A partial list of genes analyzed after negative selection of the cDNA library generated from Lin−/loSca-1+Thy-1.1loc-kit+cells
| Name . | Clone code . | Accession number . | Description . |
|---|---|---|---|
| Transcription factors | |||
| Bmi-1 | BA_HSC3_18 | M64279 | Polycomb-group transcriptional repressor; involved in cell proliferation and senescence |
| Nfe2 | BA_RA1B_64 | L09600 | AP-1–related DNA-binding protein, leucine zipper protein, hematopoietic specific |
| TBX2 | BA_RA3A_94 | AF172088 | Limb morphogenesis; immortalizing gene with tumorigenic potential |
| Ash1 | BA_RA2A_52 | NM_018489 | A SET domain, a PHD finger, 4 AT hooks, and a region with homology to the bromodomain; may be involved in adhesion-mediated transcription |
| Maid | BA_RA2B_83 | NM_010761 | Negative regulator of bHLH proteins in the mouse egg and zygote |
| LEF-1S | BA_RA5D_78 | D16503 | A lymphoid-specific protein with an HMG domain, regulates TCRα enhancer function |
| Elf1 | BA_RA6B_30 | NM_007920 | Ets-family transcription factor; highest in lymphocytes |
| ZF216 | BA_RA4C_60 | AF062071 | 1 N-terminal A20 (an inhibitor of cell death)-like zinc fingers, mediating IL-1–induced NF-kappaB activation |
| Evi-1 | BA_RA3A_50 | M21829 | 2 sets of ZF; overexpression causes abnormalities in megakaryopoiesis |
| Evi-9 | BA_RA1D_75 | NM_016707 | A ZF protein; interacts with BCL6, a known human B-cell proto-oncogene product |
| Tcf4 | BA_RA1A_07 | NM_013685 | A splicing variant of the ITF-2 transcript encoding a transcription factor that inhibits MyoD activity |
| Chx10 | BA_RA2B_69 | NM_007701 | C elegans ceh-10 homeo-domain–containing homologue; developmentally regulated |
| Putative myelin regulatory factor 1 | BA_RA4A_40 | U14648 | A brain-derived DNA-binding protein; regulates expression of myelin basic protein gene |
| KIAA0697 | BA_RA4B_88 | AB014597 | 1 TM and sequence-specific RNA binding by a novel KH domain; implicated in paraneoplastic disease and the fragile X syndrome |
| Membrane proteins | |||
| Notch1 | BA_8-3 | NM_008714 | Controls cell fate choices by inhibiting certain differentiation pathways |
| Type III multi-pass TM protein | BA_RA1A_50 | AF082535 | 4 TM; a gene similar to Homo sapiens GMP-17/NKG7/GIG-1; expressed by NK, CD8+, activated T, and macrophage R2 cells |
| Mouse homologue of Nessy | BA_RA1A_60 | NM_005768 | Putative transmembrane protein Nessy, an evolutionarily conserved gene controlled by Hox proteins during Drosophila embryogenesis |
| CD34 | BA_RA1C_19 | S69295 | Hematopoietic stem cell antigen, present in embryonic brain and adult brain, lung, and skeletal muscle |
| CGI-69 | BA_RA4D_91 | AF151827 | Similar to human CGI-69 protein |
| HSA-A | BA_RA4D_26 | X56469 | A mouse hematopoietic differentiation marker from B and T cells; signal peptide, 1 C-terminal TM |
| Human sperm surface Ag | BA_RA4B_33 | NM_003971 | A novel human testis mRNA specifically expressed in testicular haploid germ cells; carrying leucine zipper dimerization motif |
| Secreted molecules | |||
| BMP4 | BA_RA6B_87 | S65032 | A signal peptide; secreted protein; TGF-beta family; exhibits mesoderm-inducing activity |
| L2G25B | BA_RA4B_55 | J04491 | Signal peptide, CXC chemokine |
| SDF4 | BA_RA5B_24 | D50461 | A signal peptide with Ca2+ binding motif |
