsatellite markers
DXYS
MLPA probes
100
LLNOYCO3’M’51D11
LLNOYCO3’M’2E2
FISH probe (approx. location)
LLNOYCO3’M’34F5
LLNOYCO3’M’56G10
Deleted in IC - (present study)
*
100
Telomere
SNP Analysis
Not deleted (Shears et al 2003)
Key
Deleted – (Shears et al.2003)
Deleted – (present study)
Not deleted – (present study)
Gene
5651-L5105
5650-L5104
5649-L5103
5648-L6218
6293-L6219
6292-L5801
6291-L6222
5647-L5101
5646-L5100
5645-L5099
5644-L5098
5643-L5097
5642-L5096
*
PPP2R3B exon 4 Custom
2726-L1588 (PPP2R3B exon 5)
PPP2R3B exon 1 Custom
1152-L0709 (SHOX exon 6b)
1151-L0708 (Between exon 6a & 6b)
1150-L0911 (SHOX exon 6a)
1149-L0910 (SHOX exon 5)
1148-L1331 (SHOX exon 4)
1147-L0802 (SHOX exon 3)
1146-L6220 (SHOX exon 2)
1145-L0702 (SHOX exon 1 – non-coding)
1341-L6221 (LOC159015)
Putative SHOX
regulatory region
(Fukami et al. 2006)
1000
900
800
700
600
DXYS10081
Distance from telomere (kb)
500
DXYS10080
DXYS233
DXYS10139
SHOX CA repeat
DXYS10138
Direction of transcription
400
300
200
DXYS10137
445kb – 6 SNPs
Microarray probes:
2726-L1588
SHOX
PPP2R3B
PLCXD1
355kb – 8 SNPs
CTCF
Binding site
GTPBP6
(PGPL)
RP13-391G2
Not deleted
Deleted
RP13-465B17
282kb – 7 SNPs
Microsatellite markers
DXYS
MLPA probes
100
LLNOYCO3’M’51D11
LLNOYCO3’M’2E2
FISH probe (approx. location)
LLNOYCO3’M’34F5
LLNOYCO3’M’56G10
Deleted in IC - (present study)
*
100
Telomere
CTCF
Not deleted (Shears et al 2003)
Key
Deleted – (Shears et al.2003)
Deleted – (present study)
Not deleted – (present study)
Gene
CTCF
 CTCF (CCCTC - binding factor)
 Transcriptional regulator through




chromatin remodelling
epigenetic modification
control of transcriptional machinery
insulating promoter interaction with enhancers /silencers
 Can bind to a diverse array of DNA sequences using different
combinations of its 11 zinc finger domains
CTCF zinc finger domain
PPP2R3B
More SNP analysis
SNPs @ 282kb
rs7060857 C/G
rs7060861 A/G
rs7060992 C/G
rs7061128 G/T
rs35803036 A/G
rs34424779 G/T
rs7061154 A/G
rs6603263 C/T
rs28536695 C/G
rs5950823 G/T
LWD
rs5950824 C/T
rs5950825 C/G
rs5950826 A/G
HL
+
+
A
G
A
T
A
G
G
G
A
+
+
+
+
+
+
rs5950685 C/T
rs34943375 A/G
rs5950686 C/G
rs5950835 A/G
+
+
+
+
rs7473428 A/G
G
G
G
G
G
G
G
T
SNPs @ 445kb
rs5950825 C/G
G
G
G
G
G
G
G
C
C
T
T
C
rs5950826 A/G
G
+
+
PPP2R3B
G
G
G
G
G
G
G
T
C
T
T
C
rs7060857 C/G
rs5950825 C/G
G
G
G
G
G
G
G
C
C
G
C
C
rs5950826 A/G
G
A
CTCF
+
+
CTCF
rs28421260 G/A
A
G
rs28421260 G/A
A
rs5991174 G/C
G
A
T
A
G
G
G
A
G
G
C
G
A
C
A
G
