supplementary materials for · 2020. 8. 31. · quantified by thunderbird sybr qpcr mix (toyobo)...

immunology.sciencemag.org/cgi/content/full/5/51/eabb1455/DC1

Supplementary Materials for

The transcription factor E2A activates multiple enhancers that drive Rag expression

in developing T and B cells

Kazuko Miyazaki, Hitomi Watanabe, Genki Yoshikawa, Kenian Chen, Reiko Hidaka, Yuki Aitani, Kai Osawa, Rie Takeda, Yotaro Ochi, Shizue Tani-ichi, Takuya Uehata, Osamu Takeuchi, Koichi Ikuta,

Seishi Ogawa, Gen Kondoh, Yin C. Lin, Hiroyuki Ogata, Masaki Miyazaki*

*Corresponding author. Email: [email protected]

Published 4 September 2020, Sci. Immunol. 5, eabb1455 (2020)

DOI: 10.1126/sciimmunol.abb1455

The PDF file includes:

Methods Fig. S1. Characterization of R-TEn and R1B/R2B. Fig. S2. R-TEn and R1B/R2B are essential for cell type–specific Rag1/Rag2 expression. Fig. S3. R1B and R2B regulates compartmentalization, local compaction, sub-TAD, and loop formation. Fig. S4. E protein binding to enhancer and promoter regions are indispensable for Rag gene expression. Fig. S5. E-box mutations in R-TEn-p1 did not affect other gene loci. Fig. S6. Development of Rag SEs during T and B cell differentiation, in comparison with BMDM. Fig. S7. Comparative analysis of R-TEn, R1B, and R2B enhancers among vertebrates. Table S1. GSE numbers for figures. Table S2. Tag density at enhancer regions.

Supplementary Methods

Flow cytometry

Single-cell suspensions from the bone marrow and thymus were stained with FITC-, PE-,

APC-, APC-Cy7, Pacific Blue-, BV421, BV450, Alexa Fluor 780-, PerCP-Cy5.5-, PE-Cy7-,

or biotin-labeled monoclonal antibodies (BD PharMingen; CD4 (H129.19), CD44 (IM7),

CD45R/B220 (RA3-6B2), TCR(GL3), eBioscience; CD4 (GK1.5), CD8 (53.6.7),

CD49b (DX5), CD117(ACK2), IgM (11/41), BioLegend; CD3 (145-2C11), CD5 (53-7.3),

CD8 (53.6.7), CD19 (ID3), CD28 (E18), CD25 (PC61), CD69 (H1.2F3), TCR (H57),

CD45R/B220 (RA3-6B2), IgD (11-26C.2d), CD117 (2B8), TONBO; CD3 (145-2C11),

CD19 (ID3), B220 (RA3-6B2), CD11b (M1/70), Gr1 (RB6-8C5), Ter119 (TER119),

CD11c (N418)). Biotinylated antibodies were labeled with streptavidin-conjugated BV650

(BD). PE-conjugated CD1d-tetramer was generously provided by the National Institutes of

Health Tetramer Core Facility (mCD1d/PBS57). Clone 2.4G2 anti-CD32:CD16

(eBioscience) was used to block FcRs. Dead cells were removed from analysis and sort by

staining with propidium iodide (PI) (Sigma-Aldrich). Samples were collected or sorted on a

FACSAria, LSRII (BD Biosciences) and were analyzed with FlowJo software (Tree Star).

Intracellular staining was performed with Intracellular Fixation & Permeabilization Buffer

Set (eBioscience).

RNA isolation and reverse transcriptase PCR

Total RNA was isolated from sorted DN3a, CD5–CD69–DP, pro-B, or pre-B cells with

RNeasy kit (Qiagen), followed by reverse transcription with the SuperScript III RT-PCR

system (Invitrogen). Quantitative real-time PCR was performed by TB Green Premix EX

Taq (Takara).

3C assay

3C assay was performed as previously described (15). Briefly, 1 x 107 DP cells were fixed

with 2% formaldehyde. After quenching the reaction, the cells were washed and lysed by

incubation on ice in 10 mM Tris, 10 mM NaCl, 0.2% NP40 and proteinase inhibitor

cocktail. Then, nuclei were washed with PBS, and incubated in CutSmart digestion buffer

(New England Biolabs) containing 0.3% SDS, followed by the addition of Triton-X (37°C

1 h incubation). Chromatin was digested with HindIII and digested chromatin was diluted

and ligated by T4 DNA ligase according to the protocol. Then, proteinase K was added and

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ligated chromatin was incubated overnight at 65 °C to reverse cross-links. Then, DNA was

purified by DNA clean & Concentrator kit (Zymo Research). Ligation products were

quantified by Thunderbird SYBR qPCR mix (TOYOBO) using StepOne Plus (Thermo

Fisher). Primer sequences are previously reported (15).

Methylation data analysis

We downloaded the MethylC-seq data of pro-B and pro-T from GEO (GSM1867947,

GSM2685783). Reads were aligned to the reference genome mm9 using Bismark (v0.15.0)

with the parameters "--bowtie2 -N 1 -L 22 --score_min L,-0.6,-0.6". We then used

Bismark_methylation_extractor command from bismark software package to extract

context-dependent (CpG/CHG/CHH) methylation, with parameters "--paired-end

--no_overlap --report --bedGraph --counts --no_header --cytosine_report". The resulting

bedgraph files were converted to bigwig files for genome browser visualization.

ChIP-seq

ChIP-seq was mostly performed as described(21). Briefly, cells were fixed in 1%

formaldehyde/PBS for 10 min at room temperature. The reactions were quenched by 1.5 M

of glycine and the cells were washed with PBS. Cell pellets were lysed and chromatin was

sonicated by Covaris M220. Anti-H3K4me1 (Abcam, ab8895), anti-H3K27ac (Abcam,

ab4729), anti-H3K27me3 (Millipore, 07-449), anti-CTCF (Millipore, 07-729) or

anti-SMC3a (Abcam, ab9263) antibodies were pre-bound to Dynabeads Protein G

magnetic microbeads (Thermo Fisher). The sheared and diluted chromatin was

immunoprecipitated with each respective antibody overnight at 4 °C. The samples were

washed, eluted, and reverse cross-linked at 65°C overnight. After treatment with RNase A

and proteinase K, DNA fragments were purified and then ligated to NEBNext Multiplex

Oligos for Illumina (NEB) for PCR. Amplified ChIP DNA was size selected and the

libraries were sequenced single-ended (75 bp) or paired-ended (150 bp) on an Illumina

NextSeq 500 or NovaSeq (Illumina). Only read1 fastq files of PE reads were used for

ChIP-seq data analysis. Reads were aligned to reference genome mm9 by Bowtie2. Tags

that mapped uniquely were analyzed further. To visualize ChIP-seq reads on the UCSU

Genome Browser, bedGraph files were generated as described above. ChIP-seq peaks were

called using HOMER’s findPeaks command with default parameters and –style option.

Each ChIP-seq experiments were performed twice and one set of high-quality data was

used for differential peak analysis. Differential ChIP-seq peaks between control and mutant

samples were statistically analyzed using the HOMER tool getDifferentialPeaks program to

identify regions with greater than 2-fold normalized read coverage and p value less than

1e-7 (Poisson). To compare abundance of transcription factor ChIP-seq reads at the Rag

enhancer peaks across the different experiments from GEO, normalized tag densities were

calculated by HOMER’s annotatePeaks.pl program with option –size 200.

Fig. S1. Characterization of R-TEn and R1B/R2B. (A) Many transcription factors essential for T or B cell development bound to R-TEn, or R1B and R2B in T- or B-progenitor/precursor, respectively. Browser shots of ChIP-seq for transcription factors in DN2-3 and pro-B cells. (B) 2 kb R-TEn was located in 8 kb ASE region. Normalized ATAC-seq reads and ChIP-seq for E2A occupancy in DN3 and DP cells and PolII occupancy in DP cells. (C) R2B is partially overlapped with Erag. Normalized ATAC-seq reads and ChIP-seq for E2A binding in pro-B and pre-B cells are shown. Homo-Erag indicates the highly homologous region of Erag among mammalian species, which was previously described (ref. 12)

Figure S1 Miyazaki et al.

APro-T

ATAC;DN3

ICN1;8946

RBPj;8946

Bcl11b;DN3

Ikaros;DN3

Gata3;DN2b

PU.1;DN2b

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chr2:101,370,001-101,540,000

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E2A

Ebf1

P300

Rag1Rag2 Traf6R-TEn R2B R1B

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B

DN3

DP

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AC

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Chr2: 101,387,465-101,396,576

PolII: thymus

71kbp79kbp

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ASE

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chr2:101,437,284-101,443,3612 kb

R2B

peak1 peak2

Erag

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Fig. S2. R-TEn and R1B/R2B are essential for cell type–specific Rag1/Rag2 expression. (A) Flow cytometric analysis of CD28 versus intra-cellular TCR expression gated on DN3 cells (CD4–

CD8–Lin–CD44–CD25+)(upper), and TCR versus CD1d-tet expression in total thymocytes (lower) from 4-week-old wild-type control and R-TEnd/d mice. (B) Flow cytometric analysis of CD4 versus CD8 expression in total fetal thymocytes (left, upper), CD69 versus CD5 expression gated on DP cells (left, lower), CD44 versus CD25 expression gated on CD4–CD8–Lin– cells (right, upper), and CD28 and FSC gated on DN3 cells (right, lower) derived from 18.5 d.p.c. wild-type littermate control and R-TEnd/d fetus. (C) Cell numbers of total thymocytes, ETPs (CD4–CD8–Lin–CD44+CD25–Kit+), DN2 (CD4–CD8–Lin–

CD44+CD25+), DN3a (CD4–CD8–Lin–CD44–CD25+CD28–), DN3b (CD4–CD8–Lin–CD44–

CD25+CD28+), DN4 (CD4–CD8–Lin–CD44–CD25–CD28+), ISP (CD4–CD8+TCRb–), DP (CD4+CD8+), and T cell (CD3+TCR+), the ratio of DN3b to DN3a cell numbers, %CD69+ DP cells in DP cells, derived from 18.5 d.p.c. wild-type littermate control and R-TEnd/d fetus. (D) Representative flow cytometric analysis of CD19 versus B220 expression in total bone marrow cells, IgM versus IgD expression gated on CD19+B220+ cells, and CD25 versus Kit expression gated on CD19+B220+IgM–

IgD– cells, derived from 4-week-old wild-type control and R-TEnd/d mice (E) Quantitative real-time PCR analysis of the rearrangement of V-J segments in genomic DNA extracted from CD5–CD69– DP cells from 4-week-old wild-type control and R-TEnd/d mice, as seen in Fig. 2D.