| Flt3 ligand isoform E6 Δ16 | BA_RA4A_50 | S76464 | Signal peptide; flt3 ligand isoform E6 Δ16, missing 1 TM, soluble form |
| Apoptosis | |||
| Mcl 1 | BA_RA3A_85 | NM_008562 | Myeloid leukemia sequence 1; a bcl-2–related gene; expressed in the early stage of embryonic stem cells |
| Heterochromatin protein 1α | BA_RA2A_37 | AF216290 | Apoptosis-associated proteins in a human Burkitt lymphoma cell line |
| Signaling molecules | |||
| WNK1 | BA_RA1A_15 | AF227741 | 9 TM, 3 coil-coil structures; similar to MEKK; unknown function |
| ARK2 | BA_RA1A_91 | U69107 | Aurora-related kinase 2; involved in chromosomal segregation; expressed during S and G2/M phases; localized to the midbody |
| STK-1 | BA_RA1A_91 | D21099 | Expressed in a large number of proliferating cells, but not in other tissues; Xenopus lavas XLP46 protein kinase; involved in cell growth |
| LynB | Ba_RA1D_84 | M57697 | Tyrosine kinase; expressed in myeloid and B-lymphoid lineage cells |
| Truncated form of c-kit | BA_RA6B_92 | X65997 | Kinase domain |
| GAP | BA_RA5B_81 | L13151 | GTPase activating protein; inhibits ras-mediated signaling |
| RGS2 | BA_RA6B_56 | NM_00906 | RGS box; GAP for trimeric G-protein; inhibits signaling from Gq |
| Nbr1 | BA_RA1B_56 | AF008676 | B box and zinc finger domain–containing protein, unknown function; next to BRCA1gene |
| DMX-like 1 | BA_RA6A_84 | NM_005509 | 10 WD and 2 TM; highly conserved throughout revolution; involved in regulatory function |
| Sop2p-like | BA_RA3B_29 | Y08999 | 6 WD40; interacts with Arp3p and modulates profilin function |
| Cell cycle | |||
| Cyclin H | BA_RA4D_55 | AF154914 | Associates with cyclin-dependent kinase 7 and Mat1 to form the mammalian Cdk-activating kinase, CAK; suppressed by p53 |
| Clk4 | BA_RA1C_80 | NM_007714 | CDK-like kinase 4; phosphorylate spliceosome |
| PCM-1 | BA_RA5A_71 | L27841 | 6 coils; a 228-kd centrosome autoantigen with a distinct cell cycle distribution; from fetal liver |
| PACT | BA_RA5B_02 | U28789 | p53 and pRB binding protein; binding to p53 and inhibits p53 DNA binding |
| Tousled-like kinase | BA_RA4C_16 | NM_011903 | S/T kinase; 3 coils, NLS; cell cycle–dependent activity with highest activity during S phase and is regulated by phosphorylation |
| Miscellaneous | |||
| p13MTCP1 | BA_RA4D_10 | U32332 | Found in t(X;14) translocations |
| Meis 1 | BA_RA6D_67 | NM_010789 | Myeloid ecotropic viral integration site 1; a PBX1-related homeobox gene involved in myeloid leukemia |
| RA-inducible protein E3 | BA_RA6D_70 | U29539 | Present in the myeloid, B-lymphoid, and erythroid lineages, absent in nonhematopoietic cells |
| DJ-1 | BA_RA2A_33 | AB015652 | A novel oncogene that transforms mouse NIH3T3 cells in cooperation with ras |
| HMG-1–related protein | BA_RA3D_37 | S50213 | DNA-binding components of the V-(D)-J recombinase |
| LSP1 | BA_RA6D_01 | S74179 | Lymphocyte-specific protein; binds F-actin; a negative regulator of neutrophil chemotaxis |
| Mea | BA_RA2A_25 | M27938 | Male-enhanced antigen; involved in spermatogenesis |
| Name . | Clone code . | Accession number . | Description . |
|---|---|---|---|
| Transcription factors | |||
| Bmi-1 | BA_HSC3_18 | M64279 | Polycomb-group transcriptional repressor; involved in cell proliferation and senescence |
