1
Centre for Molecular Medicine Norway, P.O. Box 1137, N-0318 University of Oslo, Norway www.ncmm.uio.no Characterization of the role of CTCF in Estrogen Receptor dependent gene regulation. Elisa Fiorito 1,* , Yogita Sharma 1,* , Siv Gilfillan 1 , Baoyan Bai 1 , Alfonso Urbanucci 2 , Ian Mills 2 , Antoni Hurtado 1,3 1 Breast Cancer Research Group, Center for Molecular Medicine, University of Oslo 2 Prostate Cancer Research Group, Center for Molecular Medicine, University of Oslo 3 Department of Genetics, Institute for Cancer Research, University of Oslo * These authors contributed equally to this work. 5 2 1 -1 0 1 2 3 4 -10000 -9200 -8400 -7600 -6800 -6000 -5200 -4400 -3600 -2800 -2000 -1200 -400 600 1400 2200 3000 3800 4600 5400 6200 7000 7800 8600 9400 Binding intensity (average) CTCF sites lost (0h Estrogen unique) CTCF 0h CTCF 3h -1 0 1 2 3 4 5 -10000 -9200 -8400 -7600 -6800 -6000 -5200 -4400 -3600 -2800 -2000 -1200 -400 600 1400 2200 3000 3800 4600 5400 6200 7000 7800 8600 9400 Binding intensity (average) CTCF sites shared -1 0 1 2 3 4 5 6 -10000 -9200 -8400 -7600 -6800 -6000 -5200 -4400 -3600 -2800 -2000 -1200 -400 600 1400 2200 3000 3800 4600 5400 6200 7000 7800 8600 9400 Binding intensity (average) CTCF sites gained (3h Estrogen unique) Estrogen stimulation redistributes CTCF binding at genome wide level CTCF ChIP-seq in MCF7 cells (first replicate): Estrogen 0h Estrogen 3h CTCF sites lost (1356 peaks) CTCF sites not affected (1256 peaks) CTCF sites gained (5575 peaks) -10kb +10kb ! ! ! ! ! !! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! !! ! ! ! ! ! ! ! ! ! ! ! ! ! !! ! ! ! ! ! ! ! ! ! !! ! ! ! ! ! ! ! ! ! ! ! ! ! ! !! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! !! ! ! ! 0 50 100 150 200 250 50 100 150 200 250 300 GROSeq RPKM (0min) GROSeq RPKM (160min) ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! top100Up top100Down GROseq Reads 0 min GROseq Reads 160 min B1 CAMTA1 GROseq Reads 0 min GROseq Reads 160 min H3K9Ac_U PANK4 4 0.0 0.5 1.0 1.5 2.0 0.0 0.2 0.4 0.6 0.8 1.0 Human : Mouse Conservation (100 bp window) Fraction ●● ●● ●● ●● ●●●●● ●●●●●● ●● ●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●● ●●● ●● ●● ●●● ●● CTCF 0 Hour Random Set 0.0 0.5 1.0 1.5 2.0 2.5 0.0 0.2 0.4 0.6 0.8 1.0 Human : Chicken Conservation (100 bp window) Fraction ●● ●● ●● ●●● ●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●● ●●● ●●●●●● CTCF 0 Hour Random Set 0 1 2 3 4 0.0 0.2 0.4 0.6 0.8 1.0 Human : Mouse Conservation (100 bp window) Fraction ●● ●● ●● ●● ●● ●●● ●●●● ●●●●● ●● ●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●● ●● ●● ●●●●●● ●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● CTCF 3 Hour Random Set 0 1 2 3 4 5 6 0.0 0.2 0.4 0.6 0.8 1.0 Human : Chicken Conservation (100 bp window) Fraction ●● ●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●● ●●●●●●●●●● ●●●● CTCF 3 Hour Random Set 3 GENE 1 GENE 2 Promoter Intergenic Gene body -0,5 0 0,5 1 1,5 2 2,5 3 -10000 -8800 -7600 -6400 -5200 -4000 -2800 -1600 -400 1000 2200 3400 4600 5800 7000 8200 9400 Promoter regions CTCF distribution around CTCF sites 0h overlapping with GRO-seq regions at 0 min -0,5 0 0,5 1 1,5 2 2,5 3 -10000 -8600 -7200 -5800 -4400 -3000 -1600 -200 1400 2800 4200 5600 7000 8400 9800 Non-promoter regions CTCF 0h CTCF 3h CTCF distribution