The VISION Project The VISION project conducted a ValIdated Systematic IntegratiON of epigenetic datasets across progenitor and differentiated blood cell types in mouse and human (Heuston et al. 2018, Xiang et al. 2020, Xiang et al. 2024). The project was carried out by an international group of scientists funded by the National Institute of Diabetes, Digestive, and Kidney Diseases of the National Institutes of Health (grant R24DK106766) and with intramural support from the National Human Genome Research Institute. Key products and results of the project can be visualized on the UCSC Genome Browser using this track hub. The project website provides other servers, databases, and data downloads.
TF ChIP-seq This composite track displays signals and peak calls for selected, published transcription factor (TF) ChIP-seq experiments in mouse blood cells and cell lines, with a heavy emphasis on erythroid cells or lines with an erythroid phenotype. The cell types or lines and the protein antigen for ChIP-seq are organized in the matrix, which can also be used to select the data to display.
Cell types and cell lines A prominent cell line model examined here is the G1E system, which is an immortalized, GATA1-null cell line derived from mouse embryonic stem cells by gene targeting (Weiss, Yu, Orkin 1997). G1E cells proliferate in culture as immature erythroid progenitor cells and undergo terminal erythroid maturation when GATA1 function is restored. A stable subline of G1E, called G1E-ER4, produces a fusion of GATA1 to the ligand-binding domain of the estrogen receptor (ER). Untreated G1E-ER4 cells, carrying the inactive GATA1-ER, proliferate without differentiation, but treatment with estradiol (E2) activates the hybrid protein, effectively complementing the GATA1 loss-of-function and allowing synchronous erythroid differentiation and maturation (Gregory et al. 1999). ChIP-seq data are compiled here using GATA1-null parental line G1E, the subline G1E-ER4 (not treated with E2), and G1E-R4 cells treated with E2 (G1E-ER4+E2) in which the GATA1-ER is activated and the cells differentiate and undergo erythroid maturation in culture. A similar knock-out-and-rescue cell line is K1-ER (Coghill et al. 2001), in which the immortalized cells are null for the erythroid transcription factor (TF) KLF1 (also called EKLF). Again, activatable KLF1 function was restored using a KLF1-ER fusion. An additional cell line model used here are murine erythroleukemia (MEL) cells. While these cells can be chemically induced to mature into erythroblast-like cells with increased hemoglobin, it was difficult to obtain good TF ChIP-seq data from the induced cells, and thus only data from uninduced MEL are provided.
Many of the TF ChIP-seq experiments using the G1E system explored one of three major processes. Changes in TF occupancy over the course of erythroid maturation were examined in a time course before and after treatment of G1E-ER4 cells with E2. Changes in TF occupancy over phases of the cell cycle, with a strong emphasis on the transition from mitosis (M) to the first stage of interphase (G1), were examined in G1E-ER4 cells arrested in M phase with nocodazole and then released into G1. Several experiments have examined a time course of the effect of acute degradation on TF occupancy using the TIR-AID system for rapid degradation of the target protein, such as CTCF. Pull-down menus are provided beneath the cell type-TF matrix to select or exclude tracks in one or more of those categories of processes. Some experiments also included analysis in a sister subclone G1E-ER4-V205M, which in carries a mutant form of GATA1 (V205M) as the GATA1-ER fusion protein. The V205M mutation in GATA1 renders it non-responsive to the factor Friend of GATA1 (FOG1, official name ZFPM1). These experiments with V205M GATA1 allow FOG1-independent activities of GATA1 to be assayed.
HPC7 cells are an immortalized line that serves as a model for mouse hematopoietic progenitor cells (Pinto do O 2002). These cells are capable of differentiation in vitro into more mature myeloid cells. CH12 cells are an immortalized line that is a model for mouse B cells.
Mouse primary blood cells purified predominantly using cell surface markers include: CMP = common myeloid progenitor cell, MEP = megakaryocyte-erythrocyte progenitor cell, ERY = erythroblast, MK = megakaryocyte, GMP = granulocyte monocyte progenitor cell, MON = monocyte, NEU = neutrophil, CLP = common lymphoid progenitor cell, B = B cell, NK = natural killer cell, TCD4 = CD4+ T cell, TCD8 = CD8+ T cell, LSK = Lin-Sca1+Kit+ cells from mouse bone marrow containing hematopoietic stem and progenitor cells, CFUE = colony forming unit erythroid, FL = designates ERY derived from fetal liver, BM = designates ERY derived from adult bone marrow, CFUMK = colony forming unit megakaryocyte, iMK = immature megakaryocyte, MK_fl = megakaryocyte derived from fetal liver. A majority of the cells in the mouse fetal liver are erythroid, and this tissue served as an informative source for ChIP-seq for EP300.
