Genome-wide Research on Transcription Factor EDAG Binding Profiling  by Using ChIP-seq

DONG Xiao-Ming, ZHENG Wei-Wei, YIN Rong-Hua, ZHAN Yi-Qun, YANG Xiao-Ming, LI Chang-Yan

Chinese Journal of Biochemistry and Molecular Biology ›› 2013, Vol. 29 ›› Issue (6) : 578-584.

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PDF(988 KB)
Chinese Journal of Biochemistry and Molecular Biology ›› 2013, Vol. 29 ›› Issue (6) : 578-584.
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Genome-wide Research on Transcription Factor EDAG Binding Profiling  by Using ChIP-seq

  • DONG Xiao-Ming1), ZHENG Wei-Wei2), YIN Rong-Hua2), ZHAN Yi-Qun2), YANG Xiao-Ming2), LI Chang-Yan2)*
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Abstract

To understand the regulation of erythroid differentiationassociated gene(EDAG) during hematopoietic differentiation, EPO-induced human cord blood CD34+ cells was used for ChI-seq analysis. The human cord blood CD34+ cells were isolated and treated with EPO for 5 days to induce erythroid differentiation. Chromatin DNA was immunoprecipitated with EDAG antibody and detected by Western blotting. The obtained DNA samples were subjected to high-throughput sequencing and bioinformatic analysis. A total of 1292 enrichment peaks corresponding 975 genes was identified with a false discovery rate (FDR) <0.0001. The mapping of the peaks revealed that they mainly occurred within intergenic and intron. To confirm the reliability of the ChIP-seq data, 11 genes involved in cell growth, cell cycle, apoptosis and hematopoietic differentiation were randomly selected and validated by qPCR for EDAG association. Gene ontology (GO) analysis suggested that EDAG regulated a set of genes involved in various biological processes, including cell proliferation, metabolism, hematopoietic development and cell signaling. These results might provide a useful insight to reveal the function and mechanism of EDAG.

Key words

erythroid differentiation-associated gene (EDAG) / ChIP-seq / CD34+ cells / bioinformatics

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DONG Xiao-Ming, ZHENG Wei-Wei, YIN Rong-Hua, ZHAN Yi-Qun, YANG Xiao-Ming, LI Chang-Yan. Genome-wide Research on Transcription Factor EDAG Binding Profiling  by Using ChIP-seq[J]. Chinese Journal of Biochemistry and Molecular Biology, 2013, 29(6): 578-584