around CTCF sites 3h overlapping with GRO-seq regions at 160 min -0,5 0 0,5 1 1,5 2 2,5 3 3,5 4 4,5 -10000 -8600 -7200 -5800 -4400 -3000 -1600 -200 1400 2800 4200 5600 7000 8400 9800 Non-promoter regions -0,5 0 0,5 1 1,5 2 2,5 3 3,5 4 -10000 -8600 -7200 -5800 -4400 -3000 -1600 -200 1400 2800 4200 5600 7000 8400 9800 Promoter regions Promoter promoter GeneBody Genebody InterGenic Intergenic 0 5 10 15 20 25 CTCF Binding Sites CTCF 0 Hour CTCF 3 Hour Heatmap CTCF ChIP-seq -0,5 0 0,5 1 1,5 2 2,5 -10000 -8800 -7600 -6400 -5200 -4000 -2800 -1600 -400 1000 2200 3400 4600 5800 7000 8200 9400 Non-promoter regions Lamin B 0h Lamin B 3h -0,5 0 0,5 1 1,5 2 2,5 -10000 -8800 -7600 -6400 -5200 -4000 -2800 -1600 -400 1000 2200 3400 4600 5800 7000 8200 9400 Promoter regions -0,5 0 0,5 1 1,5 2 2,5 3 3,5 4 -10000 -8800 -7600 -6400 -5200 -4000 -2800 -1600 -400 1000 2200 3400 4600 5800 7000 8200 9400 Non-promoter regions -0,5 0 0,5 1 1,5 2 2,5 3 3,5 4 -10000 -8800 -7600 -6400 -5200 -4000 -2800 -1600 -400 1000 2200 3400 4600 5800 7000 8200 9400 Promoter regions Lamin B distribution at CTCF sites 0h overlapping with GRO-seq regions at 0 min Lamin B distribution at CTCF sites 3h overlapping with GRO-seq regions at 160 min GRO-seq expression analysis GRO-seq UP-regulated and down-regulated genes containing CTCF binding sites (at 0h and 3h of estrogen treatment) GRO-seq enrichment along gene body in UP and DOWN regulated gene GRO-seq expression validates the differences in enrichment of CTCF binding upon estrogen treatment Genomic distribution of CTCF binding sites 9% CTCF sites 0h 8.5% CTCF sites 3h 41% CTCF sites 0h 38% CTCF sites 3h 50% CTCF sites 0h 53.5% CTCF sites 3h Box-plots of GRO-seq overlapping CTCF binding sites in different genomic locations More than 50% of CTCF binding sites are overlapping in intergenic regions, suggesting a possible role for CTCF as repressor or enhancer CTCF binding sites in intergenic regions correlate with GRO-seq expression Conservation analysis of CTCF binding sites in intergenic regions CTCF binding sites are 90% conserved between human, mouse and chicken in 17% of cases at 0 hours and 26.5% of cases at 3 hours Estrogen stimulation affects Lamin B distribution around CTCF sites overlapping with GRO-seq regions After estrogen treatment, lamin B binding intensity is reduced at promoter and non promoter regions o These data suggest an inverse correlation between CTCF and Lamin B binding. CONCLUSIONS AND FUTURE PERSPECTIVES We observed a redistribution of CTCF chromatin interactions upon estrogen stimulation, suggesting a role for CTCF in estrogen dependent gene regulation. The combination of GRO-seq and CTCF binding analysis suggested that CTCF is regulating estrogen dependent transcription, possibly via the formation of different chromatin loops. The conservation and GRO-seq analysis detect the possibility of presence of active enhancers and repressors in CTCF mediated transcription regulation. Further, Lamin B and CTCF distribution suggest a role for nuclear remodeling in estrogen dependent gene regulation. Future analysis will prove the role of CTCF in chromatin loops involving enhancers and repressors. Further experiments (e.g. 3C) will validate our findings and shed light on the function of CTCF in the whole scenario.

