Global Egr1-miRNAs binding analysis in PMA-induced K562 cells using ChIP-Seq

Journal of Biomedicine and Biotechnology

Volumn 2010, Issue , 2010, Pages

  Lu, Zuhong ^a   Wang, Wei ^a   Zhou, Dequang ^b   Shi, Xiaolong ^a   Tang, Chao ^a   Xie, Xueying ^a   Tu, Jing ^a   Ge, Qinyu ^a  

^a SOUTHEAST UNIVERSITY   (China)

^b LANZHOU UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR; HEMIN; MICRORNA;

ARTICLE; BINDING SITE; BIOINFORMATICS; CELL DIFFERENTIATION; CHROMATIN IMMUNOPRECIPITATION; HUMAN; HUMAN CELL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN MOTIF; SCORING SYSTEM;

CELL LINE, TUMOR; CHROMATIN IMMUNOPRECIPITATION; COMPUTATIONAL BIOLOGY; EARLY GROWTH RESPONSE PROTEIN 1; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; K562 CELLS; MICRORNAS; POLYMERASE CHAIN REACTION; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; SEQUENCE ANALYSIS, DNA;

EID: 77956716215     PISSN: 11107243     EISSN: 11107251     Source Type: Journal    
DOI: 10.1155/2010/867517     Document Type: Article

References (37)