rs5991174 G/C
G
A
T
A
G
G
G
A
+
+
+
+
+
+
SNPs @ 355kb
+
+
+
+
PPP2R3B
G
G
G
G
G
G
G
T
rs7060857 C/G
rs5950826 A/G
G
CTCF
+
-
rs28536695 C/G
rs5950825 C/G
G
G
G
G
G
G
G
C
C
G
C
C
SNPs @ 282kb
rs7060857 C/G
rs7060861 A/G
rs7060992 C/G
rs7061128 G/T
rs35803036 A/G
rs34424779 G/T
rs7061154 A/G
rs6603263 C/T
rs28536695 C/G
rs5950823 G/T
rs5950824 C/T
rs5950684 G/A
rs5950685 C/T
rs34943375 A/G
rs5950834 G/A
rs5950686 C/G
rs5950835 A/G
rs7473428 A/G
SNPs @ 355kb
SNPs @ 445kb
SHOX
PPP2R3B
SNPs @ 282kb
rs7060857 C/G
rs7060861 A/G
rs7060992 C/G
rs7061128 G/T
rs35803036 A/G
rs34424779 G/T
rs7061154 A/G
rs6603263 C/T
rs28536695 C/G
rs5950823 G/T
rs5950824 C/T
rs28421260 G/A
A
rs5991174 G/C
rs5950835 A/G
G
A
T
A
G
G
G
rs7473428 A/G
A
SNPs @ 355kb
+
+
+
rs5950684 G/A
rs5950685 C/T
rs34943375 A/G
rs5950834 G/A
rs5950686 C/G
SNPs @ 445kb
SHOX
SNPs @ 282kb
rs7060861 A/G
rs7060992 C/G
rs7061128 G/T
rs35803036 A/G
rs34424779 G/T
rs7061154 A/G
rs6603263 C/T
rs28536695 C/G
rs5950823 G/T
rs5950824 C/T
rs5950684 G/A
rs5950685 C/T
ML
PL
rs34943375 A/G
rs5950834 G/A
rs5950686 C/G
rs5950835 A/G
rs7473428 A/G
SNPs @ 445kb
SHOX
+
+
+
+
G
G
G
G
G
G
G
T
rs5950825 C/G
rs5950826 A/G
A
rs7060861 A/G
rs7060992 C/G
rs7061128 G/T
rs35803036 A/G
rs34424779 G/T
rs7061154 A/G
rs6603263 C/T
rs5950823 G/T
rs5950824 C/T
GL
+
+
+
G
G
G
G
G
G
G
T
C
T
T
C
SNPs @ 282kb
RL
+
-
CTCF
+
rs28421260 G/A
G
rs5991174 G/C
rs5950835 A/G
G
G
C
G
A
C
A
rs7473428 A/G
G
SNPs @ 355kb
+
+
+
rs5950684 G/A
rs5950685 C/T
rs34943375 A/G
rs5950834 G/A
rs5950686 C/G
SNPs @ 445kb
SHOX
-
G
G
G
G
G
G
G
T
C
T
C
C
G
A
G
A
T
A
G
G
G
A
rs5950834 G/A
+
+
G
G
G
G
G
G
G
C
C
T
T
C
G
rs28421260 G/A
rs5950684 G/A
PPP2R3B
+
+
CTCF
rs5991174 G/C
GW
+
+
SNPs @ 355kb
SHOX
Deleted – (present study)
Not deleted – (present study)
Gene
DXYS10081
5651-L5105
5650-L5104
5649-L5103
5648-L6218
6293-L6219
6292-L5801
6291-L6222
5647-L5101
5646-L5100
5645-L5099
5644-L5098
5643-L5097
5642-L5096
*
PPP2R3B exon 4 Custom
2726-L1588 (PPP2R3B exon 5)
PPP2R3B exon 1 Custom
1152-L0709 (SHOX exon 6b)
1151-L0708 (Between exon 6a & 6b)
1150-L0911 (SHOX exon 6a)
1149-L0910 (SHOX exon 5)
1148-L1331 (SHOX exon 4)
1147-L0802 (SHOX exon 3)
1146-L6220 (SHOX exon 2)
1145-L0702 (SHOX exon 1 – non-coding)
1341-L6221 (LOC159015)
Putative SHOX
regulatory region
(Fukami et al. 2006)
1000
900
800
700
600
500
DXYS10080
DXYS233
DXYS10139
SHOX CA repeat
DXYS10138
RP13-76L22
RP13-167H21
RP13-391G2
RP13-465B17
DXYS10137
445kb – 6 SNPs
355kb – 8 SNPs