Characterization of the role of CTCF in Estrogen Receptor gene regulation

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Page 1: Characterization of the role of CTCF in Estrogen Receptor gene regulation

Centre for Molecular Medicine Norway, P.O. Box 1137, N-0318 University of Oslo, Norway www.ncmm.uio.no

Characterization of the role of CTCF in Estrogen Receptor dependent gene regulation. Elisa Fiorito1,*, Yogita Sharma1,*, Siv Gilfillan1, Baoyan Bai1, Alfonso Urbanucci2, Ian Mills2, Antoni Hurtado1,3

1 Breast Cancer Research Group, Center for Molecular Medicine, University of Oslo 2 Prostate Cancer Research Group, Center for Molecular Medicine, University of Oslo 3Department of Genetics, Institute for Cancer Research, University of Oslo

* These authors contributed equally to this work.

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CTCF sites gained (3h Estrogen unique)

Estrogen stimulation redistributes CTCF binding at genome wide level CTCF ChIP-seq in MCF7 cells (first replicate):

Estrogen 0h Estrogen 3h

CTCF sites lost (1356 peaks)

CTCF sites not affected

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CTCF sites gained (5575 peaks)

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top100Uptop100Down

Scalechr2:

i.1516i.1671i.987i.740i.678i.594i.453

i.6863i.4737i.5088i.5079i.4619i.3951i.3833i.3641i.3397i.3195i.5610i.5408i.5393i.5314i.5276i.3582i.3330i.910i.752

i.3825i.6453i.4547i.4003i.1321i.6460i.1136i.5398i.4512i.5155i.5355

50 kb11550000 11600000 11650000

GROSEQ_0m+

GROSEQ_0m-

GROSEQ_10m+

GROSEQ_10m-

GROSEQ_25m+

GROSEQ_25m-

GROSEQ_40m+

GROSEQ_40m-

POLII_U

POLII_E

ER_U

ER_E

FOXA1_U

FOXA1_E

AP2GAMMA_U

AP2GAMMA_E

p300_U

p300_E

CBP_U

CBP_E

SRC1_U

SRC1_E

SRC2_U

SRC2_E

SRC3_U

SRC3_E

H3K4me1_U

H3K4me1_E

H3K4me2_U

H3K4me2_E

H3K4me3_U

H3K4me3_E

H3K27me3_U

H3K27me3_E

H3K9Ac_U

H3K9Ac_E

H3K14Ac_U

H3K14Ac_E

DNase1_U

DNase1_E

FAIRE_U

FAIRE_E

ChIAPET

UCSC Genes Based on RefSeq, UniProt, GenBank, CCDS and Comparative GenomicsE2F6E2F6E2F6E2F6E2F6E2F6

GREB1GREB1

GREB1GREB1

GREB1

GROSEQ_0m+

100 _

0 _

GROSEQ_0m-

0 _

-100 _

GROSEQ_10m+

100 _

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GROSEQ_10m-

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0 _

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0 _

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GROSEQ_40m+

100 _

0 _

GROSEQ_40m-

0 _

-100 _

POLII_U

40 _

1 _

POLII_E

40 _

1 _

ER_U

500 _

1 _

ER_E

500 _

1 _

FOXA1_U

60 _

1 _

FOXA1_E

60 _

1 _

AP2GAMMA_U

70 _

1 _

AP2GAMMA_E

70 _

1 _

p300_U

30 _

1 _

p300_E

30 _

1 _

CBP_U

600 _

1 _

CBP_E

600 _

1 _

SRC1_U

50 _

1 _

SRC1_E

50 _

1 _

SRC2_U

400 _

1 _

SRC2_E

400 _

1 _

SRC3_U

400 _

1 _

SRC3_E

400 _

1 _

H3K4me1_U

25 _

1 _

H3K4me1_E

25 _

1 _

H3K4me2_U

50 _

1 _

H3K4me2_E

50 _

1 _

H3K4me3_U

60 _

1 _

H3K4me3_E

60 _

1 _

H3K27me3_U

50 _

1 _

H3K27me3_E

50 _

1 _

H3K9Ac_U

25 _

1 _

H3K9Ac_E

25 _

1 _

H3K14Ac_U

20 _

1 _

H3K14Ac_E

20 _

1 _

DNase1_U

300 _

1 _

DNase1_E

300 _

1 _

FAIRE_U

10 _

1 _

FAIRE_E

10 _

1 _

Scalechr2:

i.1516i.1671i.987i.740i.678i.594i.453

i.6863i.4737i.5088i.5079i.4619i.3951i.3833i.3641i.3397i.3195i.5610i.5408i.5393i.5314i.5276i.3582i.3330i.910i.752

i.3825i.6453i.4547i.4003i.1321i.6460i.1136i.5398i.4512i.5155i.5355

50 kb11550000 11600000 11650000

GROSEQ_0m+

GROSEQ_0m-

GROSEQ_10m+

GROSEQ_10m-

GROSEQ_25m+

GROSEQ_25m-

GROSEQ_40m+

GROSEQ_40m-

POLII_U

POLII_E

ER_U

ER_E

FOXA1_U

FOXA1_E

AP2GAMMA_U

AP2GAMMA_E

p300_U

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CBP_U

CBP_E

SRC1_U

SRC1_E

SRC2_U

SRC2_E

SRC3_U

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H3K4me1_U

H3K4me1_E

H3K4me2_U

H3K4me2_E

H3K4me3_U

H3K4me3_E

H3K27me3_U

H3K27me3_E

H3K9Ac_U

H3K9Ac_E

H3K14Ac_U

H3K14Ac_E

DNase1_U

DNase1_E

FAIRE_U

FAIRE_E

ChIAPET

UCSC Genes Based on RefSeq, UniProt, GenBank, CCDS and Comparative GenomicsE2F6E2F6E2F6E2F6E2F6E2F6

