2020.2.19 KBC第4回勉強会 沖 真弥　先生 「遺伝子発現の時空間的な制御のしくみ」

1. 2020. 02. 19
KBC
(Oki, Shinya)
Data-driven & technical approach

2. ChIP-Atlas
Gene
RNA polymerase
Histones
Ac AcAc
Ac Me
Me
Me Me
Me
Enhancer
Transcription factors
Where?
What?
Low High
1 500 1000
MACS2 score
ChIP-seq
Oki* et al (2018) EMBO Rep

3. Photo-isolation chemistry

4. 2007 2008 2009 2010 2011 2012 2013 2014 2015
Oki et al, Development 2007
Oki et al, Development 2009
Sumi, Oki et al, PLOS One 2013
Hachisuga, Oki et al, PNAS 2015
Oki et al, Dev Dyn 2010
Noda, Oki et al, Dev Biol 2012

5. Gene regulation
Gene
RNA polymerase
Histones
Ac AcAc
Ac Me
Me
Me Me
Me
Enhancer
Transcription factors
Where?
What?

6. ChIP-Atlas
Gene
RNA polymerase
Histones
Ac AcAc
Ac Me
Me
Me Me
Me
Enhancer
Transcription factors
Where?
What?
Low High
1 500 1000
MACS2 score
ChIP-seq
Oki* et al (2018) EMBO RepDBCLS

7. ↓"
High'throughput"sequencing"
Park PJ (2009) Nat Rev Genet
ChIP-seq:
Chromatin Immunoprecipitation with Sequencing

8. ChIP-seq data
0
20,000
40,000
60,000
80,000
100,000
120,000
140,000
2014 2015 2016 2017 2018 2019 2020
Year
ChIP-Atlas

9. @SRR032450.88510 GSM461562_1:2:16:986:806 length=36
TCTGTAAATATAAACCCTTGGTCCATGGATTGCAAA
+SRR032450.88510 GSM461562_1:2:16:986:806 length=36
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR032450.88511 GSM461562_1:2:16:990:197 length=36
TCCTCAATTGACTGATAAGGAACAAAAATATGCGCA
+SRR032450.88511 GSM461562_1:2:16:990:197 length=36
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII4
@SRR032450.88512 GSM461562_1:2:16:770:404 length=36
TGAGCTAATTGATATTGGTATTTACCATGTGGAAGA
+SRR032450.88512 GSM461562_1:2:16:770:404 length=36
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII/I
@SRR032450.88513 GSM461562_1:2:16:89:366 length=36
TACAGACACGATCTTTGTAGAAAGAAAGACCCATAG
+SRR032450.88513 GSM461562_1:2:16:89:366 length=36
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR032450.88514 GSM461562_1:2:16:47:714 length=36
TAGAGTACGTCAAAAACATTGTATTGCTGAATAAAC
+SRR032450.88514 GSM461562_1:2:16:47:714 length=36
@SRR032450.88510 GSM461562_1:2:16:986:806 length=36
TCTGTAAATATAAACCCTTGGTCCATGGATTGCAAA
+SRR032450.88510 GSM461562_1:2:16:986:806 length=36
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR032450.88511 GSM461562_1:2:16:990:197 length=36
TCCTCAATTGACTGATAAGGAACAAAAATATGCGCA

10. @SRR032450.88510 GSM461562_1:2:16:986:806 length=36
TCTGTAAATATAAACCCTTGGTCCATGGATTGCAAA
+SRR032450.88510 GSM461562_1:2:16:986:806 length=36
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR032450.88511 GSM461562_1:2:16:990:197 length=36
TCCTCAATTGACTGATAAGGAACAAAAATATGCGCA
+SRR032450.88511 GSM461562_1:2:16:990:197 length=36
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII4
@SRR032450.88512 GSM461562_1:2:16:770:404 length=36
TGAGCTAATTGATATTGGTATTTACCATGTGGAAGA
+SRR032450.88512 GSM461562_1:2:16:770:404 length=36
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII/I
@SRR032450.88513 GSM461562_1:2:16:89:366 length=36
TACAGACACGATCTTTGTAGAAAGAAAGACCCATAG
+SRR032450.88513 GSM461562_1:2:16:89:366 length=36
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR032450.88514 GSM461562_1:2:16:47:714 length=36
TAGAGTACGTCAAAAACATTGTATTGCTGAATAAAC
+SRR032450.88514 GSM461562_1:2:16:47:714 length=36
@SRR032450.88510 GSM461562_1:2:16:986:806 length=36
TCTGTAAATATAAACCCTTGGTCCATGGATTGCAAA
+SRR032450.88510 GSM461562_1:2:16:986:806 length=36
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR032450.88511 GSM461562_1:2:16:990:197 length=36
TCCTCAATTGACTGATAAGGAACAAAAATATGCGCA
Alignment
Peak-call
> 1,000 TB