A B

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Fig. S2. R-TEn and R1B/R2B are essential for cell type–specific Rag1/Rag2 expression. (F) Flow cytometric analysis of CD4 versus CD8 expression in total thymocytes derived from 4-week-old wild-type control, R1Bd/d, R2Bd/d, R1Bd/dR2Bd/d mice, and cell number of total thymocytes, as seen in Fig. 2G. (G) Quantitative real-time PCR analysis of the rearrangement of Ig, V-J2, and V-J3 segments in genomic DNA extracted from pre-B cells (CD19+B220+IgM–IgD–CD25+) from 4-week-old wild-type control and R1Bd/dR2Bd/d mice (H) Quantitative real-time PCR analysis of Rag1 and Rag2 mRNA expression in sorted CD5–CD69– DP cells from 4-week-old wild-type control, R1Bd/d, R2Bd/d and R1Bd/dR2Bd/d mice.

Fig. S3. R1B and R2B regulates compartmentalization, local compaction, sub-TAD, and loop formation. (A), (B) in situ Hi-C contact maps of wild-type and R1Bd/dR2Bd/d cultured pro-B cells are shown. Positive PC1 values (A compartment) are indicated in black, and negative PC1 values (B compartment) are displayed in gray. Changes in PC1 and distal-to-local ratio (DLR) are shown, as seen in Fig. 3C. Right panel shows contact maps, TADs and Loops score, and PC1 values in genomic regions including enhancers (green), Rag1(R1)/Rag2(R2), and neighboring genes, as seen in Fig. 3C. Color scales in the Hi-C contact maps indicate the ratios of observed versus expected interaction frequencies: blue, lower-than-expected; red, higher-than-expected.

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1M bp

Fig. S4. E protein binding to enhancer and promoter regions are indispensable for Rag gene expression. (A), (B), (C) Other T cell transcription factors are dispensable for Rag gene expression or super-enhancer formation. (A) Rag1 and Rag2 gene expressions derived from RNA-seq data of control and Bcl11b-deficient DN cells (upper), and RNA-seq data of control and Tcf1-deficient DP cells (lower). (B) Browser shots of normalized ATAC-seq reads from control and ThymoD-deficient DN2 cells (upper) and control and Tcf1-deficient DP cells (lower), and ChIP-seq of Bcl11b and Tcf1 binding in DN3 (upper) and DP cells (lower) are shown. (C) ChIP-seq of H3K27Ac in control, Satb1-deficient DP cells (upper) and Rad21-deficient DP cells (lower) and ChIP-seq data of Satb1 in DP across Rag gene loci are shown. (D) Cell number of total thymocytes derived from 4-week-old control, R-TEn-peak1 deletion (R-TEn-p1d/d), R-TEn-peak2 deletion (R-TEn-p2d/d) mice are shown. (E) Flow cytometric analysis of CD44 versus CD25 expression gated on CD4–CD8–Lin– cells (upper), and CD28 and FSC gated on DN3 cells (lower) derived from 4-week-old wild-type control and R-TEn-p1d/d mice. (F) Cell numbers of DN3a, DN3b, and DN4 cells (upper), the ration of DN3b to DN3a cells and %CD69+ cells in DP population (lower), derived from 4-week-old wild-type control and R-TEn-p1d/d mice, are shown. (G) Browser shots of normalized ATAC-seq reads in wild-type DP cells (upper) and DNA sequence conservations in R-TEn regions are shown. Blue lines indicate peak1 (R-TEn-p1) and peak2 (R-TEn-p2) in R-TEn region (middle). Green bar indicates E2A binding region in R-TEn-p1 and red boxes indicates E-box sites. Other transcription factor binding motifs are shown below. The E-box sequences (red) and the edited mutant sequences (black) in R-TEn-p1-Eboxmut/mut mouse are shown below.

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Fig. S4. E protein binding to enhancer and promoter regions are indispensable for Rag gene

expression. (H) Cell numbers of DN3a, DN3b, DN4, CD4SP, CD8SP, and T cells derived from 4-week-old wild-type control and R-TEn-p1-Eboxmut/mut mice are shown. (I) Quantitative real-time PCR analysis of Rag1 and Rag2 mRNA expression in sorted DN3a and CD5–CD69– DP cells from 4-week-old wild-type control and R-TEn-p1-Eboxmut/mut mice are shown. (J) Browser shots of normalized ATAC-seq reads of DP cells from wild-type control and R-TEn-p1-Eboxmut/mut mice and ChIP-seq of Smc1a, Satb1, and CTCF binding of wild-type control DP cells across the Rag gene cluster are shown. (K) Cell numbers of total thymocytes, DP, CD4SP, CD8SP, ETPs, DN2, DN3a, DN3b, DN4 cells (upper), total BM cells, B cell, pro-B, CD25–, pre-B, IgM+ immature B, and IgD+ mature B cells (lower), derived from 4-week-old wild-type control and R1pro-Eboxmut/mut mice are shown. (L) Model depicting a stepwise Rag expression regulated by E2A.

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Fig. S5. E-box mutations in R-TEn-p1 did not affect other gene loci. (A) Browser shots of ChIP-seq of H3K27Ac, H3K4me1, H3K27me3, and normalized ATAC-seq reads across CD4 and neighboring genes are shown in wild-type control and R-TEn-p1-Eboxmut/mut DP cells. (B) Browser shots of ChIP-seq of H3K27me3 are shown across the Ebf1 gene locus in wild-type control and R-TEn-p1-Eboxmut/mut DP cells.

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Fig. S6. Development of Rag SEs during T and B cell differentiation, in comparison with BMDM. (A) Circos diagrams representing genomic interactions across Rag gene cluster and Traf6 gene during T and B cell differentiation. Thickness of connecting lines reflects p values associated with the indicated interactions. (B), (C) PC1 and TADs and Loops scores are shown, as seen in Fig. 6B.

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FoB

BMDM

TADs and Loops score4.2

-1.3CLP

Rag2 Rag1

Traf6

Prr5l


Rag2 Rag1

Traf6

Prr5l


DN3

DP

4SP

Naïve

CD4TNaïve

CD8TR-TEnd/d

DP

BMDM

PC1 1.2

-1.3

CLP

DN2pro-B

pre-B

Spl B

FoB

R1Bd/dR2Bd/d

pro-B

BMDM

PC1 1.33

-1.22

CLP

Rag2 Rag1

Traf6

Prr5l


B

C

CLP

DN2 DP CD4T

pro-B pre-B Spl B

ATAC R-TE

n

R2B

R1B

Rag2

Rag1

Tra

f6

ATAC R-TE

n

R2B

R1B

Rag2

Rag1

Tra

f6

ATAC R-TE

n

R2B

R1B

Rag2

Rag1

Tra

f6

ATAC R-TE

n

R2B

R1B

Rag2

Rag1

Tra

f6

ATAC R-TE

n

R2B

R1B

Rag2

Rag1

Tra

f6

ATAC R-TE

n

R2B

R1B

Rag2

Rag1

Tra

f6

ATAC R-TE

n

R2B

R1B

Rag2

Rag1

Tra

f6

chr2:101,370,001-101,540,000

chr2:101,000,001-102,000,000


Fig. S6. Development of Rag SEs during T and B cell differentiation, in comparison with BMDM. (D) Contact maps of DP, pre-B, and bone marrow derived macrophage (BMDM) are shown, related to Fig. 6B. Black lines in lower panels indicate ranges shown in Fig. 6B. (E) To examine the reproducibility of results in Figure 6B, we analyzed another data set of DP (GSE79422), pre-B (GSE109671), and BMDM (GSE115524). Contact maps of DP, pre-B and BMDM with another data set were shown, as seen in Figure 6B. (F) Model depicting TAD boundary (insulator) formation in macrophages to sequester Rag1/2 gene cluster in compartment B. (G) Rag gene cluster shows B-to-A compartment switching and local compaction in DP and preB cells with differentiation from HSC, while it does not change in BMDM. Genome browser tracks of compartment changes (PC1) and compaction (DLR).

DP pre-B BMDMchr2:91,000,001-105,000,000

Scalechr2:

5M

R2TEn

RatHuman

OrangutanDog

HorseOpossum

ChickenStickleback

UCSC Genes

capture_region

RepeatMaskerMouse mRNAs

Ensembl Genes

2 Mb mm9100,000,000 101,000,000 102,000,000 103,000,000

R2TEnR2TEn_ATAC_1st_peak

R2TEn_E2A_1st_peakR2TEn_ATAC_2nd_peak

R2TEn_E2A_2nd_peakR2bEn

R2bEn_1st_peakR2bEn_2nd_peakR1Enpro_common

R1bEn

Fig_1M_regionFig_1M_region_2

R2bEnR1Enpro_common

R1bEn

NWC_promR2bEn_ATAC_1st_peak

R2bEn_ATAC_2nd_peakR2TEn_E2A_1st_peak

R2TEn_E2A_2nd_peak





R1bEn

B230118H07RikB230118H07RikB230118H07Rik

Rag2Rag1

Traf6Traf6

Prr5lPrr5lPrr5lPrr5lCommd9

Ldlrad3Ldlrad3

Trim44Fjx1Pamr1

Slc1a2Slc1a2

Slc1a2Slc1a2

Cd44Cd44

Cd44Cd44Cd44Cd44

PdhxApipApipApip

EhfElf5Elf5

CatAbtb2

Nat10

RH126499G36984

D2MIT184

RH126106 D2MIT301D2MIT437

D2MIT384D2MIT440D2MIT300

D2MIT438

M64796M29475

D2MIT161

D84655AI851288

2600010E01RIKD2MIT249

D2MIT251D6J1

FJX1

RH126741D43796

AI159670

CD44

AI481367

D2MIT388

D2MIT12

D2MIT250D2MIT389

AF035527

D2MIT97

L25069

AW539457AI429152

46.MMHAP9FRH10.SEQM-11397

20.MMHAP10FRG8.SEQMHAA54F5.SEQ

02.MMHAP67FRA8.SEQ

43.MMHAP14FRG10.SEQPMC150727P7PMC102178P1PMC196132P1PMC137757P1

PMC21337P1BB208787

PMC133542P3PMC155324P1PMC102110P1PMC209472P1

BE333972MGI:3693540MHAA70F5.SEQ

RH124837

RH135925MGI:3611292

40.MMHAP94FRF10.SEQ

RH138571MHAA38C10.SEQ

BB307780RH136410

M-08449

lincR-Cd44-5S

RAG1KO_E2A_ChIPseq_mm9_GSM546523_Sample7.1plus2_Total Tags = 5.60e+06, normalized to 1.00e+07