References

[1]许望翔,魏汉东,汪思应,等.用表达性差异显示分析技术分离人胎肝组织选择性表达基因[J].中国应用生理学杂志 (Xu W X, Wei H D, Wang S Y, et al.Isolation of specific expression gene in human fetal liver by representational difference analysis[J]. Chin J ApplPhysiol),2001,17(2):192-194                                                                     
[2] 闾军,许望翔,汪思应,等.EDAG-1,一种与造血调控密切相关新基因的分离和确认[J].生物化学与生物物理学报(Lu J, Xu W X, Wang S Y, et al. Isolation and characterization of EDAG-1, a novel gene related to regulation in hematopoietic system [J].ActaBiochimBiophysSin),2001,33(6):641-646                                                                                 
[3] 闾军,许望翔,汪思应,等.在NIH3T3细胞中高表达EDAG-1基因导致细胞恶性转化[J].生物化学与生物物理学报(Lu J, Xu W X, Wang S Y, et al. Overexpression of EDAG-1 in NIH3T3 cells leads to malignant transformation[J]. Acta Biochim Biophys Sin), 2002, 34(1):95-98    
[4] Yang L V, Nicholson R H, Kaplan J, et al. Hemogen is a novel nuclear factor specifically expressed in mouse hematopoietic development and its human homologue EDAG maps to chromosome 9q22, a region containing breakpoints of hematological neoplasms[J]. Mech Dev, 2001, 104(1-2):105-111                                                      
[5] Wurtz T, Kruger A, Christersson C, et al. A new protein expressed in bone marrow cells and osteoblasts with implication in osteoblast recruitment[J]. Exp Cell Res, 2001, 263(2):236-242                                                                     
[6] Kruger A, Ellerstrom C, Lundmark C, et al. RP59, a marker for osteoblast recruitment, is also detected in primitive mesenchymal cells, erythroid cells, and megakaryocytes[J]. Dev Dyn, 2002, 223(3):414-418                                                        
[7] Li CY, Zhan YQ, Xu CW, et al. EDAG regulates the proliferation and differentiation of hematopoietic cells and resists cell apoptosis through the activation of nuclear factor-kappa B[J]. Cell Death Differ, 2004, 11(12):1299-1308                                       
[8] Li CY, Zhan YQ,LiW, et al. Overexpression of a hematopoietic transcriptional regulator EDAG induces myelopoiesis and suppresses lymphopoiesis in transgenic mice[J]. Leukemia, 2007,21(11): 2277-2286                                                     
[9] Carey MF, Peterson CL, Smale ST, et al. Chromatin immunoprecipitation (ChIP)[J]. Cold Spring Harbor Protoc, 2009, 2009(9):pdb. prot5279
[10] Shendure J, Ji H. Next-generation DNA sequencing[J]. Nat Biotechnol,2008, 26(10):1135-1145                                   
[11] Park PJ. ChIP-seq: advantages and challenges of a maturing technology[J]. Nat Rev Genet, 2009, 10(10):669-680          
[12] Johnson D S, Mortazavi A, Myers R M, et al. Genome-wide mapping of in vivo protein-DNA interactions [J]. Science, 2007, 316(5830):1497-1502
[13] Mardis E R. ChIP-seq: welcome to the new frontier[J]. Nat Methods, 2007, 4(8):613-614                                 
[14] Baek E J, Kim H S, Kim S, et al. In vitro clinical-grade generation of red blood cells from human umbilical cord blood CD34+ cells[J]. Transfusion, 2008, 48(10):2235-2245                                                               
[15] Aleksic J, Russell S.ChIPing away at the genome: the new frontier travel guide[J].Mol Biosyst, 2009, 5(12):1421-1428              
[16] Tallack MR, Whitington T, Yuen WS,et al. A global role for KLF1 in erythropoiesis revealed by ChIP-seq in primary erythroid cells[J].Genome Res,2010, 20(8):1052-1063                                                                 
[17] Cheng Y, Wu W, Kumar SA, et al. Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression[J].Genome Res,2009,19(12):2172-2184                                  
[18] Tijssen MR, Cvejic A, Joshi A, et al. Genome-wide analysis of simultaneous GATA1/2, RUNX1, FLI1, and SCL binding in megakaryocytes identifies hematopoietic regulators[J].Dev Cell, 2011, 20(5):597-609                                                 
[19] Wilson NK, Miranda-Saavedra D, Kinston S, et al. The transcriptional program controlled by the stem cell leukemia gene Scl/Tal1 during early embryonic hematopoietic development[J].Blood,2009, 113(22):5456-5465                                
[20] Fujiwara T, O'Geen H, Keles S, et al. Discoveringhematopoieticmechanisms through genome-wide analysis of GATA factor chromatin occupancy[J].Mol Cell, 2009, 36(4):667-681                                                              
[21] Pilon AM, Ajay SS, Kumar SA, et al. Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factorerythroidKruppel-like factor during erythrocyte differentiation[J].Blood, 2011, 118(17):e139-148                                      
[22] Ding YL, Xu CW, Wang ZD, et al. Over-expression of EDAG in the myeloid cell line 32D: induction of GATA-1 expression and erythroid/megakaryocytic phenotype[J].J Cell Biochem, 2010, 110(4):866-874                                   
[23]Murre C. Helix-loop-helix proteins and lymphocyte development[J]. Nat Immunol, 2005, 6(11):1079-1086               
[24]Barndt R, Dai MF, Zhuang Y.A novel role for HEB downstream or parallel to the pre-TCR signaling pathway during alpha beta thymopoiesis[J].J Immunol, 1999,163(6):3331-3343

Funding

Supported by Talented Youth Science Foundation(No. 81222005)

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