Supplemental Figures and Figure Legends

Source Hirst REMC 1 Source Hirst REMC Source Hirst Source

1 0.9 0.8 0.7 0.6 0.9 REMC 1 0.9 0.8 0.7 0.6 Source Source B Penis_Foreskin_Melanocyte_Primary_Cells_skin03 Penis_Foreskin_Melanocyte_Primary_Cells_skin01 Penis_Foreskin_Melanocyte_Primary_Cells_skin03 0.8HUVEC Penis_Foreskin_Melanocyte_Primary_Cells_skin01 Penis_Foreskin_Fibroblast_Primary_Cells_skin02 Penis_Foreskin_Fibroblast_Primary_Cells_skin01 HUVEC H1_Derived_Mesenchymal_Stem_Cells Penis_Foreskin_Fibroblast_Primary_Cells_skin02 NHLF 0.7HSMM Penis_Foreskin_Fibroblast_Primary_Cells_skin01 Universal_Human_Reference H1_Derived_Mesenchymal_Stem_Cells NHEK Breast_vHMEC NHLF HMEC HSMM Penis_Foreskin_Keratinocyte_Primary_Cells_skin03 0.6Penis_Foreskin_Keratinocyte_Primary_Cells_skin02 Universal_Human_Reference Breast_Myoepithelial_Cells NHEK HELA A549 Breast_vHMEC HEPG2 HMEC hESC_Derived_CD56+_Mesoderm_Cultured_Cells Penis_Foreskin_Keratinocyte_Primary_Cells_skin03 H1_BMP4_Derived_Trophoblast_Cultured_Cells HUES64_Cell_Line Penis_Foreskin_Keratinocyte_Primary_Cells_skin02 H1_BMP4_Derived_Mesendoderm_Cultured_Cells Breast_Myoepithelial_Cells 4star H1_Cell_Line HELA hESC_Derived_CD56+_Ectoderm_Cultured_Cells A549 H1_Derived_Neuronal_Progenitor_Cultured_Cells hESC_Derived_CD184+_Endoderm_Cultured_Cells HEPG2 Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived hESC_Derived_CD56+_Mesoderm_Cultured_Cells Neurosphere_Cultured_Cells_Cortex_Derived Brain_Germinal_Matrix H1_BMP4_Derived_Trophoblast_Cultured_Cells Fetal_Brain_Female HUES64_Cell_Line Brain_Hippocampus_Middle Pancreas H1_BMP4_Derived_Mesendoderm_Cultured_Cells Pancreatic_Islets 4star Fetal_Intestine_Small Fetal_Intestine_Large H1_Cell_Line Lung hESC_Derived_CD56+_Ectoderm_Cultured_Cells Gastric Esophagus H1_Derived_Neuronal_Progenitor_Cultured_Cells Small_Intestine hESC_Derived_CD184+_Endoderm_Cultured_Cells Sigmoid_Colon Aorta Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived Right_Ventricle Neurosphere_Cultured_Cells_Cortex_Derived Left_Ventricle Brain_Germinal_Matrix Right_Atrium Psoas_Muscle Fetal_Brain_Female Ovary Brain_Hippocampus_Middle Spleen Thymus Pancreas Adult_Liver Pancreatic_Islets K562