63.95 -

0 _

R12BEnDel_proB_HiC_KM49 Insulation Ratio (R12BEnDel_proB_HiC_KM49_Filtered/)

6.68193 -

-1.10677 _

R2TEnDel_DP_HiC_KM41_Filtered_reduced315776392//R2TEnDel_DP_HiC_KM41_Filtered_reduced315776392 Insulation Ratio (R2TEnDel_DP_HiC

6.99369 -

-0.862841 _

R12BEnCont_proB_HiC_KM50 Insulation Ratio (R12BEnCont_proB_HiC_KM50_Filtered/)

6.90637 -

-0.904012 _

Bcell_spl_HiC_rep2_SRX3314669 Insulation Ratio (Bcell_spl_HiC_rep2_SRX3314669_Filtered/)

6.53133 -

-1.04978 _

FoB_HiC_rep2_SRX2840838 Insulation Ratio (FoB_HiC_rep2_SRX2840838_Filtered/)

6.53132 -

-1.0516 _

WT_DP_HiC_KM40_Filtered//WT_DP_HiC_KM40_Filtered Insulation Ratio (WT_DP_HiC_KM40_Filtered/)

7.02443 -

-1.07212 _

WT_CD4SP_TCC_KM906_KM11 Insulation Ratio (WT_CD4SP_TCC_KM906_KM11_Filtered/)

7.09612 -

-0.950657 _

naiveCD4T_HiC_rep2_SRX3314667 Insulation Ratio (naiveCD4T_HiC_rep2_SRX3314667_Filtered/)

6.6084 -

-1.12868 _


7.03812 -

-0.986293 _

BMDM_HiC_SRR6660238 Insulation Ratio (BMDM_HiC_SRR6660238_Filtered/)

7.85854 -

-0.99462 _

Granulo_HiC_rep1_SRX2840843 Insulation Ratio (Granulo_HiC_rep1_SRX2840843_Filtered/)

6.73827 -

-1.21367 _

neutrophil_HiC_rep3_SRX2463370 Insulation Ratio (neutrophil_HiC_rep3_SRX2463370_Filtered/)

6.193 -

-1.34423 _

0 -

R12BEnCont_proB_HiC_KM50_Filtered/ DLR (Distal Local (log2) Ratio of interactions, local<3000000 bp) 5x15kb

0.521073 -

-0.920175 _

0 -

Bcell_spl_HiC_rep2_SRX3314669_Filtered/ DLR (Distal Local (log2) Ratio of interactions, local<3000000 bp) 5x15kb

1.98662 -

-0.597458 _

Bcell_spl_HiC_rep2_SRX3314669_Filtered/ ICF (InterChromosomal interaction Fraction) 5x15kb

0.316689 -

0 _

FoB_HiC_rep2_SRX2840838_Filtered/ DLR (Distal Local (log2) Ratio of interactions, local<3000000 bp) 5x15kb

1.98627 -

-0.599627 _

FoB_HiC_rep2_SRX2840838_Filtered/ ICF (InterChromosomal interaction Fraction) 5x15kb

0.315962 -

0 _

WT_DP_HiC_KM40_Filtered/ ICF (InterChromosomal interaction Fraction) 5x15kb

0.243608 -

0 _

WT_DP_HiC_KM40_Filtered/ DLR (Distal Local (log2) Ratio of interactions, local<3000000 bp) 5x15kb

1.64819 -

-1.12609 _

0 -

WT_CD4SP_TCC_KM906_KM11_Filtered/ COV (Read Coverage) 5x15kb

8484.45 -

0 _

WT_CD4SP_TCC_KM906_KM11_Filtered/ DLR (Distal Local (log2) Ratio of interactions, local<3000000 bp) 5x15kb

1.845 -

-1.23542 _

0 -

WT_CD4SP_TCC_KM906_KM11_Filtered/ ICF (InterChromosomal interaction Fraction) 5x15kb

0.213107 -

0 _

naiveCD4T_HiC_rep2_SRX3314667_Filtered/ DLR (Distal Local (log2) Ratio of interactions, local<3000000 bp) 5x15kb

1.81825 -

-0.38647 _

naiveCD4T_HiC_rep2_SRX3314667_Filtered/ ICF (InterChromosomal interaction Fraction) 5x15kb

0.291518 -

0 _


2.04591 -

-0.393245 _


0.271412 -

0 _

BMDM_HiC_SRR6660238_Filtered/ COV (Read Coverage) 5x15kb

8000.91 -

0 _

BMDM_HiC_SRR6660238_Filtered/ ICF (InterChromosomal interaction Fraction) 5x15kb

0.241807 -

0 _

BMDM_HiC_SRR6660238_Filtered/ DLR (Distal Local (log2) Ratio of interactions, local<3000000 bp) 5x15kb

1.55545 -

-1.46394 _

Granulo_HiC_rep1_SRX2840843_Filtered/ ICF (InterChromosomal interaction Fraction) 5x15kb

0.225621 -

0 _

Granulo_HiC_rep1_SRX2840843_Filtered/ DLR (Distal Local (log2) Ratio of interactions, local<3000000 bp) 5x15kb

1.9046 -

-0.722723 _

0 -

neutrophil_HiC_rep3_SRX2463370_Filtered/ COV (Read Coverage) 5x15kb

8792.47 -

0 _

neutrophil_HiC_rep3_SRX2463370_Filtered/ ICF (InterChromosomal interaction Fraction) 5x15kb

0.415157 -

0 _

neutrophil_HiC_rep3_SRX2463370_Filtered/ DLR (Distal Local (log2) Ratio of interactions, local<3000000 bp) 5x15kb

1.36294 -

-1.34024 _

R2TEnDel_DP_HiC_KM41_Filtered_reduced315776392/ DLR (Distal Local (log2) Ratio of interactions, local<3000000 bp) 5x15kb

2.26075 -

-0.970977 _

0 -

R2TEnDel_DP_HiC_KM41_Filtered_reduced315776392/ ICF (InterChromosomal interaction Fraction) 5x15kb

0.257815 -

0 _

R12BEnCont_proB_HiC_KM50_Filtered/ COV (Read Coverage) 5x15kb

8682.57 -

0 _

R12BEnDel_proB_HiC_KM49_Filtered/ DLR (Distal Local (log2) Ratio of interactions, local<3000000 bp) 5x15kb

0.912272 -

-1.1266 _

R12BEnDel_proB_HiC_KM49_Filtered/ COV (Read Coverage) 5x15kb

8684.93 -

0 _

R12BEnCont_proB_HiC_KM50_Filtered/ ICF (InterChromosomal interaction Fraction) 5x15kb

0.197886 -

0 _

R12BEnDel_proB_HiC_KM49_Filtered/ ICF (InterChromosomal interaction Fraction) 5x15kb

0.185118 -

0 _

Cont1_DP_ATAC_KM4801_wo_chrM_mm9_reduced_19Mio Total Tags = 3.37e+07, normalized to 1.00e+07

80.59 -

0 _


84.39 -

0 _

IndId2_1_DP_ATAC_KM4803_wo_chrM_mm9 Total Tags = 1.87e+07, normalized to 1.00e+07

91.87 -

0 _

IndId2_2_DP_ATAC_KM4804_wo_chrM_mm9_reduced_17Mio Total Tags = 3.05e+07, normalized to 1.00e+07

63.87 -

0 _

H3K36me3_neutrophil_SRR5144977_mm9 Total Tags = 1.34e+07, normalized to 1.00e+07

21.55 -

0 _


10.63 -

-0.05 _


7.31 -

0 _

H3K27ac_neutrophil_SRR5144965_mm9 Total Tags = 1.28e+07, normalized to 1.00e+07

33.3 -

0 _


154.83 -

0 _


19.21 -

0 _


42.39 -

0 _

CTCF_neutrophil_SRR5144963_mm9 Total Tags = 1.30e+07, normalized to 1.00e+07

38.4 -

0 _

BMDM_CTCF_ChIP_GSM918726_mm9_reduced_30Mio Total Tags = 3.00e+07, normalized to 1.00e+07

33.51 -

0 _

Rad21_neutrophil_SRR5144961_mm9 Total Tags = 1.43e+07, normalized to 1.00e+07

73.36 -

0 _

BMDM_Rad21_ChIP_SRR6492207_mm9_reduced_28Mio Total Tags = 2.80e+07, normalized to 1.00e+07

45.31 -

0 _

Id2_Ind_proB_Dox0_ATAC_KM4701_wo_chrM_mm9 Total Tags = 1.34e+07, normalized to 1.00e+07

97.85 -

0 _

Id2_Ind_proB_Dox1.0_ATAC_KM4702_wo_chrM_mm9_reduced_15Mio Total Tags = 2.78e+07, normalized to 1.00e+07

30.09 -

0 _

Id2_Ind_proB_Dox2.0_ATAC_KM4703_wo_chrM_mm9 Total Tags = 1.01e+07, normalized to 1.00e+07

47.93 -

0 _


26.36 -

0 _


67.76 -

0 _

EHCont1_DP_ATAC_KM4501_wo_chrM_mm9_reduced_20Mio Total Tags = 3.40e+07, normalized to 1.00e+07

77.31 -

0 _

EHdKO1_DP_ATAC_KM4502_wo_chrM_mm9_reduced_19Mio Total Tags = 3.19e+07, normalized to 1.00e+07

82.31 -

0 _

WT_DP_HiC_KM40_Filtered//WT_DP_HiC_KM40_Filtered DI (WT_DP_HiC_KM40_Filtered/)

6.07962 -

-5.02661 _

0 -

R2TEnDel_DP_HiC_KM41_Filtered_reduced315776392//R2TEnDel_DP_HiC_KM41_Filtered_reduced315776392 DI (R2TEnDel_DP_HiC_KM41_Filtered

5.92912 -

-5.50629 _

R12BEnDel_proB_HiC_KM49 DI (R12BEnDel_proB_HiC_KM49_Filtered/)