GREB1GREB1

GREB1GREB1

GREB1

GROSEQ_0m+

100 _

0 _

GROSEQ_0m-

0 _

-100 _

GROSEQ_10m+

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POLII_U

40 _

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POLII_E

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ER_U

500 _

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ER_E

500 _

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FOXA1_U

60 _

1 _

FOXA1_E

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1 _

AP2GAMMA_U

70 _

1 _

AP2GAMMA_E

70 _

1 _

p300_U

30 _

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p300_E

30 _

1 _

CBP_U

600 _

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CBP_E

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1 _

SRC1_U

50 _

1 _

SRC1_E

50 _

1 _

SRC2_U

400 _

1 _

SRC2_E

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1 _

SRC3_U

400 _

1 _

SRC3_E

400 _

1 _

H3K4me1_U

25 _

1 _

H3K4me1_E

25 _

1 _

H3K4me2_U

50 _

1 _

H3K4me2_E

50 _

1 _

H3K4me3_U

60 _

1 _

H3K4me3_E

60 _

1 _

H3K27me3_U

50 _

1 _

H3K27me3_E

50 _

1 _

H3K9Ac_U

25 _

1 _

H3K9Ac_E

25 _

1 _

H3K14Ac_U

20 _

1 _

H3K14Ac_E

20 _

1 _

DNase1_U

300 _

1 _

DNase1_E

300 _

1 _

FAIRE_U

10 _

1 _

FAIRE_E

10 _

1 _

GROseq'Reads'0'min'

GROseq'Reads'160'min'

Scalechr2:

i.1516i.1671i.987i.740i.678i.594i.453

i.6863i.4737i.5088i.5079i.4619i.3951i.3833i.3641i.3397i.3195i.5610i.5408i.5393i.5314i.5276i.3582i.3330i.910i.752

i.3825i.6453i.4547i.4003i.1321i.6460i.1136i.5398i.4512i.5155i.5355

50 kb11550000 11600000 11650000

GROSEQ_0m+

GROSEQ_0m-

GROSEQ_10m+

GROSEQ_10m-

GROSEQ_25m+

GROSEQ_25m-

GROSEQ_40m+

GROSEQ_40m-

POLII_U

POLII_E

ER_U

ER_E

FOXA1_U

FOXA1_E

AP2GAMMA_U

AP2GAMMA_E

p300_U

p300_E

CBP_U

CBP_E

SRC1_U

SRC1_E

SRC2_U

SRC2_E

SRC3_U

SRC3_E

H3K4me1_U

H3K4me1_E

H3K4me2_U

H3K4me2_E

H3K4me3_U

H3K4me3_E

H3K27me3_U

H3K27me3_E

H3K9Ac_U

H3K9Ac_E

H3K14Ac_U

H3K14Ac_E

DNase1_U

DNase1_E

FAIRE_U

FAIRE_E

ChIAPET

UCSC Genes Based on RefSeq, UniProt, GenBank, CCDS and Comparative GenomicsE2F6E2F6E2F6E2F6E2F6E2F6