GM12878 Cluster Blood Fetal_Intestine_Small Erythroid Fetal_Intestine_Large BCell Monocyte Lung CD8_Naive_Primary_Cells Gastric CD4_Naive_Primary_Cells CD4_Memory_Primary_Cells Esophagus TCell2 Small_Intestine TCell1 Peripheral_Blood_Mononuclear_Primary_Cells Sigmoid_Colon Mobilized_CD34_Primary_Cells_Female Aorta MEP GMP Right_Ventricle CMP Left_Ventricle CD34.CD38. Right_Atrium Psoas_Muscle Ovary Spleen Thymus Adult_Liver K562 GM12878 Erythroid BCell 1 Monocyte CD8_Naive_Primary_Cells CD4_Naive_Primary_Cells CD4_Memory_Primary_Cells TCell2 TCell1 Peripheral_Blood_Mononuclear_Primary_Cells Mobilized_CD34_Primary_Cells_Female MEP GMP CMP CD34.CD38. CD34.CD38. CMP GMP MEP Mobilized_CD34_Primary_Cells_Female Peripheral_Blood_Mononuclear_Primary_Cells TCell1 TCell2 CD4_Memory_Primary_Cells CD4_Naive_Primary_Cells CD8_Naive_Primary_Cells Monocyte BCell Erythroid GM12878 K562 Adult_Liver Thymus Spleen Ovary Psoas_Muscle Right_Atrium Left_Ventricle Right_Ventricle Aorta Sigmoid_Colon Small_Intestine Esophagus Gastric Lung Fetal_Intestine_Large Fetal_Intestine_Small Pancreatic_Islets Pancreas Brain_Hippocampus_Middle Fetal_Brain_Female Brain_Germinal_Matrix Neurosphere_Cultured_Cells_Cortex_Derived Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived hESC_Derived_CD184+_Endoderm_Cultured_Cells H1_Derived_Neuronal_Progenitor_Cultured_Cells hESC_Derived_CD56+_Ectoderm_Cultured_Cells H1_Cell_Line 4star H1_BMP4_Derived_Mesendoderm_Cultured_Cells HUES64_Cell_Line H1_BMP4_Derived_Trophoblast_Cultured_Cells hESC_Derived_CD56+_Mesoderm_Cultured_Cells HEPG2 A549 HELA Breast_Myoepithelial_Cells Penis_Foreskin_Keratinocyte_Primary_Cells_skin02 Penis_Foreskin_Keratinocyte_Primary_Cells_skin03 HMEC Breast_vHMEC NHEK Universal_Human_Reference HSMM NHLF H1_Derived_Mesenchymal_Stem_Cells Penis_Foreskin_Fibroblast_Primary_Cells_skin01 Penis_Foreskin_Fibroblast_Primary_Cells_skin02 HUVEC Penis_Foreskin_Melanocyte_Primary_Cells_skin01 Penis_Foreskin_Melanocyte_Primary_Cells_skin03 Figure S1. Related to Figure 1. Sorting strategy for hematopoietic populations profiled in this study. A) Representative examples of sorting strategies for CD34+CD38-, CMP, GMP, MEP, monocyte, erythroid precursors and B cell isolated from pool of cord blood. B) Unsupervised hierarchical clustering and heatmap of pairwise spearman correlations for protein coding gene RPKM values across blood cell types profiled in this study in the context of all cell types profiled by NIH Epigenome RoadMap Consortium. The cluster of blood cell types is indicated by the shaded box.

A CD14 CD19 CD34 C 250 150 200 60 150 100 40 100 20 50 50 D 0 0 0 CD38 CD7 FLT3 CD34.CD38. 60 CMP GMP 60 40 100 MEP 40 Monocyte Erythroid

1.00 RPKM RPKM 20 50 E 20 BCell TCell1 0 0 0 3 GYPA ITGAM PTPRC black 1.00 2000 80 300 1500 60 1000 40 200 F 500 20 100 0 2 0 0

B G H Log10(q-value) 0.75 TAL1 3 3 Mark

22 H3K27me3 1 Mark H3K36me3 H3K27me3 1 1 H3K36me3 H3K4me3 log10(RPKM) H3K4me3

0.75 log10(RPKM) 00

Log10(RPKM) Cell -1-1 - CMP MEP GMP B-Cell T-Cell H1 Monocyte Erythroid 0 CD34+CD38- CMP GMP MEP T Cell MPO B Cell CD34+CD38− MonocyteErythroid CD34+CD38 CMP Cell GMP 0.50 Cella$n Cell H1 MEP CB CD34+ CD38- MPL 1 CD34+CD38− -1CMP Monocyte TFRC 0.5 GMP CMP Erythroid VWF MEP GMP B−Cell 0 0.50 TAL1 Group CMP GMP MEP T-Cell a$n B-CellMEP T−Cell Erythroid/Megakaryocyte EPOR -0.5 Monocyte Erythroid Monocyte/Granulocyte Monocyte GATA1 -1 CD34+CD38-CD34+CD38- Compartment Erythroid GATA3 B−Cell HOXB5 T−Cell ID2 NR4A20.25

IL3RA 3

ELANE CSF2RA CEBPA 0.25 MPO CD33 SPI1 Group

0.00

H1 CD34+CD38− CMP GMP MEP Monocyte Erythroid B−Cell T−Cell a$Cell

0.00

H1 CD34+CD38− CMP GMP MEP Monocyte Erythroid B−Cell T−Cell a$Cell Figure S2. Related to Figure 1. Each progenitor populations possesses a unique expression profile. A) Expression (RPKM) of cell type specific cell surface marker genes across cell types as indicated by the colour legend on the bottom right. B) Expression of previously identified progenitor population specific genes across CD34+CD38-, CMP, GMP and MEP. Gene ontology analysis of GMP (C), MEP (D), CD34+CD38- (E), and CMP (F) up-regulated genes identified by DEFine (FDR > 0.01). G) Genome browser view of H3K4me3 density in progenitor populations at the TAL1 and MPO locus across CD34+CD38-, CMP, GMP and MEP. H) Expression of genes marked with H3K4me3, H3K27me3 or H3K36me3 across each cell type.