3.57126 -

-2.67824 _

0 -

R12BEnCont_proB_HiC_KM50 DI (R12BEnCont_proB_HiC_KM50_Filtered/)

2.94087 -

-2.67216 _

Bcell_spl_HiC_rep2_SRX3314669 DI (Bcell_spl_HiC_rep2_SRX3314669_Filtered/)

3.72397 -

-3.8282 _

FoB_HiC_rep2_SRX2840838 DI (FoB_HiC_rep2_SRX2840838_Filtered/)

3.72399 -

-3.83718 _

WT_CD4SP_TCC_KM906_KM11 DI (WT_CD4SP_TCC_KM906_KM11_Filtered/)

5.06659 -

-4.82989 _

naiveCD4T_HiC_rep2_SRX3314667 DI (naiveCD4T_HiC_rep2_SRX3314667_Filtered/)

4.9661 -

-3.86829 _

0 -


5.26336 -

-3.18212 _

0 -

BMDM_HiC_SRR6660238 DI (BMDM_HiC_SRR6660238_Filtered/)

4.18498 -

-3.63586 _

0 -

Granulo_HiC_rep1_SRX2840843 DI (Granulo_HiC_rep1_SRX2840843_Filtered/)

5.64464 -

-3.53896 _

0 -

neutrophil_HiC_rep3_SRX2463370 DI (neutrophil_HiC_rep3_SRX2463370_Filtered/)

3.88639 -

-3.39212 _

R2TEn_vs_WT Correlation difference (WT_DP_HiC_KM40_Filtered vs. R2TEnDel_DP_HiC_KM41_Filtered_reduced315776392)

1 -

-1 _

WT_DP_HiC_KM40 PC1

1.26523 -

-1.27631 _

R2TEnDel_DP_HiC_KM41_red315776392 PC1

1.27106 -

-1.31777 _

R12BEnDel_proB_HiC_KM49_50kb PC1

1.41234 -

-1.22558 _

R12BEnCont_proB_HiC_KM50_50kb PC1

1.4378 -

-1.13167 _

Bcell_spl_HiC_rep2_SRX3314669_50k PC1

1.42539 -

-1.23421 _

FoB_HiC_rep2_SRX2840838_50k PC1

1.42511 -

-1.23416 _

WT_CD4SP_TCC_KM906_KM11_Filtered_new PC1

1.36541 -

-1.26966 _

naiveCD4T_HiC_rep2_SRX3314667_50k PC1

1.35785 -

-1.2689 _


1.32558 -

-1.25762 _

BMDM_HiC_SRR6660238 PC1

1.48659 -

-1.20179 _

Granulo_HiC_rep1_SRX2840843_50k PC1

1.45955 -

-1.25405 _

neutrophil_HiC_rep3_SRX2463370 PC1

1.6531 -

-1.09518 _

0 -

neutrophil_HiC_rep3_SRX2463370_40k PC1

1.68212 -

-1.08445 _

0 -

PreB_HiC_SRR6512775_50k PC1

1.28393 -

-1.31009 _

Satb1_DP_SRR5059419_mm9 Total Tags = 1.80e+07, normalized to 1.00e+07

68.54 -

0 _


51 -

0 _

Satb1_Scid.adh.2c2_Mock_rep1_SRR5183702_mm9 Total Tags = 2.70e+07, normalized to 1.00e+07

37 -

0 _


22.72 -

0 _

Satb1_Thy_SRR1810468_mm9 Total Tags = 3.17e+07, normalized to 1.00e+07

24.77 -

0 _

Cont_proB_polII_KM4402_mm9 Total Tags = 1.27e+07, normalized to 1.00e+07

38.44 -

0 _

R12Bddel_proB_polII_KM4404_mm9 Total Tags = 1.64e+07, normalized to 1.00e+07

2.56 -

0 _

preBAdh_H3K27me3_SRR4241635_mm9 Total Tags = 2.77e+07, normalized to 1.00e+07

16.71 -

0 _


9.78 -

0 _

preBAdh_H3K27ac_SRR4241633_mm9 Total Tags = 2.12e+07, normalized to 1.00e+07

54.79 -

0 _


50 -

0 _


48.71 -

0 _


19.54 -

0 _

preBAdh_Ets1_SRR4241625_mm9 Total Tags = 2.33e+07, normalized to 1.00e+07

12.4 -

0 _

preBAdh_Ikaros_SRR4241638_mm9 Total Tags = 2.12e+07, normalized to 1.00e+07

36.34 -

0 _

preBAdh_Irf4_SRR4241642_mm9 Total Tags = 9.06e+06, normalized to 1.00e+07

55.4 -

0 _

preBAdh_Med1_SRR4241646_mm9 Total Tags = 2.10e+07, normalized to 1.00e+07

6.73 -

0 _

preBAdh_Pax5_SRR4241648_mm9 Total Tags = 2.15e+07, normalized to 1.00e+07

108.05 -

0 _

preBAdh_polII_SRR4241650_mm9 Total Tags = 2.64e+07, normalized to 1.00e+07

57.66 -

0 _

preBAdh_Ebf1_SRR4241623_mm9 Total Tags = 1.63e+07, normalized to 1.00e+07

42.01 -

0 _

preBAdh_E2A_SRR4241621_mm9 Total Tags = 2.17e+07, normalized to 1.00e+07

50.38 -

0 _

preBAdh_AIO_SRR4241619_mm9 Total Tags = 2.07e+07, normalized to 1.00e+07

8 -

0 _

C10_Foxo1_SRR4167498_mm9 Total Tags = 1.63e+07, normalized to 1.00e+07

4.02 -

0 _

C10_Ebf1_SRR4167499_mm9 Total Tags = 9.86e+07, normalized to 1.00e+07

33.65 -

0 _

preBAdh_Tead1_SRR4241652_mm9 Total Tags = 2.26e+07, normalized to 1.00e+07

53.75 -

0 _

haC10_Foxo1_SRR2125714_mm9 Total Tags = 1.63e+07, normalized to 1.00e+07

4 -

0 _

rag2KO_proB_Ebf1_rep2_SRR3222626_mm9 Total Tags = 2.77e+07, normalized to 1.00e+07

35.96 -

0 _

proB_p300_ChIPseq_SRR543411_mm9 Total Tags = 2.26e+07, normalized to 1.00e+07

10.98 -

0 _

rag2KO_proB_Ebf1_SRR3222625_mm9 Total Tags = 1.38e+07, normalized to 1.00e+07

37.93 -

0 _

proB_Ebf1_Yin_SRR057383_mm9 Total Tags = 2.60e+06, normalized to 1.00e+07

38.82 -

0 _

proB_Foxo_Yin_SRX021879_mm9 Total Tags = 1.10e+07, normalized to 1.00e+07

29.54 -

0 _

proB_rad21_Yin_SRR543409_mm9 Total Tags = 1.22e+07, normalized to 1.00e+07

31.63 -

0 _

WT_proB_Ebf1_SRR2040083_mm9 Total Tags = 2.37e+07, normalized to 1.00e+07

15.1 -

0 _

TH_proB_Ebf1_SRX1038472_mm9 Total Tags = 3.24e+07, normalized to 1.00e+07

11.39 -

0 _

R12B_Cont_proB_ATAC_KM3801_rep1_mm9 Total Tags = 1.85e+07, normalized to 1.00e+07

100 -

5 _

R12B_Cont_proB_ATAC_KM3802_rep2_mm9_reduced_20Mio Total Tags = 3.20e+07, normalized to 1.00e+07

83.8 -

0 _

R12BEn_del_proB_ATAC_KM3803_rep1_mm9_reduced_20Mio Total Tags = 3.20e+07, normalized to 1.00e+07

76.89 -

0 _

R12BEn_del_proB_ATAC_KM3804_rep2_mm9 Total Tags = 1.37e+07, normalized to 1.00e+07

42 -

5 _

R12BEn_Cont_preB_ATAC_KM3805_mm9_reduced_20Mio Total Tags = 3.23e+07, normalized to 1.00e+07

73.07 -

0 _

R12BEn_Cont_preB_ATAC_KM3806_mm9 Total Tags = 1.44e+07, normalized to 1.00e+07

60 -

5 _

R12BEn_del_preB_ATAC_KM3807_mm9 Total Tags = 1.11e+07, normalized to 1.00e+07

63 -

5 _


72 -

5 _

8946_ICN1_rep1_SRR1812024_mm9 Total Tags = 1.72e+07, normalized to 1.00e+07

40 -

4 _

8946_Rbpj_SRR1812026_mm9 Total Tags = 2.38e+07, normalized to 1.00e+07

55 -

4 _

DN2_ATAC_thymoDKO_SRR5082029_mm9 Total Tags = 2.47e+07, normalized to 1.00e+07

84.77 -

0 _

ATAC_Tcf1_Cont_DP_rep1_SRR5582460_mm9_reduced_25Mio Total Tags = 3.96e+07, normalized to 1.00e+07

56.35 -

0 _

OP9_DN2_rep1_ATAC_SRR5082025_mm9 Total Tags = 4.25e+07, normalized to 1.00e+07

52.62 -

0 _

day2_DN4_E2A_SRR307057_mm9 Total Tags = 8.42e+06, normalized to 1.00e+07

11.87 -

0 _

ATAC_Tcf1_KO_DP_rep2_SRR5582463_mm9_reduced_19Mio Total Tags = 3.36e+07, normalized to 1.00e+07

18.38 -

0 _

ATAC_Tcf1_KO_DP_SRR5582462_mm9_reduced_19Mio Total Tags = 3.29e+07, normalized to 1.00e+07

16.17 -

0 _

DN2_ATAC_thymoDKO_rep2_SRR5082030_mm9 Total Tags = 1.96e+07, normalized to 1.00e+07

87.83 -

0 _

WT_DN2_CTCF_ChIPseq_SRR5082054_mm9 Total Tags = 2.32e+07, normalized to 1.00e+07

48.56 -

0 _

Thymus_CTCF_GSM918734_mm9 Total Tags = 1.69e+07, normalized to 1.00e+07

56.1 -

0 _

DN2_15min_cont_SMC3_ChIPseq_SRR5276340_mm9_reduced_25Mio Total Tags = 2.50e+07, normalized to 1.00e+07