GREB1GREB1

GREB1GREB1

GREB1

GROSEQ_0m+

100 _

0 _

GROSEQ_0m-

0 _

-100 _

GROSEQ_10m+

100 _

0 _

GROSEQ_10m-

0 _

-100 _

GROSEQ_25m+

100 _

0 _

GROSEQ_25m-

0 _

-100 _

GROSEQ_40m+

100 _

0 _

GROSEQ_40m-

0 _

-100 _

POLII_U

40 _

1 _

POLII_E

40 _

1 _

ER_U

500 _

1 _

ER_E

500 _

1 _

FOXA1_U

60 _

1 _

FOXA1_E

60 _

1 _

AP2GAMMA_U

70 _

1 _

AP2GAMMA_E

70 _

1 _

p300_U

30 _

1 _

p300_E

30 _

1 _

CBP_U

600 _

1 _

CBP_E

600 _

1 _

SRC1_U

50 _

1 _

SRC1_E

50 _

1 _

SRC2_U

400 _

1 _

SRC2_E

400 _

1 _

SRC3_U

400 _

1 _

SRC3_E

400 _

1 _

H3K4me1_U

25 _

1 _

H3K4me1_E

25 _

1 _

H3K4me2_U

50 _

1 _

H3K4me2_E

50 _

1 _

H3K4me3_U

60 _

1 _

H3K4me3_E

60 _

1 _

H3K27me3_U

50 _

1 _

H3K27me3_E

50 _

1 _

H3K9Ac_U

25 _

1 _

H3K9Ac_E

25 _

1 _

H3K14Ac_U

20 _

1 _

H3K14Ac_E

20 _

1 _

DNase1_U

300 _

1 _

DNase1_E

300 _

1 _

FAIRE_U

10 _

1 _

FAIRE_E

10 _

1 _

CAMTA1&

GROseq'Reads'0'min'

GROseq'Reads'160'min'

Scalechr11:

i.1461i.1643i.1611

i.41i.6941i.5834i.1681i.660

i.3472i.4945i.5086i.5522i.6256i.5275

50 kb72570000 72580000 72590000 72600000 72610000 72620000 72630000 72640000 72650000 72660000 72670000

GROSEQ_0m+

GROSEQ_0m-

GROSEQ_10m+

GROSEQ_10m-

GROSEQ_25m+

GROSEQ_25m-

GROSEQ_40m+

GROSEQ_40m-

POLII_U

POLII_E

ER_U

ER_E

FOXA1_U

FOXA1_E

AP2GAMMA_U

AP2GAMMA_E

p300_U

p300_E

CBP_U

CBP_E

SRC1_U

SRC1_E

SRC2_U

SRC2_E

SRC3_U

SRC3_E

H3K4me1_U

H3K4me1_E

H3K4me2_U

H3K4me2_E

H3K4me3_U

H3K4me3_E

H3K27me3_U

H3K27me3_E

H3K9Ac_U

H3K9Ac_E

H3K14Ac_U

H3K14Ac_E

DNase1_U

DNase1_E

FAIRE_U

FAIRE_E

ChIAPET

UCSC Genes Based on RefSeq, UniProt, GenBank, CCDS and Comparative GenomicsP2RY2P2RY2P2RY2

P2RY2

P2RY6P2RY6P2RY6P2RY6

P2RY6P2RY6P2RY6

GROSEQ_0m+

100 _

0 _

GROSEQ_0m-

0 _

-100 _

GROSEQ_10m+

100 _

0 _

GROSEQ_10m-

0 _

-100 _

GROSEQ_25m+

100 _

0 _

GROSEQ_25m-

0 _

-100 _

GROSEQ_40m+

100 _

0 _

GROSEQ_40m-

0 _

-100 _

POLII_U

30 _

1 _

POLII_E

30 _

1 _

ER_U

50 _

1 _

ER_E

50 _

1 _

FOXA1_U

30 _

1 _

FOXA1_E

30 _

1 _

AP2GAMMA_U

70 _

1 _

AP2GAMMA_E

70 _

1 _

p300_U

15 _

1 _

p300_E

15 _

1 _

CBP_U

150 _

1 _

CBP_E

150 _

1 _

SRC1_U

25 _

1 _

SRC1_E

25 _

1 _

SRC2_U

150 _

1 _

SRC2_E

150 _

1 _

SRC3_U

120 _

1 _

SRC3_E

120 _

1 _

H3K4me1_U

25 _

1 _

H3K4me1_E

25 _

1 _

H3K4me2_U

25 _

1 _

H3K4me2_E

25 _

1 _

H3K4me3_U

60 _

1 _

H3K4me3_E

60 _

1 _

H3K27me3_U

30 _

1 _

H3K27me3_E

30 _

1 _

H3K9Ac_U

15 _

1 _

H3K9Ac_E

15 _

1 _

H3K14Ac_U

20 _

1 _

H3K14Ac_E

20 _

1 _

DNase1_U

150 _

1 _

DNase1_E

150 _

1 _

FAIRE_U

10 _

1 _

FAIRE_E

10 _

1 _

Scalechr11:

i.1461i.1643i.1611

i.41i.6941i.5834i.1681

i.660i.3472i.4945i.5086i.5522i.6256i.5275

50 kb72570000 72580000 72590000 72600000 72610000 72620000 72630000 72640000 72650000 72660000 72670000