a$Cell

Cell − T Cell − B Erythroid Monocyte MEP GMP CMP − CD34+CD38 H1 ✱✱✱ 0.00 DMSO Control ✱✱✱ DMSO Control ✱✱✱ DMSO Control A GMP vs Erythroid GMP vs MEP GMP vs MEP✱✱✱ MEP vs Monocyte ATRA ✱✱✱✱✱✱ DMSOATRA Control ✱✱✱ ATRA 4 ✱✱✱ ✱✱✱ GMP up-regulated GMP up-regulated MEP up-regulated MEP 4up-regulated ✱✱✱ GSK-J4 4 ✱✱✱✱✱✱ ✱✱✱ ATRA GSK-J4 ✱✱✱ ✱✱✱ GSK-J4 ✱✱✱ ✱✱✱ DMSO Control✱✱✱ DMSO Control ✱✱✱ ✱✱✱ 300 4 ✱✱✱ ✱✱✱ ns ✱✱✱ EPZ ✱✱✱ns ✱✱✱ ✱✱✱ ATRA GSK-J4EPZ ATRA ns ✱✱✱ EPZ 4 ✱✱✱ ✱✱✱ DMSO Control ✱✱✱ 4 ✱✱✱ ✱✱✱ ✱✱✱ GSK-J4✱✱✱✱✱✱ GSK-J4 ✱✱✱ CMP ATRA + GSK-J4 ✱✱✱ ✱✱✱ ✱✱✱ DMSO Control ✱✱✱ DMSO Control ns ✱✱✱ ✱✱✱ ✱✱✱EPZ✱✱✱✱✱✱ DMSO ControlATRA✱✱✱ ✱✱✱ ATRA + GSK-J4 ns ✱✱✱ ns ✱✱✱EPZ ✱✱✱ ATRA EPZ + GSK-J4 ✱✱✱ ✱✱✱ ✱✱✱ 4✱✱✱ ATRA ✱✱✱✱✱✱ GMP DMSO ControlATRA✱✱✱ 200 ✱✱✱ ✱✱✱ ✱✱✱ ✱✱✱3 ✱✱✱ DMSO Control ✱✱✱ ns ATRA GSK-J4 ATRA + EPZ ✱✱✱ ✱✱✱ ATRA✱✱✱ + GSK-J4 ATRA + GSK-J4ATRA + GSK-J4 ✱✱✱4 ✱✱✱ 4 ✱✱✱✱✱✱ ✱✱✱ 4 ATRA✱✱✱ +GSK-J4 EPZ 3 ✱✱✱ ✱✱✱✱✱ ns ATRA GSK-J4 ATRA + EPZ ✱✱✱3 ✱✱✱ ns✱✱✱✱✱✱ ✱✱✱ ✱✱✱✱✱✱✱✱✱ns ATRA ✱✱✱ GSK-J4EPZ MEP ✱✱✱ 3 ATRA + EPZ ATRA + EPZ 4 ✱✱✱ ✱✱✱ ✱✱✱ 3 ns ns ✱✱ns✱✱✱ ✱✱✱EPZ ✱✱✱ ns ✱✱✱ GSK-J4EPZ✱✱ 3 ns 4 ✱✱✱✱✱ ✱✱✱ ns✱✱✱✱✱ATRA +GSK-J4 EPZ ✱✱✱ ✱✱✱ EPZ ATRA + GSK-J4 ✱✱✱ ✱✱✱ ✱✱✱ ✱✱✱ ✱✱✱ns✱✱✱ ✱✱✱ Monocyte EPZ ✱✱ ✱✱✱✱✱✱ ✱✱✱ATRA + GSK-J4 ✱✱✱ ✱✱✱✱✱✱ ATRA + GSK-J4 100 ✱✱✱ ✱✱✱ns ✱✱✱ ✱✱✱ 3✱✱✱ EPZ ns ✱✱✱ ATRA +✱✱✱ ATRAGSK-J4 + EPZ ✱✱✱ ✱✱✱ ✱✱✱✱✱✱✱✱✱ ✱✱✱ ✱✱✱ Erythroid ATRA +✱✱✱ GSK-J4 3 ✱✱✱ns ATRA + EPZ ✱✱✱3✱✱ ATRA + EPZ ns ATRA + EPZ ✱✱✱ ✱✱✱ 3 ATRAns + GSK-J4 ✱✱✱ ✱✱