23.02 -

0 _

WT_DP_Smc1a_rep1_SRR1575166_mm9 Total Tags = 4.87e+07, normalized to 1.00e+07

212.6 -

0 _

proB_CTCF_SRR543408_mm9 Total Tags = 1.04e+07, normalized to 1.00e+07

75.35 -

0 _

R2En-DN3-1_ATAC_KM3105_mm9 Total Tags = 2.18e+07, normalized to 1.00e+07

112.42 -

0 _


117.78 -

0 _

B6-DN3-2_ATAC_KM3108_mm9 Total Tags = 1.92e+07, normalized to 1.00e+07

97.98 -

0 _

B6-2_ATAC_KM3104_mm9 Total Tags = 1.72e+07, normalized to 1.00e+07

125 -

0 _

R2En-DP-1_ATAC_KM3101_mm9 Total Tags = 2.02e+07, normalized to 1.00e+07

125 -

0 _


174.34 -

0 _

A12-E2A-E47ER_6h Total Tags = 2.51e+06, normalized to 1.00e+07

115.6 -

0 _

E2A_d0_mm9 Total Tags = 8.49e+06, normalized to 1.00e+07

23.3 -

0 _

Id_dKO_Thy_p300_KM_2205_R1_ChIPseq_mm9 Total Tags = 9.78e+06, normalized to 1.00e+07

158.24 -

0 _

mT-ALL_SRR1577081_mm9 Total Tags = 1.35e+07, normalized to 1.00e+07

82.88 -

0 _

B6_DP_Bcl11b_rep2_SRR3269915_mm9 Total Tags = 3.46e+07, normalized to 1.00e+07

60 -

4 _

WT_DP_Ikaros_SRR1565988_mm9 Total Tags = 2.49e+07, normalized to 1.00e+07

12 -

4 _

B6_DP_Tcf1_SRR846897_mm9 Total Tags = 1.59e+07, normalized to 1.00e+07

135.33 -

0 _

DP_Runx1_ChIPseq_SRR770062_mm9 Total Tags = 5.44e+06, normalized to 1.00e+07

31 -

4 _

DP_Gata3_SRR038545_mm9spc Total Tags = 6.34e+06, normalized to 1.00e+07

85 -

4 _

WT_DP_K27ac_rep1_SRR1575161_mm9_reduced_30Mio Total Tags = 3.00e+07, normalized to 1.00e+07

104 -

4 _

OP9_DN3_Bcl11b_ChIPseq_rep1_SRR5171243_mm9spc Total Tags = 2.54e+07, normalized to 1.00e+07

42 -

4 _

WT_DN3_Ikaros_SRR1565986_mm9 Total Tags = 1.99e+07, normalized to 1.00e+07

80 -

5 _

OP9_FLDN2b_Gata3_ChIPseq_SRR330838_mm9spc Total Tags = 1.88e+07, normalized to 1.00e+07

65 -

5 _

OP9_FLDN2b_PU.1_ChIPseq_SRR330835_mm9spc Total Tags = 1.80e+07, normalized to 1.00e+07

60 -

5 _

OP9_FLDN1_Gata3_ChIPseq_SRR330837_mm9spc Total Tags = 3.16e+07, normalized to 1.00e+07

52.93 -

0 _

DN_Gata3_SRR038544_mm9spc Total Tags = 6.22e+06, normalized to 1.00e+07

118.11 -

0 _

OP9_FLDN2a_PU.1_ChIPseq_SRR330834_mm9spc Total Tags = 9.37e+06, normalized to 1.00e+07

523.81 -

0 _

thyDP_TCRaKO_Gata3_ChIPseq_SRR330839_mm9spc Total Tags = 8.52e+06, normalized to 1.00e+07

241.17 -

-0.05 _

OP9_FLDN1_PU.1_ChIPseq_SRR330833_mm9spc Total Tags = 8.95e+06, normalized to 1.00e+07

315.92 -

0 _


102.88 -

0 _

thyDP_TCRaKO_PU.1_ChIPseq_SRR330836_mm9spc Total Tags = 2.00e+07, normalized to 1.00e+07

8.8 -

0 _

gdT_Notch1_SRR1236287_mm9 Total Tags = 3.09e+07, normalized to 1.00e+07

50.17 -

0 _

LTHSC.34+.BM_1_ATAC_SRR5799537_wo_chrM_mm9 Total Tags = 1.10e+07, normalized to 1.00e+07

46 -

5 _

LTHSC.34-.BM_1_ATAC_SRR5799538_wo_chrM_mm9 Total Tags = 8.42e+06, normalized to 1.00e+07

78.75 -

0 _

STHSC.150-.BM_1_ATAC_SRR5799539_wo_chrM_mm9 Total Tags = 8.98e+06, normalized to 1.00e+07

50 -

5 _

MMP3.48+.BM_1_ATAC_SRR5799528_wo_chrM_mm9 Total Tags = 8.89e+06, normalized to 1.00e+07

58 -

5 _


100 -

5 _

proB.FrA.BM_1_ATAC_SRR5799448_wo_chrM_mm9 Total Tags = 9.07e+06, normalized to 1.00e+07

76 -

5 _

proB.FrBC.BM_1_ATAC_SRR5799450_wo_chrM_mm9 Total Tags = 9.60e+06, normalized to 1.00e+07

82 -

5 _

preB.FrD.BM_2_ATAC_SRR5799453_wo_chrM_mm9 Total Tags = 8.50e+06, normalized to 1.00e+07

95 -

5 _

B.FrE.BM_2_ATAC_SRR5799455_wo_chrM_mm9 Total Tags = 8.04e+06, normalized to 1.00e+07

68 -

5 _

CMP_ATAC_SRX667510_wo_chrM_mm9 Total Tags = 2.77e+07, normalized to 1.00e+07

96 -

5 _

MEP_ATAC_SRX667511_wo_chrM_mm9 Total Tags = 2.23e+07, normalized to 1.00e+07

43 -

4 _

GMP_ATAC_SRX667503_wo_chrM_mm9 Total Tags = 2.68e+07, normalized to 1.00e+07

47 -

5 _

GN.BM_2_ATAC_SRR5799406_wo_chrM_mm9 Total Tags = 1.01e+07, normalized to 1.00e+07

28 -

4 _

EryA_ATAC_SRR3001797_wo_chrM_mm9 Total Tags = 5.15e+06, normalized to 1.00e+07

130 -

5 _

ILC2.SI_1_ATAC_SRR5799483_wo_chrM_mm9 Total Tags = 1.14e+07, normalized to 1.00e+07

39 -

4 _


99.67 -

0 _


67.22 -

0 _


75.04 -

0 _


35.12 -

0 _

proB.CLP.BM_2_ATAC_SRR5799447_wo_chrM_mm9 Total Tags = 7.67e+06, normalized to 1.00e+07

119.11 -

0 _

preT.DN1.Th_2_ATAC_SRR5799384_wo_chrM_mm9 Total Tags = 7.68e+06, normalized to 1.00e+07

86.35 -

0 _

preT.DN2a.Th_2_ATAC_SRR5799386_wo_chrM_mm9 Total Tags = 6.95e+06, normalized to 1.00e+07

103.28 -

0 _

preT.DN2b.Th_1_ATAC_SRR5799387_wo_chrM_mm9 Total Tags = 7.87e+06, normalized to 1.00e+07

74.62 -

0 _

T.DN4.Th_1_ATAC_SRR5799390_wo_chrM_mm9 Total Tags = 8.65e+06, normalized to 1.00e+07

65.35 -

0 _

T.DP.Th_2_ATAC_SRR5799547_wo_chrM_mm9 Total Tags = 1.79e+07, normalized to 1.00e+07

24.95 -

0 _


50 -

5 _

T.ISP.Th_2_ATAC_SRR5799393_wo_chrM_mm9 Total Tags = 6.52e+06, normalized to 1.00e+07

31 -

4 _


36 -

4 _


84.25 -

0 _


50 -

5 _

preT.DN1.Th_rep1_ATAC_SRR5799383_wo_chrM_mm9 Total Tags = 6.81e+06, normalized to 1.00e+07

48 -

5 _


40 -

4 _


56 -

5 _


60 -

5 _


55 -

5 _


60 -

5 _

B6-DP-1_ATAC_KM3103_mm9 Total Tags = 2.51e+07, normalized to 1.00e+07

95 -

5 _

ATAC_Cont_KM80123_trimmed_mm9 Total Tags = 8.52e+07, normalized to 1.00e+07

66 -

5 _

T.8.Th_1_ATAC_SRR5799396_wo_chrM_mm9 Total Tags = 1.02e+07, normalized to 1.00e+07

88 -

5 _

Tgd.g2+d17.24a+.Th_1_ATAC_SRR5799422_wo_chrM_mm9 Total Tags = 9.43e+06, normalized to 1.00e+07

48 -

5 _

Tgd.g1.1+d1.24a+.Th_2_ATAC_SRR5799427_wo_chrM_mm9 Total Tags = 7.19e+06, normalized to 1.00e+07

183 -

0 _


69.89 -

0 _

Tgd.g2+d1_1_ATAC_SRR5799424_wo_chrM_mm9 Total Tags = 1.03e+07, normalized to 1.00e+07

54.74 -

0 _


53.83 -

0 _


45 -

4 _


148.17 -

0 _


70.87 -

0 _


62.2 -

0 _


21 -

3 _


90.11 -

0 _

dKO.methyC

1 -

0 _

Cont.methyC

1 -

0 _

Lymp.methyC

1 -

0 _

preproB.methyC

1 -

0 _

proB.methyC

1 -

0 _

proT.methyC

1 -

0 _

Cont_CTCF_ChIPseq_KM2704_R1_truseq_trimmed_mm9 Total Tags = 2.58e+07, normalized to 1.00e+07

23.51 -

0 _

Cont_p300_ChIPseq_KM2704_R1_truseq_trimmed_mm9 Total Tags = 2.68e+07, normalized to 1.00e+07

2.38 -

0 _

Cont_E2A_ChIPseq_KM2706_R1_truseq_trimmed_mm9 Total Tags = 2.14e+07, normalized to 1.00e+07

4.38 -

0 _

Myc_MP_ChIPseq_SRR5100876_mm9 Total Tags = 1.26e+07, normalized to 1.00e+07

7.4 -

0 _

ATAC_Cont2_KM802_trimmed_mm9 Total Tags = 2.85e+07, normalized to 1.00e+07

141.47 -

0 _


133.75 -

0 _

ATAC_lymphoma_KM1402_trimmed Total Tags = 9.35e+07, normalized to 1.00e+07

68.89 -

0 _

ATAC_lymohoma_KM2403_trimmed50 Total Tags = 4.90e+07, normalized to 1.00e+07

179.8 -

0 _

DN2_15min_cont_polII_SRR5276334_mm9_reduced_25Mio Total Tags = 2.50e+07, normalized to 1.00e+07