11. Alignment
Peak-call
Sample metadata
Curation
SRX330668 Ezh2 ES cells
SRX310198 Ctcf Mast cells
SRX1092953 Cebpa Liver
Foxa2
ID TFs Cells
FastQ (Sequence raw data)

12. ID Original sample metadata
ERX200492
ArrayExpress-Sex=male; ArrayExpress-CellType=B-Lymphocyte;
ArrayExpress-Immunoprecipitate=CTCF; ArrayExpress-Species=Homo
SRX1024932
source_name=chronic myelogenous leukemia cell line; cell line=K562;
antibody=AGO2
SRX212431
source_name=CD4+CD25+CD45RA+ expanded naive regulatory T cells;
donor=S030b; cell type=CD4+CD25+CD45RA+ expanded naive regulatory
SRX831872
source_name=Pre-activated CD8+ T cells; tissue=Peripheral blood; cell
type=Pre-activated CD8+ T cells; chip antibody=STAT5B (Invitrogen,
SRX100477
source_name=HepG2; biomaterial_provider=ATCC; datatype=ChipSeq;
datatype description=Chromatin IP Sequencing; cell
SRX530184
source_name=primary human hepatocytes; tissue=Liver; chip
antibody=FXR (1:1 mixture of sc-1204x and sc-13063x, ChIP grade,
SRX159094
source_name=HuH7 cells, mitotic block and release; cell type=HuH7;
cycling state=mitotic; antibody=FoxA1; vendor/catalog/lot=Abcam
SRX644410
source_name=PANC1 Pancreatic cancer cell line; antibody=ETS1 (Santa
Cruz, sc-350, lot #F1312); cell line=PANC1
BEFORE

13. ID Antigen Cell type Class Cell type
ERX200492 CTCF Blood B-Lymphocytes
SRX1024932 AGO2 Blood K-562
SRX212431 STAT5A Blood CD4-Positive T-Lymphocytes
SRX831872 STAT5B Blood CD8-Positive T-Lymphocytes
SRX100477 FOXA1 Liver Hep G2
SRX530184 NR1H4 Liver Hepatocytes
SRX159094 FOXA1 Liver HuH-7
SRX644410 ETS1 Pancreas PANC-1
AFTER
1,500 /

14. Foxa2
&
Alignment
Peak-call
Curation
SRX330668 Ezh2 ES cells
SRX310198 Ctcf Mast cells
SRX1092953 Cebpa Liver
ID
Sample metadata
TFs Cells
FastQ (Sequence raw data)