GROSEQ_0m+

GROSEQ_0m-

GROSEQ_10m+

GROSEQ_10m-

GROSEQ_25m+

GROSEQ_25m-

GROSEQ_40m+

GROSEQ_40m-

POLII_U

POLII_E

ER_U

ER_E

FOXA1_U

FOXA1_E

AP2GAMMA_U

AP2GAMMA_E

p300_U

p300_E

CBP_U

CBP_E

SRC1_U

SRC1_E

SRC2_U

SRC2_E

SRC3_U

SRC3_E

H3K4me1_U

H3K4me1_E

H3K4me2_U

H3K4me2_E

H3K4me3_U

H3K4me3_E

H3K27me3_U

H3K27me3_E

H3K9Ac_U

H3K9Ac_E

H3K14Ac_U

H3K14Ac_E

DNase1_U

DNase1_E

FAIRE_U

FAIRE_E

ChIAPET

UCSC Genes Based on RefSeq, UniProt, GenBank, CCDS and Comparative GenomicsP2RY2P2RY2P2RY2

P2RY2

P2RY6P2RY6P2RY6P2RY6

P2RY6P2RY6P2RY6

GROSEQ_0m+

100 _

0 _

GROSEQ_0m-

0 _

-100 _

GROSEQ_10m+

100 _

0 _

GROSEQ_10m-

0 _

-100 _

GROSEQ_25m+

100 _

0 _

GROSEQ_25m-

0 _

-100 _

GROSEQ_40m+

100 _

0 _

GROSEQ_40m-

0 _

-100 _

POLII_U

30 _

1 _

POLII_E

30 _

1 _

ER_U

50 _

1 _

ER_E

50 _

1 _

FOXA1_U

30 _

1 _

FOXA1_E

30 _

1 _

AP2GAMMA_U

70 _

1 _

AP2GAMMA_E

70 _

1 _

p300_U

15 _

1 _

p300_E

15 _

1 _

CBP_U

150 _

1 _

CBP_E

150 _

1 _

SRC1_U

25 _

1 _

SRC1_E

25 _

1 _

SRC2_U

150 _

1 _

SRC2_E

150 _

1 _

SRC3_U

120 _

1 _

SRC3_E

120 _

1 _

H3K4me1_U

25 _

1 _

H3K4me1_E

25 _

1 _

H3K4me2_U

25 _

1 _

H3K4me2_E

25 _

1 _

H3K4me3_U

60 _

1 _

H3K4me3_E

60 _

1 _

H3K27me3_U

30 _

1 _

H3K27me3_E

30 _

1 _

H3K9Ac_U

15 _

1 _

H3K9Ac_E

15 _

1 _

H3K14Ac_U

20 _

1 _

H3K14Ac_E

20 _

1 _

DNase1_U

150 _

1 _

DNase1_E

150 _

1 _

FAIRE_U

10 _

1 _

FAIRE_E

10 _

1 _

Scalechr11:

i.1461i.1643i.1611

i.41i.6941i.5834i.1681i.660

i.3472i.4945i.5086i.5522i.6256i.5275

50 kb72570000 72580000 72590000 72600000 72610000 72620000 72630000 72640000 72650000 72660000 72670000

GROSEQ_0m+

GROSEQ_0m-

GROSEQ_10m+

GROSEQ_10m-

GROSEQ_25m+

GROSEQ_25m-

GROSEQ_40m+

GROSEQ_40m-

POLII_U

POLII_E

ER_U

ER_E

FOXA1_U

FOXA1_E

AP2GAMMA_U

AP2GAMMA_E

p300_U

p300_E

CBP_U

CBP_E

SRC1_U

SRC1_E

SRC2_U

SRC2_E

SRC3_U

SRC3_E

H3K4me1_U

H3K4me1_E

H3K4me2_U

H3K4me2_E

H3K4me3_U

H3K4me3_E

H3K27me3_U

H3K27me3_E

H3K9Ac_U

H3K9Ac_E

H3K14Ac_U

H3K14Ac_E

DNase1_U

DNase1_E

FAIRE_U

FAIRE_E

ChIAPET

UCSC Genes Based on RefSeq, UniProt, GenBank, CCDS and Comparative GenomicsP2RY2P2RY2P2RY2