10.73 -

0 _

Thymus_polII_GSM918742_mm9 Total Tags = 2.06e+07, normalized to 1.00e+07

59.66 -

0 _

Thymus 8w Pol2

17.3228 -

0.191412 _

Thymus H3K4m1

13.2375 -

0.116118 _

Thymus H3K4m3

56.3006 -

0.121863 _

Thymus H3K27m3

3.76 -

0.13 _

Thymus H3K36m3

4.65 -

0.12 _

Thymus 8w CTCF5 -

0.2 _

Thymus H3K27a5 -

0.2 _

WT_LSK_K3K27me3_exp1_SRR1565982_mm9 Total Tags = 1.78e+07, normalized to 1.00e+07

12.25 -

0 _

WT_DN1_K3K27me3_SRR1565963_mm9 Total Tags = 3.28e+07, normalized to 1.00e+07

9.96 -

0 _


9.92 -

0 _


26.29 -

0 _


21.84 -

0 _

WT_DP_H3K27me3_SRR038558_mm9 Total Tags = 7.50e+06, normalized to 1.00e+07

56.81 -

0 _


50.74 -

0 _

Cont_CD4_H3K4me3_KM703_R1_mm9 Total Tags = 2.03e+07, normalized to 1.00e+07

156.15 -

0 _

Cont_CD4_H3K27ac_KM704_R1_mm9 Total Tags = 2.01e+07, normalized to 1.00e+07

11.9 -

0 _


13.67 -

0 _

Cont_CD4_Inp_KM705_R1_mm9 Total Tags = 1.59e+07, normalized to 1.00e+07

4.21 -

0 _

GSM310074_mm9-Th2-13hr-Stat5a Total Tags = 8.30e+06, normalized to 1.00e+07

37.37 -

0 _

GSM310075_mm9-Th2-13hr-Stat5b Total Tags = 9.02e+06, normalized to 1.00e+07

58.71 -

0 _

ivTh1_Dec1_SRR6988802_mm9 Total Tags = 3.56e+07, normalized to 1.00e+07

46.84 -

0 _

chr2:98,600,001-103,600,000

Scalechr2:

5M

R2TEn

RatHuman

OrangutanDog

HorseOpossum

ChickenStickleback

UCSC Genes

capture_region


Ensembl Genes

2 Mb mm9100,000,000 101,000,000 102,000,000 103,000,000





R1bEn


R2bEnR1Enpro_common

R1bEn



R2TEn_E2A_2nd_peak





R1bEn


Rag2Rag1

Traf6Traf6


Ldlrad3Ldlrad3

Trim44Fjx1Pamr1

Slc1a2Slc1a2

Slc1a2Slc1a2

Cd44Cd44

Cd44Cd44Cd44Cd44

PdhxApipApipApip

EhfElf5Elf5CatAbtb2

Nat10

RH126499G36984

D2MIT184



D2MIT438

M64796M29475

D2MIT161

D84655AI851288

2600010E01RIKD2MIT249

D2MIT251D6J1

FJX1

RH126741D43796

AI159670

CD44

AI481367

D2MIT388

D2MIT12

D2MIT250D2MIT389

AF035527

D2MIT97

L25069

AW539457AI429152



02.MMHAP67FRA8.SEQ


PMC21337P1BB208787



RH124837

RH135925MGI:3611292

40.MMHAP94FRF10.SEQ


BB307780RH136410

M-08449

lincR-Cd44-5S


63.95 -

0 _


6.68193 -

-1.10677 _


6.99369 -

-0.862841 _


6.90637 -

-0.904012 _


6.53133 -

-1.04978 _


6.53132 -

-1.0516 _


7.02443 -

-1.07212 _


7.09612 -

-0.950657 _


6.6084 -

-1.12868 _


7.03812 -

-0.986293 _


7.85854 -

-0.99462 _


6.73827 -

-1.21367 _


6.193 -

-1.34423 _

0 -


0.521073 -

-0.920175 _

0 -


1.98662 -

-0.597458 _


0.316689 -

0 _


1.98627 -

-0.599627 _


0.315962 -

0 _


0.243608 -

0 _


1.64819 -

-1.12609 _

0 -


8484.45 -

0 _


1.845 -

-1.23542 _

0 -


0.213107 -

0 _


1.81825 -

-0.38647 _


0.291518 -

0 _


2.04591 -

-0.393245 _


0.271412 -

0 _


8000.91 -

0 _


0.241807 -

0 _


1.55545 -

-1.46394 _


0.225621 -

0 _


1.9046 -

-0.722723 _

0 -


8792.47 -

0 _


0.415157 -

0 _


1.36294 -

-1.34024 _


2.26075 -

-0.970977 _

0 -


0.257815 -

0 _


8682.57 -

0 _


0.912272 -

-1.1266 _


8684.93 -

0 _


0.197886 -

0 _


0.185118 -

0 _


80.59 -

0 _


84.39 -

0 _


91.87 -

0 _


63.87 -

0 _


21.55 -

0 _


10.63 -

-0.05 _


7.31 -

0 _


33.3 -

0 _


154.83 -

0 _


19.21 -

0 _


42.39 -

0 _


38.4 -

0 _


33.51 -

0 _


73.36 -

0 _


45.31 -

0 _


97.85 -

0 _


30.09 -

0 _


47.93 -

0 _


26.36 -

0 _


67.76 -

0 _


77.31 -

0 _


82.31 -

0 _


6.07962 -

-5.02661 _

0 -


5.92912 -

-5.50629 _


3.57126 -

-2.67824 _

0 -


2.94087 -

-2.67216 _


3.72397 -

-3.8282 _


3.72399 -

-3.83718 _


5.06659 -

-4.82989 _


4.9661 -

-3.86829 _

0 -


5.26336 -

-3.18212 _

0 -


4.18498 -

-3.63586 _

0 -


5.64464 -

-3.53896 _

0 -


3.88639 -

-3.39212 _


1 -

-1 _

WT_DP_HiC_KM40 PC1

1.26523 -

-1.27631 _


1.27106 -

-1.31777 _


1.41234 -

-1.22558 _


1.4378 -

-1.13167 _


1.42539 -

-1.23421 _


1.42511 -

-1.23416 _


1.36541 -

-1.26966 _


1.35785 -

-1.2689 _


1.32558 -

-1.25762 _


1.48659 -

-1.20179 _


1.45955 -

-1.25405 _


1.6531 -

-1.09518 _

0 -


1.68212 -

-1.08445 _

0 -


1.28393 -

-1.31009 _


68.54 -

0 _


51 -

0 _


37 -

0 _


22.72 -

0 _


24.77 -

0 _


38.44 -

0 _


2.56 -

0 _


16.71 -

0 _


9.78 -

0 _


54.79 -

0 _


50 -

0 _


48.71 -

0 _


19.54 -

0 _


12.4 -

0 _


36.34 -

0 _


55.4 -

0 _


6.73 -

0 _


108.05 -

0 _


57.66 -

0 _


42.01 -

0 _


50.38 -

0 _


8 -

0 _


4.02 -

0 _


33.65 -

0 _


53.75 -

0 _


4 -

0 _


35.96 -

0 _


10.98 -

0 _


37.93 -

0 _


38.82 -

0 _


29.54 -

0 _


31.63 -

0 _


15.1 -

0 _


11.39 -

0 _


100 -

5 _


83.8 -

0 _


76.89 -

0 _


42 -

5 _


73.07 -

0 _


60 -

5 _


63 -

5 _


72 -

5 _


40 -

4 _


55 -

4 _


84.77 -

0 _


56.35 -

0 _


52.62 -

0 _


11.87 -

0 _


18.38 -

0 _


16.17 -

0 _


87.83 -

0 _


48.56 -

0 _


56.1 -

0 _


23.02 -

0 _


212.6 -

0 _


75.35 -

0 _


112.42 -

0 _


117.78 -

0 _


97.98 -

0 _


125 -

0 _


125 -

0 _


174.34 -

0 _


115.6 -

0 _


23.3 -

0 _


158.24 -

0 _


82.88 -

0 _


60 -

4 _


12 -

4 _


135.33 -

0 _


31 -

4 _


85 -

4 _


104 -

4 _


42 -

4 _


80 -

5 _


65 -

5 _


60 -

5 _


52.93 -

0 _


118.11 -

0 _


523.81 -

0 _


241.17 -

-0.05 _


315.92 -

0 _


102.88 -

0 _


8.8 -

0 _


50.17 -

0 _


46 -

5 _


78.75 -

0 _


50 -

5 _


58 -

5 _


100 -

5 _


76 -

5 _


82 -

5 _


95 -

5 _


68 -

5 _


96 -

5 _


43 -

4 _


47 -

5 _


28 -

4 _


130 -

5 _


39 -

4 _


99.67 -

0 _


67.22 -

0 _


75.04 -

0 _


35.12 -

0 _


119.11 -

0 _


86.35 -

0 _


103.28 -

0 _


74.62 -

0 _


65.35 -

0 _


24.95 -

0 _


50 -

5 _


31 -

4 _


36 -

4 _


84.25 -

0 _


50 -

5 _


48 -

5 _


40 -

4 _


56 -

5 _


60 -

5 _


55 -

5 _


60 -

5 _


95 -

5 _


66 -

5 _


88 -

5 _


48 -

5 _


183 -

0 _


69.89 -

0 _


54.74 -

0 _


53.83 -

0 _


45 -

4 _


148.17 -

0 _


70.87 -

0 _


62.2 -

0 _


21 -

3 _


90.11 -

0 _

dKO.methyC

1 -

0 _

Cont.methyC

1 -

0 _

Lymp.methyC

1 -

0 _

preproB.methyC

1 -

0 _

proB.methyC

1 -

0 _

proT.methyC

1 -

0 _


23.51 -

0 _


2.38 -

0 _


4.38 -

0 _


7.4 -

0 _


141.47 -

0 _


133.75 -

0 _


68.89 -

0 _


179.8 -

0 _


10.73 -

0 _


59.66 -

0 _

Thymus 8w Pol2

17.3228 -

0.191412 _

Thymus H3K4m1

13.2375 -

0.116118 _

Thymus H3K4m3

56.3006 -

0.121863 _

Thymus H3K27m3

3.76 -

0.13 _

Thymus H3K36m3

4.65 -

0.12 _

Thymus 8w CTCF5 -

0.2 _

Thymus H3K27a5 -

0.2 _


12.25 -

0 _


9.96 -

0 _


9.92 -

0 _


26.29 -

0 _


21.84 -

0 _


56.81 -

0 _


50.74 -

0 _


156.15 -

0 _


11.9 -

0 _


13.67 -

0 _


4.21 -

0 _


37.37 -

0 _


58.71 -

0 _


46.84 -

0 _

Scalechr2:

5M

R2TEn

RatHuman

OrangutanDog

HorseOpossum

ChickenStickleback

UCSC Genes

capture_region


Ensembl Genes

2 Mb mm9100,000,000 101,000,000 102,000,000 103,000,000





R1bEn


R2bEnR1Enpro_common

R1bEn



R2TEn_E2A_2nd_peak





R1bEn


Rag2Rag1

Traf6Traf6


Ldlrad3Ldlrad3

Trim44Fjx1Pamr1

Slc1a2Slc1a2

Slc1a2Slc1a2

Cd44Cd44

Cd44Cd44Cd44Cd44

PdhxApipApipApip

EhfElf5Elf5CatAbtb2

Nat10

RH126499G36984

D2MIT184



D2MIT438

M64796M29475

D2MIT161

D84655AI851288

2600010E01RIKD2MIT249

D2MIT251D6J1

FJX1

RH126741D43796

AI159670

CD44

AI481367

D2MIT388

D2MIT12

D2MIT250D2MIT389

AF035527

D2MIT97

L25069

AW539457AI429152



02.MMHAP67FRA8.SEQ


PMC21337P1BB208787



RH124837

RH135925MGI:3611292

40.MMHAP94FRF10.SEQ


BB307780RH136410

M-08449

lincR-Cd44-5S


63.95 -

0 _


6.68193 -

-1.10677 _


6.99369 -

-0.862841 _


6.90637 -

-0.904012 _


6.53133 -

-1.04978 _


6.53132 -

-1.0516 _


7.02443 -

-1.07212 _


7.09612 -

-0.950657 _


6.6084 -

-1.12868 _


7.03812 -

-0.986293 _


7.85854 -

-0.99462 _


6.73827 -

-1.21367 _


6.193 -

-1.34423 _

0 -


0.521073 -

-0.920175 _

0 -


1.98662 -

-0.597458 _


0.316689 -

0 _


1.98627 -

-0.599627 _


0.315962 -

0 _


0.243608 -

0 _


1.64819 -

-1.12609 _

0 -


8484.45 -

0 _


1.845 -

-1.23542 _

0 -


0.213107 -

0 _


1.81825 -

-0.38647 _


0.291518 -

0 _


2.04591 -

-0.393245 _


0.271412 -

0 _


8000.91 -

0 _


0.241807 -

0 _


1.55545 -

-1.46394 _


0.225621 -

0 _


1.9046 -

-0.722723 _

0 -


8792.47 -

0 _


0.415157 -

0 _


1.36294 -

-1.34024 _


2.26075 -

-0.970977 _

0 -


0.257815 -

0 _


8682.57 -

0 _


0.912272 -

-1.1266 _


8684.93 -

0 _


0.197886 -

0 _


0.185118 -

0 _


80.59 -

0 _


84.39 -

0 _


91.87 -

0 _


63.87 -

0 _


21.55 -

0 _


10.63 -

-0.05 _


7.31 -

0 _


33.3 -

0 _


154.83 -

0 _


19.21 -

0 _


42.39 -

0 _


38.4 -

0 _


33.51 -

0 _


73.36 -

0 _


45.31 -

0 _


97.85 -

0 _


30.09 -

0 _


47.93 -

0 _


26.36 -

0 _


67.76 -

0 _


77.31 -

0 _


82.31 -

0 _


6.07962 -

-5.02661 _

0 -


5.92912 -

-5.50629 _


3.57126 -

-2.67824 _

0 -


2.94087 -

-2.67216 _


3.72397 -

-3.8282 _


3.72399 -

-3.83718 _


5.06659 -

-4.82989 _


4.9661 -

-3.86829 _

0 -


5.26336 -

-3.18212 _

0 -


4.18498 -

-3.63586 _

0 -


5.64464 -

-3.53896 _

0 -


3.88639 -

-3.39212 _


1 -

-1 _

WT_DP_HiC_KM40 PC1

1.26523 -

-1.27631 _


1.27106 -

-1.31777 _


1.41234 -

-1.22558 _


1.4378 -

-1.13167 _


1.42539 -

-1.23421 _


1.42511 -

-1.23416 _


1.36541 -

-1.26966 _


1.35785 -

-1.2689 _


1.32558 -

-1.25762 _


1.48659 -

-1.20179 _


1.45955 -

-1.25405 _


1.6531 -

-1.09518 _

0 -


1.68212 -

-1.08445 _

0 -


1.28393 -

-1.31009 _


68.54 -

0 _


51 -

0 _


37 -

0 _


22.72 -

0 _


24.77 -

0 _


38.44 -

0 _


2.56 -

0 _


16.71 -

0 _


9.78 -

0 _


54.79 -

0 _


50 -

0 _


48.71 -

0 _


19.54 -

0 _


12.4 -

0 _


36.34 -

0 _


55.4 -

0 _


6.73 -

0 _


108.05 -

0 _


57.66 -

0 _


42.01 -

0 _


50.38 -

0 _


8 -

0 _


4.02 -

0 _


33.65 -

0 _


53.75 -

0 _


4 -

0 _


35.96 -

0 _


10.98 -

0 _


37.93 -

0 _


38.82 -

0 _


29.54 -

0 _


31.63 -

0 _


15.1 -

0 _


11.39 -

0 _


100 -

5 _


83.8 -

0 _


76.89 -

0 _


42 -

5 _


73.07 -

0 _


60 -

5 _


63 -

5 _


72 -

5 _


40 -

4 _


55 -

4 _


84.77 -

0 _


56.35 -

0 _


52.62 -

0 _


11.87 -

0 _


18.38 -

0 _


16.17 -

0 _


87.83 -

0 _


48.56 -

0 _


56.1 -

0 _


23.02 -

0 _


212.6 -

0 _


75.35 -

0 _


112.42 -

0 _


117.78 -

0 _


97.98 -

0 _


125 -

0 _


125 -

0 _


174.34 -

0 _


115.6 -

0 _


23.3 -

0 _


158.24 -

0 _


82.88 -

0 _


60 -

4 _


12 -

4 _


135.33 -

0 _


31 -

4 _


85 -

4 _


104 -

4 _


42 -

4 _


80 -

5 _


65 -

5 _


60 -

5 _


52.93 -

0 _


118.11 -

0 _


523.81 -

0 _


241.17 -

-0.05 _


315.92 -

0 _


102.88 -

0 _


8.8 -

0 _


50.17 -

0 _


46 -

5 _


78.75 -

0 _


50 -

5 _


58 -

5 _


100 -

5 _


76 -

5 _


82 -

5 _


95 -

5 _


68 -

5 _


96 -

5 _


43 -

4 _


47 -

5 _


28 -

4 _


130 -

5 _


39 -

4 _


99.67 -

0 _


67.22 -

0 _


75.04 -

0 _


35.12 -

0 _


119.11 -

0 _


86.35 -

0 _


103.28 -

0 _


74.62 -

0 _


65.35 -

0 _


24.95 -

0 _


50 -

5 _


31 -

4 _


36 -

4 _


84.25 -

0 _


50 -

5 _


48 -

5 _


40 -

4 _


56 -

5 _


60 -

5 _


55 -

5 _


60 -

5 _


95 -

5 _


66 -

5 _


88 -

5 _


48 -

5 _


183 -

0 _


69.89 -

0 _


54.74 -

0 _


53.83 -

0 _


45 -

4 _


148.17 -

0 _


70.87 -

0 _


62.2 -

0 _


21 -

3 _


90.11 -

0 _

dKO.methyC

1 -

0 _

Cont.methyC

1 -

0 _

Lymp.methyC

1 -

0 _

preproB.methyC

1 -

0 _

proB.methyC

1 -

0 _

proT.methyC

1 -

0 _


23.51 -

0 _


2.38 -

0 _


4.38 -

0 _


7.4 -

0 _


141.47 -

0 _


133.75 -

0 _


68.89 -

0 _


179.8 -

0 _


10.73 -

0 _


59.66 -

0 _

Thymus 8w Pol2

17.3228 -

0.191412 _

Thymus H3K4m1

13.2375 -

0.116118 _

Thymus H3K4m3

56.3006 -

0.121863 _

Thymus H3K27m3

3.76 -

0.13 _

Thymus H3K36m3

4.65 -

0.12 _

Thymus 8w CTCF5 -

0.2 _

Thymus H3K27a5 -

0.2 _


12.25 -

0 _


9.96 -

0 _


9.92 -

0 _


26.29 -

0 _


21.84 -

0 _


56.81 -

0 _


50.74 -

0 _


156.15 -

0 _


11.9 -

0 _


13.67 -

0 _


4.21 -

0 _


37.37 -

0 _


58.71 -

0 _


46.84 -

0 _

2

-20

D

E


chr2:101,320,000-102,000,000

DP1.6

-1.3

1.65

-2.3

preB

BMDM

ΔP

C1

(vs H

SC

)Δ

DL

R (

vs H

SC

)

R2/R1gene

DP

preB

BMDM

F

R-TEn

Rag1/2Traf6

Compartment A

R2B

R1B

T/B precursor

CTCF

Cohesin

Macrophage

R-TEn

Rag1/2

Com

partment A

Traf6

Compartment B

R2B

Boundary

(Insulator)

G

R2R1

Traf6

Prr5l Ldlrad3R-TEn

R2BR1BTAD-Bd1 TAD-Bd3

R2R1

Traf6

Prr5l Ldlrad3R-TEn


R2R1

Traf6

Prr5l Ldlrad3R-TEn


DP pre-B BMDM

Fig. S7. Comparative analysis of R-TEn, R1B, and R2B enhancers among vertebrates. (A) Genome browser view of the upstream regions of Rag1 and Rag2 genes among vertebrates. Green regions indicate genomic regions that are similar to human sequences. R1B, R2B and R-TEn are highlighted.