H3K4em3 tag density tag H3K4em3 ✱✱ ✱✱✱2 ✱✱✱ ✱✱✱ 3✱✱ ns ATRA + EPZ 2 ✱✱✱ 2 ATRA + EPZ ✱✱✱ 3 ns ✱✱✱ ✱✱✱ ✱✱✱ ✱✱ Normalized H3K4me3 tags H3K4me3 Normalized ✱✱ ✱✱✱ 2 ✱✱✱ 0 2 ✱✱✱ ✱✱✱ ✱✱✱ 2 ✱✱✱ 2 2 ✱✱✱ 2 B GMP vs Erythroid GMP vs MEP 2 GMP vs MEP MEP vs Monocyte 1 1 2 CMP GMP MEP CMP2 GMP MEP CMP GMP MEP CMP GMP MEP GMP up-regulated GMP up-regulated MEP up-regulated MEP up-regulated MonocyteErythroid MonocyteErythroid 1 MonocyteErythroid MonocyteErythroid ✱✱✱ 1 ✱✱✱ DMSO Control DMSO Control 1 1 1 1 ✱✱✱ DMSO Control ✱✱✱ DMSO Control

0 ✱✱✱ 0 ✱✱✱✱✱✱✱✱✱ ✱✱✱✱✱✱ ATRADMSO Control 1 DMSO✱✱✱✱✱✱ ControlATRA DMSO ControlDMSO Control

✱✱✱✱✱✱ 1 4 3 days ATRA 6 days 4 9DMSO days✱✱✱ Control ✱✱✱ DMSO Control 1 3 days 6 days 9 days✱✱✱ DMSO ✱✱✱Control ✱✱✱ ATRAGSK-J4 0.25 CMP ✱✱✱ ATRAGSK-J4 ✱✱✱✱✱✱ ATRA 4 ✱✱✱ ✱✱✱ GSK-J4 4 ✱✱✱ ✱✱✱ ✱✱✱ DMSO Control ✱✱✱ 4 ✱✱✱✱✱✱ ATRA✱✱✱✱✱✱ 0 ✱✱✱✱✱✱ns ✱✱✱ 4 ATRA EPZ GSK-J4✱✱✱ 40 ✱✱✱ ✱✱✱ns ATRA EPZ GSK-J4 ✱✱✱✱✱✱✱✱✱✱✱✱ GMP ATRA GSK-J4 ATRA 4 ns ✱✱✱✱✱✱ 0 EPZ 0 ✱✱✱✱✱✱ 3 days 6 days 0 9 days✱✱✱ ✱✱✱ ATRA ✱✱✱ GSK-J4✱✱✱ ns ✱✱✱✱✱✱ ATRAEPZ + GSK-J4 4 4 ✱✱✱✱✱✱ns3 days ✱✱✱6 days✱✱✱4 9 days ATRAEPZ + GSK-J4✱✱✱40 ✱✱✱ns3 days ✱✱✱6 days 9 days EPZ 1.00 ✱✱✱ ✱✱✱✱✱✱ ✱✱✱ ✱✱✱✱✱✱ ATRA + GSK-J4 ✱✱✱3 ✱✱✱days ✱✱✱GSK-J4 6 days 9 days4✱✱✱ GSK-J4✱✱✱ ✱✱✱ ✱✱✱MEP ✱✱✱ GSK-J4 GSK-J4 GSK-J4 ✱✱✱ns 0 EPZ 03 ATRA✱✱✱ + EPZ 3 days 6 ATRAdays + + EPZ GSK-J4 9 days ✱✱✱ 3✱✱✱✱✱✱ ✱✱✱✱✱✱ns ✱✱✱ ✱✱✱ATRAns− + GSK-J4 ✱✱✱ ✱✱✱✱✱✱ ✱✱✱ATRA + GSK-J4 3 days✱✱✱ 6ATRA days + EPZ 9 days✱✱✱✱✱ 0✱✱✱✱✱ns ✱✱✱ ✱✱✱ EPZ 03 ✱✱✱ns ✱✱✱ ns ATRA + GSK-J4✱✱✱ 3ns 3 days ns ✱✱✱ 6 daysEPZ ATRA +9 EPZ days✱✱✱Monocyte✱✱✱EPZ 20 ns✱✱✱ ✱✱3✱✱✱ ns EPZ ATRA✱✱✱ + EPZ 3✱✱ns ns ATRA + EPZ EPZ ✱✱✱✱✱✱ ✱✱ ✱✱✱ 3 days✱✱✱✱✱✱ 6 days ✱✱✱ATRA +9 GSK-J4 days 0 3 3 days ns 6 days ATRA +9 EPZ days ✱✱✱ ✱✱✱ ✱✱✱ ✱✱✱✱✱ ✱✱✱ ✱✱ ✱✱✱ ✱✱✱ Erythroid ✱✱✱ ✱✱✱ ✱✱✱ ATRA + GSK-J4 ✱✱✱ ✱✱✱3 ATRA + GSK-J4✱✱✱ns ✱✱✱ ATRA + GSK-J4ATRA + EPZ ATRA + GSK-J4

H3K27em3 tag density tag H3K27em3 ✱✱✱ ✱✱✱ 3 days ✱✱✱ 6 days✱✱✱2 ✱✱✱9 days ✱✱✱2 ✱✱✱ ✱✱✱ ✱✱✱ ✱✱✱✱✱ ✱✱✱ 2 ✱✱✱