Sources of data The data were generated in several laboratories and published in many different papers, using a variety of approaches to obtain the primary cells. Details on the sources of the data are in the following table.
| Factor | G1E system | Erythroid maturation series | M to G1 transition | Acute degradation | Ref. G1E system | G1E PMID | Other cell types | Ref. Other cell types | Other PMID |
|---|---|---|---|---|---|---|---|---|---|
| PolII= POL2 | yes | yes | yes | Hsiung Gen Res 2015; Hsiung Genes Dev 2016; Zhang Nature 2019 | 25373146; 27340175; 31776509 | ||||
| GATA1 | yes | yes | Cheng Gen Res 2009; Jain Genom Data 2015 | 19887574; 25729644 | ERY, MK | Pimkin Gen Res 2014; Yue Nature 2014 | 25319996; 25409824 | ||
| TAL1 | yes | yes | Wu Gen Res 2011; Wu Gen Res 2014 | 21795386; 25319994 | ERY, MK, MEL, HPC7 | Pimkin Gen Res 2014; Yue Nature 2014; Wilson Blood 2016 | 25319996; 25409824; 26809507 | ||
| GATA2 | yes | Trompouki Cell 2011 | 22036566 | HPC7 | Wilson Blood 2016 | 26809507 | |||
| LDB1 | yes | yes | Vermunt Mol Cell 2023; Aboreden Mol Cell 2025 | 36868189; 39721581 | HPC7 | Wilson Blood 2016 | 26809507 | ||
| YY1 | yes | yes | yes | Lam Nat Gen 2024 | 39210046 | ||||
| KLF1 | K1-ER; FL cells | Gillinder NAR 2016; Mukherjee Cell Rep 2022 | 28180284; 36543143 | ||||||
| FLI1 | MK, HPC7 | Pimkin Gen Res 2014; Yue Nature 2014; Wilson Blood 2016 | 25319996; 25409824; 26809507 | ||||||
| RUNX1 | HPC7 | Wilson Blood 2016 | 26809507 | ||||||
| LMO2 | HPC7 | Wilson Blood 2016 | 26809507 | ||||||
| TCF3 | HPC7 | Wilson Blood 2016 | 26809507 | ||||||
| EP300 | FL, MEL, CH12 | Yue Nature 2014; ENCODE Nature 2020 | 25409824; 32728249 | ||||||
| CHD4 | yes | yes | Vermunt Mol Cell 2023 | 36868189 | |||||
| MTA2 | yes | yes | Vermunt Mol Cell 2023 | 36868189 | |||||
| CTCF | yes | yes | yes | yes | Zhang Nature 2019; Luan Cell Reports 2021 | 31776509; 33626344 | LSK, HPC7, CMP, GMP, MEP, CFU-E, ERY-fl, ERY, MEL, CFU-Mk, iMk, NEU, MON, CH12, T_CD4, T_CD8 | Yue Nature 2014; Wilson Blood 2016; Keller G3 2021; Zhu Genes Dev 2017; Vahedi Nature 2015; Shih PNAS 2012; ENCODE Nature 2020 | 25409824; 26809507; 33788948; 28167501; 25686607; 23169622; 32728249 |
| RAD21 | yes | yes | yes | yes | Zhang Nature 2019; Luan Cell Reports 2021 | 31776509; 33626344 | ERY, HPC7 | Hua Nature 2021; Wilson Blood 2016 | 34108683; 26809507 |
| SA1 | yes | Luan, Blobel lab | |||||||
| SA2 | yes | Luan, Blobel lab | |||||||
| SMC1 | yes | yes | Hsu, Blobel lab | ||||||
| BRD2 | yes | yes | Stonestrom Blood 2015 | 25696920 | |||||
| BRD3 | yes | yes | Stonestrom Blood 2015 | 25696920 | |||||
| BRD4 | yes | yes | Stonestrom Blood 2015 | 25696920 | |||||
| BRD2-HA | yes | yes | Stonestrom Blood 2015 | 25696920 | |||||
| BRD3-HA | yes | yes | Stonestrom Blood 2015 | 25696920 | |||||
| HIC2-HA | yes | Huang Nat Gen 2022 | 35941187 | ||||||
| NELFE | yes | yes | Vermunt, Blobel lab |
Users can choose the tracks to display using the check boxes in the matrix of TFs and cell types or the list of tracks. In addition, pull-down menus are provided below the TF-cell type matrix to select subsets of tracks examining phases of the cell cycle (such as M to G1), impacts on TF binding upon acute degradation of the TF, and binding patterns across an erythroid maturation series.