| Nfe2 | BA_RA1B_64 | L09600 | AP-1–related DNA-binding protein, leucine zipper protein, hematopoietic specific |
| TBX2 | BA_RA3A_94 | AF172088 | Limb morphogenesis; immortalizing gene with tumorigenic potential |
| Ash1 | BA_RA2A_52 | NM_018489 | A SET domain, a PHD finger, 4 AT hooks, and a region with homology to the bromodomain; may be involved in adhesion-mediated transcription |
| Maid | BA_RA2B_83 | NM_010761 | Negative regulator of bHLH proteins in the mouse egg and zygote |
| LEF-1S | BA_RA5D_78 | D16503 | A lymphoid-specific protein with an HMG domain, regulates TCRα enhancer function |
| Elf1 | BA_RA6B_30 | NM_007920 | Ets-family transcription factor; highest in lymphocytes |
| ZF216 | BA_RA4C_60 | AF062071 | 1 N-terminal A20 (an inhibitor of cell death)-like zinc fingers, mediating IL-1–induced NF-kappaB activation |
| Evi-1 | BA_RA3A_50 | M21829 | 2 sets of ZF; overexpression causes abnormalities in megakaryopoiesis |
| Evi-9 | BA_RA1D_75 | NM_016707 | A ZF protein; interacts with BCL6, a known human B-cell proto-oncogene product |
| Tcf4 | BA_RA1A_07 | NM_013685 | A splicing variant of the ITF-2 transcript encoding a transcription factor that inhibits MyoD activity |
| Chx10 | BA_RA2B_69 | NM_007701 | C elegans ceh-10 homeo-domain–containing homologue; developmentally regulated |
| Putative myelin regulatory factor 1 | BA_RA4A_40 | U14648 | A brain-derived DNA-binding protein; regulates expression of myelin basic protein gene |
| KIAA0697 | BA_RA4B_88 | AB014597 | 1 TM and sequence-specific RNA binding by a novel KH domain; implicated in paraneoplastic disease and the fragile X syndrome |
| Membrane proteins | |||
| Notch1 | BA_8-3 | NM_008714 | Controls cell fate choices by inhibiting certain differentiation pathways |
| Type III multi-pass TM protein | BA_RA1A_50 | AF082535 | 4 TM; a gene similar to Homo sapiens GMP-17/NKG7/GIG-1; expressed by NK, CD8+, activated T, and macrophage R2 cells |
| Mouse homologue of Nessy | BA_RA1A_60 | NM_005768 | Putative transmembrane protein Nessy, an evolutionarily conserved gene controlled by Hox proteins during Drosophila embryogenesis |
| CD34 | BA_RA1C_19 | S69295 | Hematopoietic stem cell antigen, present in embryonic brain and adult brain, lung, and skeletal muscle |
| CGI-69 | BA_RA4D_91 | AF151827 | Similar to human CGI-69 protein |
| HSA-A | BA_RA4D_26 | X56469 | A mouse hematopoietic differentiation marker from B and T cells; signal peptide, 1 C-terminal TM |
| Human sperm surface Ag | BA_RA4B_33 | NM_003971 | A novel human testis mRNA specifically expressed in testicular haploid germ cells; carrying leucine zipper dimerization motif |
| Secreted molecules | |||
| BMP4 | BA_RA6B_87 | S65032 | A signal peptide; secreted protein; TGF-beta family; exhibits mesoderm-inducing activity |
| L2G25B | BA_RA4B_55 | J04491 | Signal peptide, CXC chemokine |
| SDF4 | BA_RA5B_24 | D50461 | A signal peptide with Ca2+ binding motif |
| Flt3 ligand isoform E6 Δ16 | BA_RA4A_50 | S76464 | Signal peptide; flt3 ligand isoform E6 Δ16, missing 1 TM, soluble form |
| Apoptosis | |||
| Mcl 1 | BA_RA3A_85 | NM_008562 | Myeloid leukemia sequence 1; a bcl-2–related gene; expressed in the early stage of embryonic stem cells |
| Heterochromatin protein 1α | BA_RA2A_37 | AF216290 | Apoptosis-associated proteins in a human Burkitt lymphoma cell line |