✱✱✱Cell 3 3 ns 3 2 ATRA + EPZ ns 3 ATRA + EPZ Cell ATRA + EPZ ATRA + EPZ Normalized H3K27me3 tags H3K27me3 Normalized ns 2 2 ns ✱✱✱

0 − 2 ✱✱ ✱✱ − H1 CD34+CD38 CMP GMP MEP Monocyte Erythroid B T ✱✱ 1 CD34CD38 ✱✱ 5 Monocyte 6 Erythriod GMP CMP 1.00 2 MEP 8 Tcell1 3 GMP 2 CMP 7 Bcell ✱✱✱ ✱✱✱ 1 ✱✱✱ 4 MEP ✱✱✱ C 1 CD34CD38

CMP GMP MEP D CMP GMP1 MEP E CMP GMP MEPF ✱✱✱ CMP GMP MEP 1 ✱✱✱ ✱✱✱5 Monocyte ✱✱✱ 6 Erythriod

1 Cell 1 Cell − T 1 Distribution of transcription factor-binding loci to relative TSS

Erythroid Erythroid 10 TSS 10 20 30 Erythroid 40 50 Erythroid 1 Monocyte Monocyte Monocyte Monocyte 8 Tcell1 3 GMP 2 CMP 7 Bcell

Tcell1 4 MEP

Tcell1 2 2 2 2 1

Cell − B 0 0

Promoter (<=1kb) 40 0 3 days 6 days 0 9 days3 days 6 days 9 days Bcell 0 0

3 days 6 days 9 days Distribution of transcription factor-binding loci to relative TSS PromoterPromoter (1-2kb) (<=1kb) 3 daysBinding sites (%) (5'->3') 6 days 9 days

0 3 days 6 days 9 days 3 days 6 days 9 days Erythroid 10 TSS 10 20 30 40 50 20 Bcell Erythriod3 days 6 days 9 days 5' UTR 0 Cell Promoter (1-2kb) 3 days 6 days 9 days −

3' UTR T Tcell1 1 Monocyte 1 1 1

Monocyte TSS

Erythriod 1st Exon5' UTR

MEP Other Exon 50 40 30 20

Promoter (<=1kb) a$n 20 MEP 3' UTR 0.50 Binding sites (%) (5'->3')

Bcell 1st Intron Cell GMP Promoter (1-2kb) − 0.75 Monocyte GMP Other Intron B 1st Exon 40

0 0 0 0 CMP Downstream (<=3kb) Tcell1 Erythriod 3 daysCMP 6 days5' UTR 3 days Other9 days Exon6 days 3 daysPercentage of enriched regions 9 days 6 days 3 days 9 days 6 days 9 days

MEP Distal Intergenic G Feature − CD34+CD38 3' UTR >100kb 10-100kb 5-10kb 3-5kb 1-3kb 0-1kb H3K27me3 Occupancy (MB) Occupancy H3K27me3 Promoter (<=1kb)

Bcell CD34CD38 1st Intron 40 Monocyte H1 Promoter (1-2kb) 1st Exon Other Intron Erythroid

GMP 00 25 50 75 1000 25 50 75 100 20

25 50 75 50 40 30 20

0.75 100 Tcell1 Cell Erythriod MEP 5' UTR PercentageOther Exon PercentageDownstream (<=3kb) CMP 1st Intron TSS Promoter (<=1kb) 3' UTR Distal Intergenic Cell

Bcell Monocyte 20 Monocyte GMP Promoter (1-2kb) 1st Exon Other Intron CD34CD38 H1 Erythriod 5' UTR Other Exon Downstream (<=3kb) 40 MEP CD34+CD38− CMP MEP a$Cell 3' UTR0 Distal Intergenic Feature 25 1st50 Intron 75 Percentage of enriched regions 100 CMP

Monocyte >100kb 10-100kb 5-10kb 3-5kb 1-3kb 0-1kb

GMP 1st Exon Other Intron Cell CD34CD38 GMP 0.75 0.50 Other Exon Downstream (<=3kb) a$n MEP H1 MEP GMP CMP 0 1st Intron 25 50 75 Distal Intergenic CD34+CD38− Monocyte 100 Other Intron GMP CD34CD38 CMP Erythroid Downstream (<=3kb) GMP B−Cell CMP