P2RY2

P2RY6P2RY6P2RY6P2RY6

P2RY6P2RY6P2RY6

GROSEQ_0m+

100 _

0 _

GROSEQ_0m-

0 _

-100 _

GROSEQ_10m+

100 _

0 _

GROSEQ_10m-

0 _

-100 _

GROSEQ_25m+

100 _

0 _

GROSEQ_25m-

0 _

-100 _

GROSEQ_40m+

100 _

0 _

GROSEQ_40m-

0 _

-100 _

POLII_U

30 _

1 _

POLII_E

30 _

1 _

ER_U

50 _

1 _

ER_E

50 _

1 _

FOXA1_U

30 _

1 _

FOXA1_E

30 _

1 _

AP2GAMMA_U

70 _

1 _

AP2GAMMA_E

70 _

1 _

p300_U

15 _

1 _

p300_E

15 _

1 _

CBP_U

150 _

1 _

CBP_E

150 _

1 _

SRC1_U

25 _

1 _

SRC1_E

25 _

1 _

SRC2_U

150 _

1 _

SRC2_E

150 _

1 _

SRC3_U

120 _

1 _

SRC3_E

120 _

1 _

H3K4me1_U

25 _

1 _

H3K4me1_E

25 _

1 _

H3K4me2_U

25 _

1 _

H3K4me2_E

25 _

1 _

H3K4me3_U

60 _

1 _

H3K4me3_E

60 _

1 _

H3K27me3_U

30 _

1 _

H3K27me3_E

30 _

1 _

H3K9Ac_U

15 _

1 _

H3K9Ac_E

15 _

1 _

H3K14Ac_U

20 _

1 _

H3K14Ac_E

20 _

1 _

DNase1_U

150 _

1 _

DNase1_E

150 _

1 _

FAIRE_U

10 _

1 _

FAIRE_E

10 _

1 _

PANK4&

4

0.0 0.5 1.0 1.5 2.0

0.0

0.2

0.4

0.6

0.8

1.0

Human : Mouse

Conservation (100 bp window)

Frac

tion

●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

●●●●●●●●●●●●●●●●●●●●●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

●●●●●●●●●●●●●●●●●●●●●●●

●●

●●●●●●●●●

CTCF 0 HourRandom Set

0.0 0.5 1.0 1.5 2.0 2.5

0.0

0.2

0.4

0.6

0.8

1.0

Human : Chicken

Conservation (100 bp window)

Frac

tion

●●

●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●

●●

●●●●●●●●●●

CTCF 0 HourRandom Set

0 1 2 3 4

0.0

0.2

0.4

0.6

0.8

1.0

Human : Mouse

Conservation (100 bp window)

Frac

tion

●●

●●

●●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

●●

●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

CTCF 3 HourRandom Set

0 1 2 3 4 5 6

0.0

0.2

0.4

0.6

0.8

1.0

Human : Chicken

Conservation (100 bp window)

Frac

tion

●●

●●●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

●●

●●●●●●●●●●●●●●●

CTCF 3 HourRandom Set

0.0 0.5 1.0 1.5 2.0

0.0

0.2

0.4

0.6

0.8

1.0

Human : Mouse

Conservation (100 bp window)

Frac

tion

●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

●●●●●●●●●●●●●●●●●●●●●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

●●●●●●●●●●●●●●●●●●●●●●●

●●

●●●●●●●●●

CTCF 0 HourRandom Set

0.0 0.5 1.0 1.5 2.0 2.5

0.0

0.2

0.4

0.6

0.8

1.0

Human : Chicken

Conservation (100 bp window)

Frac

tion

●●

●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●

●●

●●●●●●●●●●

CTCF 0 HourRandom Set

0 1 2 3 4

0.0

0.2

0.4

0.6

0.8

1.0

Human : Mouse

Conservation (100 bp window)

Frac

tion

●●

●●

●●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

●●

●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

CTCF 3 HourRandom Set

0 1 2 3 4 5 6

0.0

0.2

0.4

0.6

0.8

1.0

Human : Chicken

Conservation (100 bp window)

Frac

tion

●●

●●●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●

●●

●●●●●●●●●●●●●●●

CTCF 3 HourRandom Set

3

GENE 1 GENE 2

Promoter Intergenic Gene body

-0,5 0

0,5 1

1,5 2

2,5 3

-100

00

-880

0 -7

600

-640

0 -5

200

-400

0 -2

800

-160

0 -4

00

1000

22

00

3400

46

00

5800

70

00

8200

94

00

Promoter regions

CTCF distribution around CTCF sites 0h overlapping with GRO-seq regions at 0 min

-0,5 0

0,5 1

1,5 2

2,5 3

-100

00

-860

0 -7

200

-580

0 -4

400

-300

0 -1

600

-200

14

00

2800

42

00

5600

70

00

8400

98

00

Non-promoter regions

CTCF 0h

CTCF 3h

CTCF distribution around CTCF sites 3h overlapping with GRO-seq regions at 160 min