| Signaling molecules | |||
| WNK1 | BA_RA1A_15 | AF227741 | 9 TM, 3 coil-coil structures; similar to MEKK; unknown function |
| ARK2 | BA_RA1A_91 | U69107 | Aurora-related kinase 2; involved in chromosomal segregation; expressed during S and G2/M phases; localized to the midbody |
| STK-1 | BA_RA1A_91 | D21099 | Expressed in a large number of proliferating cells, but not in other tissues; Xenopus lavas XLP46 protein kinase; involved in cell growth |
| LynB | Ba_RA1D_84 | M57697 | Tyrosine kinase; expressed in myeloid and B-lymphoid lineage cells |
| Truncated form of c-kit | BA_RA6B_92 | X65997 | Kinase domain |
| GAP | BA_RA5B_81 | L13151 | GTPase activating protein; inhibits ras-mediated signaling |
| RGS2 | BA_RA6B_56 | NM_00906 | RGS box; GAP for trimeric G-protein; inhibits signaling from Gq |
| Nbr1 | BA_RA1B_56 | AF008676 | B box and zinc finger domain–containing protein, unknown function; next to BRCA1gene |
| DMX-like 1 | BA_RA6A_84 | NM_005509 | 10 WD and 2 TM; highly conserved throughout revolution; involved in regulatory function |
| Sop2p-like | BA_RA3B_29 | Y08999 | 6 WD40; interacts with Arp3p and modulates profilin function |
| Cell cycle | |||
| Cyclin H | BA_RA4D_55 | AF154914 | Associates with cyclin-dependent kinase 7 and Mat1 to form the mammalian Cdk-activating kinase, CAK; suppressed by p53 |
| Clk4 | BA_RA1C_80 | NM_007714 | CDK-like kinase 4; phosphorylate spliceosome |
| PCM-1 | BA_RA5A_71 | L27841 | 6 coils; a 228-kd centrosome autoantigen with a distinct cell cycle distribution; from fetal liver |
| PACT | BA_RA5B_02 | U28789 | p53 and pRB binding protein; binding to p53 and inhibits p53 DNA binding |
| Tousled-like kinase | BA_RA4C_16 | NM_011903 | S/T kinase; 3 coils, NLS; cell cycle–dependent activity with highest activity during S phase and is regulated by phosphorylation |
| Miscellaneous | |||
| p13MTCP1 | BA_RA4D_10 | U32332 | Found in t(X;14) translocations |
| Meis 1 | BA_RA6D_67 | NM_010789 | Myeloid ecotropic viral integration site 1; a PBX1-related homeobox gene involved in myeloid leukemia |
| RA-inducible protein E3 | BA_RA6D_70 | U29539 | Present in the myeloid, B-lymphoid, and erythroid lineages, absent in nonhematopoietic cells |
| DJ-1 | BA_RA2A_33 | AB015652 | A novel oncogene that transforms mouse NIH3T3 cells in cooperation with ras |
| HMG-1–related protein | BA_RA3D_37 | S50213 | DNA-binding components of the V-(D)-J recombinase |
| LSP1 | BA_RA6D_01 | S74179 | Lymphocyte-specific protein; binds F-actin; a negative regulator of neutrophil chemotaxis |
| Mea | BA_RA2A_25 | M27938 | Male-enhanced antigen; involved in spermatogenesis |
In clone codes, RA refers to the clones that have been negatively selected by subtraction with mature hematopoietic cells. Note that Bmi-1 and Notch 1 were identified during the sequencing of the random clones. ZF indicates zinc finger; TM, transmembrane; KH, K homology RNA-binding domain; HMG, high-mobility group; TCR, T-cell receptor; RRM, RNA recognition motif.
The EST (expressed sequence tag) sequences that are predominantly expressed in hematopoietic stem cells are available at the web-accessible database at www.systemsbiology.org/research/stemcells. This EST database also applies to Tables 2 and 3.