CMP 0.50 Distal Intergenic − a$n 0 25 50 75 MEP T−Cell 100 CD34CD38 Monocyte

Erythroid CD34+CD38 0 25 50 75 B−Cell

100 H1 5 T−Cell

0.25 1.00

1.00 0.75 0.50 0.25 0.00 a$n

0.25

0.00

H1 CD34+CD38− CMP GMP MEP Monocyte Erythroid B−Cell T−Cell a$Cell

0.00

H1 CD34+CD38− CMP GMP MEP Monocyte Erythroid B−Cell T−Cell a$Cell Figure S3. Related to Figure 1 and 2. H3K27me3 signal is stable at promoters across progenitor populations. H3K4me3 (A) and H3K27me3 (B) tag density ±2 Kb of transcription start sites of genes up-regulated in GMP and MEP across CMP, GMP, MEP, monocyte and erythroid precursor as indicated by the colour legend on the bottom right. C) Plot of the cumulative number of base pairs marked by H3K27me3 across cell types indicated by colour legend on the bottom right. Percentage of H3K27me3- (D) and H3K4me3-(E) enriched regions at genomic features. Percentage of H3K27me3 (F) and H3K4me3 (G) enriched regions with respect to their binned distance to the TSS of coding genes across cell types indicated by colours. Distance from TSS for each bin indicated in the bottom panel (*** P < 0.001).

1.00 A 1 0.8 0.6 0.4 0.2 1 0.8 0.6 0.4 0.2 1 0.8 0.6 0.4 0.2 1 0.8 0.6 0.4 0.2 11 0.8 0.6 0.4 0.2 0 1 0 1 0 1 0 1 0 1 1 1 1 1 Biavlent Enhancer Biavlent Enhancer Biavlent Enhancer Biavlent Enhancer Biavlent Enhancer 0.8 0.8 0.8 0.8 0.8 Poised Enhancer Poised Enhancer Poised Enhancer Poised Enhancer Poised Enhancer

Poised Genic Enhnacer 0.6Poised Genic Enhnacer 0.6Poised Genic Enhnacer 0.6Poised Genic Enhnacer 0.6Poised Genic Enhnacer 0.6

Strong Active Flanking Promoters 0.4Strong Active Flanking Promoters 0.4Strong Active Flanking Promoters 0.4Strong Active Flanking Promoters 0.4Strong Active Flanking Promoters 0.4 Biavlent Enhancer Biavlent Enhancer Poised Enhnacer Genic Poised Promoters Flanking Active Strong prmoter flanking Weak Promoters Flanking Active Promoters Active Strong Promoters Active promoters Bivalent repressed Polycomb regions Repressed Heterochromatin Finger Zinc Other 1 regions Transcribed 2 regions Transcribed 1 Enhnacer Genic Active 2 Enhnacer Genic Active Biavlent Enhancer Biavlent Enhancer Poised Enhnacer Genic Poised Promoters Flanking Active Strong prmoter flanking Weak Promoters Flanking Active Promoters Active Strong Promoters Active promoters Bivalent repressed Polycomb regions Repressed Heterochromatin Finger Zinc Other 1 regions Transcribed 2 regions Transcribed 1 Enhnacer Genic Active 2 Enhnacer Genic Active Biavlent Enhancer Biavlent Enhancer Poised Enhnacer Genic Poised Promoters Flanking Active Strong prmoter flanking Weak Promoters Flanking Active Promoters Active Strong Promoters Active promoters Bivalent repressed Polycomb regions Repressed Heterochromatin Finger Zinc Other 1 regions Transcribed 2 regions Transcribed 1 Enhnacer Genic Active 2 Enhnacer Genic Active Biavlent Enhancer Biavlent Enhancer Poised Enhnacer Genic Poised Promoters Flanking Active Strong prmoter flanking Weak Promoters Flanking Active Promoters Active Strong Promoters Active promoters Bivalent repressed Polycomb regions Repressed Heterochromatin Finger Zinc Other 1 regions Transcribed 2 regions Transcribed 1 Enhnacer Genic Active 2 Enhnacer Genic Active Biavlent Enhancer Biavlent Enhancer Poised Enhnacer Genic Poised Promoters Flanking Active Strong prmoter flanking Weak Promoters Flanking Active WeakPromoters Active Strong flankingPromoters Active promoters Bivalent prmoterrepressed Polycomb regions Repressed Heterochromatin 0.2Finger Zinc WeakOther flanking1 regions Transcribed prmoter2 regions Transcribed 1 Enhnacer Genic Active 2 Enhnacer Genic Active 0.2Weak flanking prmoter 0.2Weak flanking prmoter Weak flanking prmoter 0.2 0.2 LAD LAD LAD LAD LAD Active Flanking Promoters Active Flanking Promoters Active Flanking Promoters Active Flanking Promoters Active Flanking Promoters TSS+/-2Kb TSS+/-2Kb TSS+/-2Kb TSS+/-2Kb TSS+/-2Kb Strong Active Promoters Strong Active Promoters TSS Strong Active Promoters TSS Strong Active Promoters TSS Strong Active Promoters TSS TSS TES TES TES TES TES Active Promoters Active Promoters Active Promoters Active Promoters Active Promoters Gene Gene Gene Gene Gene Exon Bivalent promoters Bivalent promoters Exon Bivalent promoters Exon Bivalent promoters Exon Bivalent promoters Exon CpGIsland CpGIsland CpGIsland CpGIsland CpGIsland Polycomb repressed Polycomb repressed Polycomb repressed GenomePolycomb % repressed Genome % GenomePolycomb % repressed RepressedGenome % Genome % Repressed regions Repressed regions Repressed regions Repressed regions RepressedDually regions Repressed Heterochromatin Heterochromatin Heterochromatin Heterochromatin Heterochromatin 0.75 Zinc Finger Zinc Finger Zinc Finger Zinc Finger Zinc Finger Other Other Other Other Other