15. Home page
Oki, S.*, et al (2018) EMBO Rep.

16. Peak Browser
Foxa2

17. Peak Browser
TFs and
others
All cell
types
Click
M. musculus

18. Low High
1 500 1000
MACS2 score
Low High
1 500 1000
MACS2 score
Peak Browser
Foxa2

19. Low High
1 500 1000
MACS2 score
Low High
1 500 1000
MACS2 score
Peak Browser

20. Enrichment Analysis
Query
Result

21. Enrichment Analysis
TSS 5,000 bp
Click
Hepatocyte
Hepatocyte

22. Enrichment Analysis
HNF4A
FOXA2
HNF4G
Hepatocyte
Hepatocyte

23. in silico ChIPTF enrichment
Thousands of ChIP-seq data: : : : : :
Hepatocyte

24. TFs enriched for hepatocyte-specific genes
Top15
–Log10P
0
Liver
Liver
Liver
Liver
Liver
Liver
Liver
Liver
Liver
Liver
Liver
Liver
Liver
Liver
Liver
SRX100505 HNF4A Hep G2
SRX100449 HNF4G Hep G2
SRX100544 EP300 Hep G2
SRX100497 RXRA Hep G2
SRX150698 HNF4A Hep G2
SRX100448 FOXA2 Hep G2
SRX100477 FOXA1 Hep G2
SRX1531773 MED1 Hep G2
SRX100506 FOXA1 Hep G2
SRX100538 HDAC2 Hep G2
SRX018625 HNF4A Hep G2
SRX100552 SP1 Hep G2
SRX018626 HNF4A Hep G2
SRX190331 TEAD4 Hep G2
SRX190234 CEBPB Hep G2
30 60 90 120
Oki*, et al., 2018 EMBO Rep.
TF Cell

25. Top15
–Log10P
for Endothelial cells-specific genes
0
CDV (Cardiovascular)
CDV
CDV
CDV
CDV
CDV
CDV
CDV
CDV
CDV
CDV
CDV
CDV
CDV
Uterus
SRX393516 TAL1 Endothelia
SRX393518 TAL1 Endothelia
SRX2355072 JUN HAEC
SRX150664 FOS HUVEC
SRX2355073 JUN HAEC
SRX070879 FOS HUVEC
SRX150427 GATA2 HUVEC
SRX150358 JUN HUVEC
SRX1116232 EP300 HUVEC
SRX2355074 JUNB HAEC
SRX070877 GATA2 HUVEC
SRX2355085 RELA HAEC
SRX070876 GATA2 HUVEC
SRX070878 FOS HUVEC
SRX1674506 MBD3 HeLa
50 100 150
Oki*, et al., 2018 EMBO Rep.
TF Cell

26. Top15
–Log10P
Blood
Blood
Blood
Blood
Blood
Blood
Blood
Blood
Blood
Blood
Blood
Blood
Blood
Blood
Blood
SRX2770854 SPI1 Macrophages
SRX2770856 SPI1 Macrophages
SRX093189 SPI1 Macrophages
SRX3244991 SPI1 Macrophages
SRX097097 SMAD1 U-937
SRX1023791 SPI1 Macrophages
SRX2770857 SPI1 Macrophages
SRX627428 SPI1 Dendritic cells
SRX1023790 SPI1 Macrophages
SRX1023793 SPI1 Macrophages
SRX627430 SPI1 Dendritic cells
SRX103224 SPI1 THP-1
SRX2268284 SPI1 THP-1
SRX2268286 SPI1 THP-1
SRX2770855 SPI1 Macrophages
300 60 90 120
Oki*, et al., 2018 EMBO Rep.
for Macrophage-specific genes
TF Cell

27. Top15
–Log10P
0
Blood
Blood
Blood
Blood
Blood
Blood
Blood
Blood
Blood
Blood
Blood
Blood
Blood
Blood
BloodSRX373733 ETS1 CUTLL1
SRX1880278 BRD4 Jurkat
SRX725582 MYB Jurkat
SRX1046558 RAG2 Thymus
SRX658611 MYB Jurkat
SRX159138 NOTCH1 T-ALL
SRX326887 GABPA Jurkat
SRX100541 ELF1 GM12878
SRX198034 BRD4 CD4+ T-cells
SRX190349 RUNX3 GM12878
SRX1497394 MYC RAJI
SRX265233 EP300 ME-1
SRX190216 CREB1 GM12878
SRX369136 BRD4 CUTLL1
SRX971780 KMT2D OCI-LY-7
80 160 240
Oki*, et al., 2018 EMBO Rep.
for T cell-specific genes
TF Cell

28. Acknowledgement
PIC Apr 2020 ~
DBCLS
RIKEN
RIKEN
DDBJ
NBDC
ChIP-Atlas
H29
R1 H30 B ( )
H31 B ( )
H29 H29 AMED