ARag1 Rag2 R-TEnR2BR1B

Lizard(–)Xenopus(–)

Opossum(–)

Ma

mm

al

Bir

dR

ep

tile

Fis

hA

gn

ath

an

s

Am

ph

ibia

≈

≈ ≈


Fig. S7. Comparative analysis of R-TEn, R1B, and R2B enhancers among vertebrates. (B) Genome browser view of R-TEn (B-1) and R2B (B-2) enhancer regions among vertebrates. Green regions indicate genomic regions that are similar to human sequences. Blue dot lines indicate the border between placentalis and maruspialia (B-1), mammal and bird (B-2), turtle and lizard (B-1), and reptile and amphibia (B-1 and B-2).

Fig. S7. Comparative analysis of R-TEn, R1B, and R2B enhancers among vertebrates. (B) Genome browser view of R1B (B-3) enhancer regions among vertebrates. Black regions indicate genomic regions that are similar to human sequences. Blue dot lines indicate the border between placentalis and maruspialia.

R1BM

am

ma

lB

ird

Eu

the

ria

/ P

lace

nta

liaM

aru

sp

ialia

B-3Figure S7 Miyazaki et al.

Fig. S7. Comparative analysis of R-TEn, R1B, and R2B enhancers among vertebrates. (C-1) 100 kb regions containing Rag2 and its upstream sequence are compared among vertebrates in the dot matrix. Tick marks on the axes are placed at 10 kb intervals. Red and Blue dots indicate sequence similarities detected by BLASTN (E-value < 0.1) in the same and opposite orientations, respectively.

human

mouse

armadillo

chicken

zebrafish

Tasmaniandevil

turtle

elephant shark

frog

R2B peak2 (human)

R2B (mouse)

R-TEn (mouse)

hum

an

mouse

arm

ad

illo

ch

icken

fro

g

zebra

fish

Tasm

ania

nde

vil

turt

le

ele

phan

t shark

Rag2 upstream

Rag2 (mouse)

R-TEn peak1 (human)

C-1Figure S7 Miyazaki et al.

Fig. S7. Comparative analysis of R-TEn, R1B, and R2B enhancers among vertebrates. (C-2) Dot plot for the Rag1 upstream regions among vertebrates. The regions containing Rag1 gene and its upstream sequence up to the start of Traf6 are compared. Tick marks on the axes are placed at 10 kb intervals. Red and Blue dots indicate sequence similarities detected by BLASTIN (E-value < 0.1) for the same and opposite orientations, respectively.

human

mouse

armadillo

chicken

zebrafish

tasmaniandevil

turtle

elephant shark

frog

Rag1 (mouse)

R1B (mouse)

Rag1 upstream

hu

ma

n

mo

use

arm

ad

illo

ch

icke

n

fro

g

ze

bra

fish

Ta

sm

an

ian

de

vil

turt

le

ele

ph

an

t sh

ark

C-2Figure S7 Miyazaki et al.

Fig. S7. Comparative analysis of R-TEn, R1B, and R2B enhancers among vertebrates. (D-1) Genome browser view showing the sequence conservation of the R-TEn-peak1 regions. Red boxes indicate seven E-box sequences in R-TEn-peak1 region in mouse (E1-E7). Black regions indicate genomic regions similar to human sequences.

D-1 Figure S7 Miyazaki et al.

200bp

E1E2E3E4E5E6E7

E1; human (-)

E6; human(-)

E7;missing

Ma

mm

al

Bir

dR

ep

tile

Fis

hA

gn

ath

an

s

Am

ph

ibia

R-TEn-peak1

E-box

Fig. S7. Comparative analysis of R-TEn, R1B, and R2B enhancers among vertebrates. (D-2) Upper and lower two panels show the DNA sequences in E-box3 and 4 (E3 and E4), E-box2 (E2), and E-box5 (E5) among vertebrates. E-box motifs in E2 and E3 are conserved among mammals, birds and reptiles. However, E-box motif in E5 is conserved among mammals, but rarely conserved among birds and reptiles. E-box motif in E4 is less conserved among mammals.

E5E2

R-TEn-p1 E-boxD-2

R-TEn-p1 E-box

E3E4

Conservation

100 vertebrates

Mam

ma

lB

ird

Re

ptile

Fis

h

Ag

na

tha

ns

Am

ph

ibia

Ma

mm

al

Bir

dR

ep

tile

Fis

h

Ag

na

tha

ns

Am

ph

ibia

R-TEn-p1 E-box R-TEn-p1 E-box

Conservation

100 vertebrates


Table S1. GSE numbers for figures.

Figure GEO_number

Fig. 1A GSE30518

GSE21978

GSE40173

Fig. 1B GSE30518

GSE21978

GSE90958

GSE40173

GSE26257

Fig. 1C GSE30518

GSE72670

GSE90958

Fig. 1D GSE21978

GSE72670

GSE90958

Fig. 1E GSE79875

GSE61148

GSE46662

GSE44578

GSE20898

GSE86897

GSE109671

Fig. 6A GSE100738

Fig. 6B GSE109671

GSE109965

Fig. 6C GSE109671

GSE109965

GSE61428

GSE109909

GSE49847

GSE108583

Fig. S1A GSE21978

GSE40173

GSE66146

GSE93572

GSE61148

GSE31233

GSE78844

Fig. S1B GSE30518

GSE89847

GSE36027

Fig. S1C GSE86897

GSE21978

Fig. S4A GSE110882

GSE99159

Fig. S4B GSE90958

GSE93572

GSE99159

GSE46662

Fig. S4C DRP003376

GSE90635

GSE61428

Fig. S4J GSE61428

GSE90635

Fig. S6A GSE90958

GSE109671

GSE79422

GSE100738

GSE105918

Fig. S6B, S6C GSE90958

GSE109671

GSE109965

GSE79422

GSE105918

GSE99151

Fig. S6D GSE109671

GSE109965

Fig. S6E GSE79422

GSE109671

GSE115524

Fig. S6G GSE79422

GSE109671

GSE109965

Table S2. Tag density at enhancer regions.

peak_name R-TEn-peak1 R-TEn-peak2 R2B-peak1 R2B-peak2 R1B

Chr chr2 chr2 chr2 chr2 chr2

Start 101391496 101392573 101439010 101440789 101505598

End 101391696 101392773 101439210 101440989 101505798

DN3:E2A ChIPseq Normalized Tag Count 23.09 9.45 2.1 1.05 3.15

A12(DP):E2A ChIPseq Normalized Tag Count 156.4 50.92 0 7.27 43.65

proB:E2A ChIPseq Normalized Tag Count 0 0 32.14 51.79 82.14

proB:p300 ChIPseq Normalized Tag Count 0.98 0.19 4.7 7.44 5.29

DP:Bcl11b ChIPseq Normalized Tag Count 86.78 28.35 1.45 4.05 5.5

DP:Ikaros ChIPseq Normalized Tag Count 20.5 6.43 4.02 1.61 1.61

DP:Tcf１ ChIPseq Normalized Tag Count 163.32 28.27 18.84 6.28 8.79

DP:Runx1 ChIPseq Normalized Tag Count 44.13 3.68 0 1.84 0

DP:Gata3 ChIPseq Normalized Tag Count 56.78 1.58 4.73 1.58 0

preB:E2A ChIPseq Normalized Tag Count 0.92 0.46 10.61 56.73 66.87

preB:Ebf1 ChIPseq Normalized Tag Count 1.84 0.61 9.79 13.46 7.34

preB:Pax5 ChIPseq Normalized Tag Count 0.93 0 219.05 16.31 27.96

preB:Ets1 ChIPseq Normalized Tag Count 0.86 0.43 15.89 16.32 5.58

preB:Ikaros ChIPseq Normalized Tag Count 1.42 0 40.61 64.69 15.11

preB:Irf4 ChIPseq Normalized Tag Count 0 0 9.93 6.62 5.52

8946Tcell_leukemia_cell:ICN1 ChIPseq Normalized Tag Count 41.27 4.65 0 2.33 2.33

8946Tcell_leukemia_cell:Rbpj ChIPseq Normalized Tag Count 60.49 20.58 3.78 12.18 9.24

DN3:Bcl11b ChIPseq Normalized Tag Count 79.94 3.94 11.42 24.42 7.09

DN3:Ikaros ChIPseq Normalized Tag Count 89.36 13.55 17.57 9.54 10.54

DN2b:Gata3 ChIPseq Normalized Tag Count 16.52 1.07 1.07 1.07 0.53

DN2b:PU.1 ChIPseq Normalized Tag Count 6.1 0 0 3.88 5.55

DN3:Ctrl_ATAC Normalized Tag Count 62.19 14.87 18.78 12.92 18.18

DN3:R-TEnd/d _ATAC Normalized Tag Count 0 0 14.66 14.4 29.83

DP:Ctrl_ATAC Normalized Tag Count 107.73 136.78 18.22 23.52 45.18

DP:R-TEnd/d _ATAC Normalized Tag Count 0 0 0.5 1.38 33.21

proB:Ctrl_ATAC Normalized Tag Count 0.68 0 55.4 110.69 84.98

proB:R1Bd/dR2Bd/d _ATAC Normalized Tag Count 0.75 0.5 0 0 0

preB:Ctrl_ATAC Normalized Tag Count 1.36 3.46 29.79 43.02 86.53

preB: R1Bd/dR2Bd/d _ATAC Normalized Tag Count 2.15 1.51 0 0 0

DP:Tcf3/Tcf12 Ctrl_ATAC Normalized Tag Count 63.43 89.18 4.5 7.31 20.47

DP: Tcf3/Tcf12 dKO _ATAC Normalized Tag Count 19.17 17.04 10.33 5.11 14.91

DP:R-TEn-p1-Ebox_Ctrl_ATAC Normalized Tag Count 74.66 85.7 10.12 11.65 24.99

DP:R-TEn-p1-Ebox_Mut_ATAC Normalized Tag Count 0 0.28 0.56 2.36 21.28

DN3:R1pro-Ebox_Ctrl_ATAC Normalized Tag Count 45.12 7.22 6.62 10.83 10.23

DN3:R1pro-Ebox_Mut_ATAC Normalized Tag Count 33.86 6.57 9.6 8.08 6.57

proB:R1pro-Ebox_Ctrl_ATAC Normalized Tag Count 1.61 0.54 75.24 116.08 105.87

proB:R1pro-Ebox_Mut_ATAC Normalized Tag Count 0 0.98 79.58 121.08 85.44

supplementary materials for · 2020. 8. 31. · quantified by thunderbird sybr qpcr mix (toyobo)...

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