Transcribed regions 1 Transcribed regions 1 Transcribed regions 1 Transcribed regions 1 Transcribed regions 1

Transcribed regions 2 Transcribed regions 2 Transcribed regions 2 Transcribed regions 2 Transcribed regions 2

Active Genic Enhnacer 1 Active Genic Enhnacer 1 Active Genic Enhnacer 1 Active Genic Enhnacer 1 Active Genic Enhnacer 1

Active Genic Enhnacer 2 Active Genic Enhnacer 2 Active Genic Enhnacer 2 Active Genic Enhnacer 2 Active Genic Enhnacer 2 Exon Gene Gene Exon Gene Gene Gene TSS TSS+/ Exon TSS TSS+/ Exon TSS TSS+/ Exon Genome % CpGIsland Exon Gene TES TSS TSS+/-2Kb LAD TES TSS TSS+/ TES TES TSS TSS+/ Genome % Genome % Genome TES % Genome % Genome % Genome TES CpGIsland LAD CpGIsland LAD CpGIsland LAD CpGIsland LAD CpGIsland LAD Genome % CpGIsland Exon Gene TES TSS TSS+/-2Kb LAD Genome % CpGIsland Exon Gene TES TSS TSS+/-2Kb LAD Genome % CpGIsland Exon Gene TES TSS TSS+/-2Kb LAD Genome % CpGIsland Exon Gene TES TSS TSS+/-2Kb LAD - - - - - 2Kb 2Kb 2Kb 2Kb 2Kb Cell

H1 B Chr20:49,650,000-50,050,000 200Kb CD34+CD38− 100 CMP 0 GMP 0.50 a$n MEP Monocyte Erythroid B−Cell T−Cell LOCKS C D E F 1.0

0.75 0.25

Methylation 0.5

0.25

Fractional 0

0.00

H1 CD34+CD38− CMP GMP MEP Monocyte Erythroid B−Cell T−Cell a$Cell Figure S4. Related to Figure 4. ChromHMM identified polycomb repressed regions are enriched in LADs in progenitor cells. A) Enrichment of ChromHMM chromatin states within genomic features for T cells (navy), monocyte (brown), GMP (yellow), CMP (orange) and CD34+CD38- cells (green). B) Genome browser view of Fractional DNA methylation on chromosome 20 across cell types as indicated by colour legend. A H3K27me3 LOCK (FDR < 0.05) present in progenitor cells but lost in monocyte and erythroid precursor is indicated by the shaded box. Fractional CpG methylation signal within ChromHMM defined H3K9me3 (C), H3K27me3 repressed (D) and H3K9me3/H3K27me3 (E) regions and genome-wide (F) across cell types as indicated by colour legend.

1.00

0.75

Cell A B H1 CD34+CD38− 60000 CMP CD34+ CD38- CD34+ CD38- CMP 10000 CMP GMP 0.50 GMP GMP a$n 40000 MEP MEP MEP Monocyte MonocyteMonocyte Erythroid Erythroid 5000 B Cell B Cell Number of Enhancers of Number 20000 Erythroid T Cell T Cell Number of Active Enhancers Active of Number

Number of Enhancers B−Cell 100 Number of Active Enhancers 100 T−Cell 0 0

black C 75 D E 75 F

100 100 100 100 100 GMP & MEP 100 PoisedFirst poised in CD34+CD38- in CD34+CD38-

black black black CMP & MEP PoisedFirst poised in Commited in myeloid Myeloid progenitors Progenitors 0.25 7575 75 75 7575 GMP & MEP GMP & MEP GMP & MEP Poised in CD34+CD38- CMP & MEP CMP &CMP MEP & GMP Specific CMP & MEP 50 Poised in Commited Myeloid Progenitors CMP & GMP CMP & GMP CMP & GMP 5050 50 50 50 Specific 50 CMP & GMP & MEP CMP & GMP & MEP CMP & GMP & MEP 50 Proportion Proportion Proportion CMP & GMP & MEP MEP Unique MEP Unique MEP Unique black