The pull-down menus at the top of the page provide choices to examine peak calls or signal tracks. Parameters for track configurations, including y-axis settings, are accessed by clicking the down arrow for "Peaks", "Signal", or "Fold-change".
Many of the ChIP-seq TF datasets on the selected TFs in erythroid cells and neutrophils were generated in collaborations during the mouse ENCODE and VISION projects. More information on sample sources and ChIP-seq methods is in the references in the Table. Additional datasets were downloaded from GEO and SRA or from the ENCODE data portal. Sequencing reads were mapped to the mouse GRCm38/mm10 genome assembly using the VISION project pipeline (Xiang et al., 2020), which is similar to the ENCODE pipeline except the mapping retains multi-mapped reads.
The data processing, downloads, generation of the tracks displayed, and development of the track hub were done by Belinda Giardine. Data to include was selected and curated by Ross Hardison.
Coghill E, Eccleston S, Fox V, Cerruti L, Brown C, Cunningham J, Jane S, Perkins A. Erythroid Kruppel-like factor (EKLF) coordinates erythroid cell proliferation and hemoglobinization in cell lines derived from EKLF null mice. Blood. 2001 Mar 15;97(6):1861-8. doi: 10.1182/blood.v97.6.1861. PMID: 11238130.
Gregory T, Yu C, Ma A, Orkin SH, Blobel GA, Weiss MJ. GATA-1 and erythropoietin cooperate to promote erythroid cell survival by regulating bcl-xL expression. Blood. 1999; 94:87-96. PMID: 10381501.
Heuston EF, Keller CA, Lichtenberg J, Giardine B, Anderson SM; NIH Intramural Sequencing Center; Hardison RC, Bodine DM. Establishment of regulatory elements during erythro-megakaryopoiesis identifies hematopoietic lineage-commitment points. Epigenetics Chromatin. 2018 May 28;11(1):22. PMID: 29807547; PMCID: PMC5971425.
Pinto do O P, Richter K, Carlsson L. Hematopoietic progenitor/stem cells immortalized by Lhx2 generate functional hematopoietic cells in vivo. Blood. 2002 Jun 1;99(11):3939-46. doi: 10.1182/blood.v99.11.3939. PMID: 12010792.
Weiss MJ, Yu C, Orkin SH. Erythroid-cell-specific properties of transcription factor GATA-1 revealed by phenotypic rescue of a gene-targeted cell line. Mol Cell Biol. 1997; 17:1642-1651. PMID: 9032291; PMCID: PMC231889.
Xiang G, Keller CA, Heuston E, Giardine BM, An L, Wixom AQ, Miller A, Cockburn A, Sauria MEG, Weaver K, Lichtenberg J, Göttgens B, Li Q, Bodine D, Mahony S, Taylor J, Blobel GA, Weiss MJ, Cheng Y, Yue F, Hughes J, Higgs DR, Zhang Y, Hardison RC. An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis. Genome Res. 2020 Mar;30(3):472-484. PMID: 32132109; PMCID: PMC7111515.
Xiang G, He X, Giardine BM, Isaac KJ, Taylor DJ, McCoy RC, Jansen C, Keller CA, Wixom AQ, Cockburn A, Miller A, Qi Q, He Y, Li Y, Lichtenberg J, Heuston EF, Anderson SM, Luan J, Vermunt MW, Yue F, Sauria MEG, Schatz MC, Taylor J, Göttgens B, Hughes JR, Higgs DR, Weiss MJ, Cheng Y, Blobel GA, Bodine DM, Zhang Y, Li Q, Mahony S, Hardison RC. Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. Genome Res. 2024 Aug 20;34(7):1089-1105. PMID: 38951027; PMCID: PMC11368181.
These ChIP-seq data are available for use without restrictions.
Ross Hardison rch8@psu.edu