Distance from telomere (kb)
400
300
200
300kb – 9 SNPs
Microarray probes:
2726-L1588
SHOX
PPP2R3B
PLCXD1
309kb – 9 SNPs
CTCF
Binding site
GTPBP6
(PGPL)
RP13-391G2
305kb – 5 SNPs
Microsatellite markers
DXYS
MLPA probes
100
Not deleted
Deleted
RP13-465B17
282kb – 7 SNPs
Direction of transcription
LLNOYCO3’M’51D11
LLNOYCO3’M’2E2
FISH probe (approx. location)
LLNOYCO3’M’34F5
LLNOYCO3’M’56G10
Deleted in IC - (present study)
*
100
Telomere
Microarray analysis
Not deleted (Shears et al 2003)
Key
Deleted – (Shears et al.2003)
Conclusions
 Deletion of this CTCF binding site could affect
regulation of its target gene.
 Could the target be PPP2R3B?
Deregulation of PPP2R3B could result in
deregulation of the cell cycle
Another B subunit of PP2A is present at 4p16.1, a
region linked to HL in a study by Goldin et al.
(2006).
 The CTCF binding site could regulate another,
more distant gene.
 Further studies required.
Map of PAR1
Not deleted (Shears et al 2003)
Deleted – (Shears et al.2003)
Not deleted – (present study)
Deleted – (present study)
END OF
PAR1
Gene
Deleted in IC - (present study)
*
LLNOYCO3’M’56G10
LLNOYCO3’M’34F5
LLNOYCO3’M’51D11
Direction of transcription
RP13-465B17
RP13-391G2
Microarray probes:
CXYorf2
Not deleted
Deleted
GTPBP6
(PGPL)
SLC25A6
(ANT3)
PLCXD1
Telomere
DXYS228
2726-L1588
MLPA probes
DXYS234
Distance from telomere (kb)
100
DXS6814
DXYS
Microsatellite markers
DXYS233
SHOX CA repeat
LLNOYCO3’M’2E2
FISH probe (approx. location)
100
CRLF2
SHOX
PPP2R3B
200
300
400
500
600
700
800
900
CSF2RA
1300
1000
IL3RA
1400
ZBED1
ASMTL
1500
CXYorf3
(XE7)
ASMT
P2RYB
1600
2500 1700
CD99 (MIC2)
2600 1800
XG
2700
Conclusions
 Deletion of this CTCF binding site could affect
regulation of its target gene.
 Could the target be PPP2R3B?
Deregulation of PPP2R3B could result in
deregulation of the cell cycle
Another B subunit of PP2A is present at 4p16.1, a
region linked to HL in a study by Goldin et al.
(2006).
 The CTCF binding site could regulate another,
more distant gene.
 Further studies required.
Acknowledgements
Thanks to the following people for their help:
 David Gokhale
 Vicky Stinton
 G Malcolm Taylor
 Ciaron McAnulty
 Frances White
 Una Maye
 Julie Sibbring
 Emma McCarthy
 Roger Mountford
 Andrew Wallace
 Simon Thomas
 Kevin Baker
 Gareth Evans
 John Radford
 All at Liverpool Molecular Genetics Laboratory for their help, advice, interest
and patience.
References
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