Proportion GMP Unique GMP Unique GMP Unique 25 25 CMP Unique 25 CMP Unique CMP UniqueMEP Unique Percentage 25

Percentage black 25 Specific Specific Specific 25Enhancers Active of Proportion GMP Unique 0 0 0 0 0 CMP Unique25 0 25 Enhancers Active of Proportion MEP GMP CMP Tcell Bcell Tcell Bcell Tcell Bcell Erythroid Erythroid Monocyte Monocyte Specific ErythroidMonocyte MEP CMP GMP T Cell T Cell B Cell B B Cell B T Cell B Cell B Erythroid Erythroid Erythroid Monocyte Monocyte 0 Monocyte 0

Tcell Bcell 0.00 Tcell Bcell ErythroidMonocyte ErythroidMonocyte H1 CD34+CD38− CMP GMP MEP Monocyte Erythroid B−Cell T−Cell a$Cell

Figure S5. Related to Figure 5. Total number of enhancers decreased in erythroid precursor, monocyte and differentiated lymphoid cells. A) Total number of enhancers (active and primed enhancers) across cell types as indicated by the colour legend. B) Total number of active enhancers across cell types as indicated by the colour legend. C) Percentage of active enhancers that are shared between or unique to each progenitor populations as indicated by the color legend. D) Percentage of active enhancers that are present in progenitor populations or de novo (specific) in differentiated cells as indicated by the colour legend. E) Percentage of active enhancers that are poised in progenitor populations or de novo in differentiated cells as indicated by the colour legends. F) Percentage of active enhancers present in differentiated cells that are first poised in CD34+CD38- cells, progenitor cells, or appear de novo in erythroid precursors, monocytes or lymphoid cells as indicated by the colour legend.

100

ubiquitin-dependent protein catabolic process A transition metal ion homeostasis tetrapyrrole biosynthetic process regulation of erythrocyte differentiation porphyrin-containing compound metabolic process porphyrin-containing compound biosynthetic process 75 myeloid cell homeostasis myeloid cell development megakaryocyte differentiation First Appear in CD34+CD38- hemostasis PoisedFirst appear in CD34+CD38- in CD34+CD38- hemopoiesis First Appear in Committed Myeloid Progenitors heme metabolic process PoisedFirst appear in Commited in myeloid Myeloid progenitors Progenitors erythrocyte homeostasis erythrocyte differentiation Specific erythrocyte development 50 chromosome organization chromatin remodeling cellular response to DNA damage stimulus blood coagulation black 0

B 20 -40 -20 25 Proportion of Active Enhancers Active of Proportion

Tcell Bcell

ErythroidMonocyte 0 50 50 150 100 C -Log10(q-value) CD34+CD38- GMP Monocyte Erythroid High tetrapyrrole metabolic process Erythroid E tetrapyrroletetrapyrrole biosynthetic metabolic process protoporphyrinogentetrapyrrole IXbiosynthetic metabolic process MEP CMP B-Cell porphyrin-containingprotoporphyrinogen compound IX metabolic process porphyrin-containingporphyrin-containing compound compound biosynthetic metabolic process porphyrin-containing compoundmyeloid biosynthetic cell homeostasis process myeloidheme metabolic cell homeostasis process hemeheme biosynthetic metabolic process Erythroid T-Cell hemeerythrocyte biosynthetic homeostasis process Low erythrocyteerythrocyte differentiation homeostasis

erythrocyte differentiation 0

10 20 30 Erythroid 0 0 Monocyte

10 20 30 Erythroid 10 20 Monocyte 30 Monocyte D F regulation of innate immune response Monocyte CD34+CD38- GMP Monocyte regulationregulation of innate of immunedefense response regulationregulation of of cytokine defense production response Enriched positive regulationregulation of immune of cytokine system production process positivepositive regulation regulation of immune of immune system response process positive regulationinnate of immune response MEP CMP B-Cell immune response-activatinginnate signal immune transduction response immune response-activating signalimmune transduction response immuneendocytosis response activation of immuneendocytosis response No Change 0 activation of immune response 0 30 60 90 30 90 Erythroid T-Cell 60 0

-Log10(q30 -value)60 90 Depleted

Figure S6. Related to Figure 5 and 6. Lineage-specific enhancers are marked by H3K27ac in hematopoietic progenitor subsets. GREAT gene ontology analysis of active enhancers in erythroid precursor (A) and monocytes (B) that are first apparent in CD34+CD38- or other progenitor subsets. C) SOM plot of rank normalized H3K27ac signal contained within the hematopoietic enhancer catalogue across cell types profiled in this study. D) SOM plot of rank normalized H3K27ac signal within hematopoietic enhancers with respect to CD34+CD38- for each cell type. Gene ontology analysis of super enhancers in erythroid precursor (E) and monocyte (F).