Global Egr1-miRNAs binding analysis in PMA-induced K562 cells using ChIP-Seq.
Although much is known about microRNAs' regulation in gene expression and their contributions in cell fate, to date, globally lineage-(cell-) specific identification of the binding events between a transcription factor and its targeting microRNA genes is still waiting for elucidation. In this paper, we performed a ChIP-Seq experiment to find the targeting microRNA genes of a transcription factor, Egr1, in human erythroleukemia cell line K562. We found Egr1 binding sites near the promoters of 124 distinct microRNA genes, accounting for about 42% of the miRNAs which have high-confidence predicted promoters (294). We also found EGR1 bind to another 63 pre-miRNAs. We chose 12 of the 187 microRNAs with Egr1 binding sites to perform ChIP-PCR assays and the positive binding signal from ChIP-PCR confirmed the ChIP-Seq results. Our experiments provide the first global binding profile between Egr1 and its targeting microRNA genes in PMA-treated K562 cells, which may facilitate the understanding of pathways controlling microRNA biology in this specific cell line.
Wang
Wei
W
State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing 210096, China.
Zhou
Dequang
D
Shi
Xiaolong
X
Tang
Chao
C
Xie
Xueying
X
Tu
Jing
J
Ge
Qinyu
Q
Lu
Zuhong
Z
D045744:Cell Line, Tumor; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D019295:Computational Biology; D051766:Early Growth Response Protein 1 / Q000235:genetics*; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D020014:K562 Cells; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D016133:Polymerase Chain Reaction; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding; D017422:Sequence Analysis, DNA / Q000379:methods*
C497325:EGR1 protein, human; D051766:Early Growth Response Protein 1; D035683:MicroRNAs
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