-0,5 0

0,5 1

1,5 2

2,5 3

3,5 4

4,5 -1

0000

-8

600

-720

0 -5

800

-440

0 -3

000

-160

0 -2

00

1400

28

00

4200

56

00

7000

84

00

9800

Non-promoter regions

-0,5 0

0,5 1

1,5 2

2,5 3

3,5 4

-100

00

-860

0 -7

200

-580

0 -4

400

-300

0 -1

600

-200

14

00

2800

42

00

5600

70

00

8400

98

00

Promoter regions

●●

Prom

oter

prom

oter

Gen

eBod

y

Gen

ebod

y

Inte

rGen

ic

Inte

rgen

ic

0

5

10

15

20

25

CTC

F Bi

ndin

g Si

tes

CTCF 0 HourCTCF 3 Hour

Heatmap CTCF ChIP-seq

-0,5

0

0,5

1

1,5

2

2,5

-100

00

-880

0 -7

600

-640

0 -5

200

-400

0 -2

800

-160

0 -4

00

1000

22

00

3400

46

00

5800

70

00

8200

94

00

Non-promoter regions

Lamin B 0h

Lamin B 3h

-0,5 0

0,5 1

1,5 2

2,5

-100

00

-880

0 -7

600

-640

0 -5

200

-400

0 -2

800

-160

0 -4

00

1000

22

00

3400

46

00

5800

70

00

8200

94

00

Promoter regions

-0,5 0

0,5 1

1,5 2

2,5 3

3,5 4

-100

00

-880

0 -7

600

-640

0 -5

200

-400

0 -2

800

-160

0 -4

00

1000

22

00

3400

46

00

5800

70

00

8200

94

00

Non-promoter regions

-0,5 0

0,5 1

1,5 2

2,5 3

3,5 4

-100

00

-880

0 -7

600

-640

0 -5

200

-400

0 -2

800

-160

0 -4

00

1000

22

00

3400

46

00

5800

70

00

8200

94

00

Promoter regions

Lamin B distribution at CTCF sites 0h overlapping with GRO-seq regions at 0 min

Lamin B distribution at CTCF sites 3h overlapping with GRO-seq regions at 160 min

GRO-seq expression analysis

GRO-seq UP-regulated and down-regulated

genes containing CTCF binding sites (at 0h and

3h of estrogen treatment)

GRO-seq enrichment along gene body in UP and DOWN regulated gene

•  GRO-seq expression validates the differences in enrichment of CTCF binding upon estrogen treatment

Genomic distribution of CTCF binding sites

9% CTCF sites 0h 8.5% CTCF sites 3h

41% CTCF sites 0h 38% CTCF sites 3h

50% CTCF sites 0h 53.5% CTCF sites 3h

Box-plots of GRO-seq overlapping CTCF binding sites in different genomic

locations

•  More than 50% of CTCF binding sites are overlapping in intergenic regions, suggesting a possible role for CTCF as repressor or enhancer

•  CTCF binding sites in intergenic regions correlate with GRO-seq expression

Conservation analysis of CTCF binding sites in intergenic regions

•  CTCF binding sites are 90% conserved between human, mouse and chicken in 17% of cases at 0 hours and 26.5% of cases at 3 hours

Estrogen stimulation affects Lamin B distribution around CTCF sites overlapping with GRO-seq regions

•  After estrogen treatment, lamin B binding intensity is reduced at promoter and non promoter regions overlapping with CTCF sites. •  These data suggest an inverse correlation between CTCF and Lamin B binding.

CONCLUSIONS AND FUTURE PERSPECTIVES

•  We observed a redistribution of CTCF chromatin interactions upon estrogen stimulation, suggesting a role for CTCF in estrogen dependent gene regulation.

•  The combination of GRO-seq and CTCF binding analysis suggested that CTCF is regulating estrogen dependent transcription, possibly via the formation of different chromatin loops.

•  The conservation and GRO-seq analysis detect the possibility of presence of active enhancers and repressors in CTCF mediated transcription regulation.

•  Further, Lamin B and CTCF distribution suggest a role for nuclear remodeling in estrogen dependent gene regulation.

•  Future analysis will prove the role of CTCF in chromatin loops involving enhancers and repressors. Further experiments (e.g. 3C) will validate our findings and shed light on the function of CTCF in the whole scenario.