1. He L., Hannon G. J., MicroRNAs: small RNAs with a big role in gene regulation Nature Reviews Genetics 2004 5 7 522 531
2. Bartel D. P., MicroRNAs: genomics, biogenesis, mechanism, and function Cell 2004 116 2 281 297
3. Griffiths-Jones S., Saini H. K., Dongen S. V., Enright A. J., miRBase: tools for microRNA genomics Nucleic Acids Research 2008 36 D154 D158
4. Sassen S., Miska E. A., Caldas C., MicroRNAimplications for cancer Virchows Archiv 2008 452 1 1 10
5. Ambros V., The functions of animal microRNAs Nature 2004 431 7006 350 355
6. Huo X.-F., Yu J., Peng H., Du Z.-W., Liu X.-L., Ma Y.-N., Zhang X., Zhang Y., Zhao H.-L., Zhang J.-W., Differential expression changes in K562 cells during the hemin-induced erythroid differentiation and the phorbol myristate acetate (PMA)-induced megakaryocytic differentiation Molecular and Cellular Biochemistry 2006 292 1-2 155 167
7. Green A. R., DeLuca E., Begley C. G., Antisense SCL suppresses self-renewal and enhances spontaneous erythroid differentiation of the human leukaemic cell line K562 The EMBO Journal 1991 10 13 4153 4158
8. Cheng T., Wang Y. S., Dai W., Transcription factor egr-1 is involved in phorbol 12-myristate 13-acetate- induced megakaryocytic differentiation of K562 cells The Journal of Biological Chemistry 1994 269 49 30848 30853
9. Green A. R., Rockman S., DeLuca E., Begley C. G., Induced myeloid differentiation of K562 cells with downregulation of erythroid and megakaryocytic transcription factors: a novel experimental model for hemopoietic lineage restriction Experimental Hematology 1993 21 4 525 531
10. Ben-Ami O., Pencovich N., Lotem J., Levanon D., Groner Y., A regulatory interplay between miR-27a and Runx1 during megakaryopoiesis Proceedings of the National Academy of Sciences of the United States of America 2009 106 1 238 243
11. Navarro F., Gutman D., Meire E., Cceres M., Rigoutsos I., Bentwich Z., Lieberman J., miR-34a contributes to megakaryocytic differentiation of K562 cells independently of p53 Blood 2009 114 10 2181 2192
12. Yuan J.-Y., Wang F., Yu J., Yang G.-H., Liu X.-L., Zhang J.-W., MicroRNA-223 reversibly regulates erythroid and megakaryocytic differentiation of K562 cells Journal of Cellular and Molecular Medicine 2009 13 11-12 4551 4559
13. Yang G.-H., Wang F., Yu J., Wang X.-S., Yuan J.-Y., Zhang J.-W., MicroRNAs are involved in erythroid differentiation control Journal of Cellular Biochemistry 2009 107 3 548 556
14. Garzon R., Pichiorri F., Palumbo T., Iuliano R., Cimmino A., Aqeilan R., Volinia S., Bhatt D., Alder H., Marcucci G., Calin G. A., Liu C.-G., Bloomfield C. D., Andreeff M., Croce C. M., MicroRNA fingerprints during human megakaryocytopoiesis Proceedings of the National Academy of Sciences of the United States of America 2006 103 13 5078 5083
15. Lu J., Guo S. Q., Ebert B. L., Zhang H., Peng X., Bosco J., Pretz J., Schlanger R., Wang J. Y., Mak R. H., Dombkowski D. M., Preffer F. I., Scadden D. T., Golub T. R., MicroRNA-mediated control of cell fate in megakaryocyte- erythrocyte progenitors Developmental Cell 2008 14 6 843 853
16. Gashler A., Sukhatme V. P., Early growth response protein 1 (Egr-1): prototype of a zinc-finger family of transcription factors Progress in Nucleic Acid Research and Molecular Biology 1995 50 191 224
17. Silverman E. S., Collins T., Pathways of Egr-1-mediated gene transcription in vascular biology American Journal of Pathology 1999 154 3 665 670
18. Liu C. T., Yao J., Mercola D., Adamson E., The transcription factor EGR-1 directly transactivates the fibronectin gene and enhances attachment of human glioblastoma cell line U251 The Journal of Biological Chemistry 2000 275 27 20315 20323
19. Gitenay D., Baron V. T., Is EGR1 a potential target for prostate cancer therapy? Future Oncology 2009 5 7 993 1003
20. Sharma A., Kumar M., Aich J., Hariharan M., Brahmachari S. K., Agrawal A., Ghosh B., Posttranscriptional regulation of interleukin-10 expression by hsa-miR-106a Proceedings of the National Academy of Sciences of the United States of America 2009 106 14 5761 5766
21. Johnson D. S., Mortazavi A., Myers R. M., Wold B., Genome-wide mapping of in vivo protein-DNA interactions Science 2007 316 5830 1497 1502
22. Boyd K. E., Wells J., Gutman J., Bartley S. M., Farnham P. J., c-Myc target gene specificity is determined by a post-DNA-binding mechanism Proceedings of the National Academy of Sciences of the United States of America 1998 95 23 13887 13892
23. SOLiD Analysis Tools,. http://solidsoftwaretools.com/gf/project/corona/
24. Ji H. K., Jiang H., Ma W. X., Johnson D. S., Myers R. M., Wong W. H., An integrated software system for analyzing ChIP-chip and ChIP-seq data Nature Biotechnology 2008 26 11 1293 1300
25. Liu C., Adamson E., Mercola D., Transcription factor EGR-1 suppresses the growth and transformation of human HT-1080 fibrosarcoma cells by induction of transforming growth factor 1 Proceedings of the National Academy of Sciences of the United States of America 1996 93 21 11831 11836
26. Marson A., Levine S. S., Cole M. F., Frampton G. M., Brambrink T., Johnstone S., Guenther M. G., Johnston W. K., Wernig M., Newman J., Calabrese J. M., Dennis L. M., Volkert T. L., Gupta S., Love J., Hannett N., Sharp P. A., Bartel D. P., Jaenisch R., Young R. A., Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic dtem cells Cell 2008 134 3 521 533
27. Kuhn R. M., Karolchik D., Zweig A. S., Wang T., Smith K. E., Rosenbloom K. R., Rhead B., Raney B. J., Pohl A., Pheasant M., Meyer L., Hsu F., Hinrichs A. S., Harte R. A., Giardine B., Fujita P., Diekhans M., Dreszer T., Clawson H., Barber G. P., Haussler D., Kent W. J., The UCSC genome browser database: update 2009 Nucleic Acids Research 2009 37 D755 D761
28. Boyer L. A., Lee T. I., Cole M. F., Johnstone S. E., Levine S. S., Zucker J. P., Guenther M. G., Kumar R. M., Murray H. L., Jenner R. G., Gifford D. K., Melton D. A., Jaenisch R., Young R. A., Core transcriptional regulatory circuitry in human embryonic stem cells Cell 2005 122 6 947 956
29. Papadopoulos G. L., Reczko M., Simossis V. A., Sethupathy P., Hatzigeorgiou A. G., The database of experimentally supported targets: a functional update of TarBase Nucleic Acids Research 2009 37 D155 D158
30. Zheng Q., Wang X. J., GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis Nucleic Acids Research 2008 36 W358 W363
31. Bryne J. C., Valen E., Tang M.-H. E., Marstrand T., Winther O., Da piedade I., Krogh A., Lenhard B., Sandelin A., JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update Nucleic Acids Research 2008 36 D102 D106
32. Kubosaki A., Tomaru Y., Tagami M., Arner E., Miura H., Suzuki T., Suzuki M., Suzuki H., Hayashizaki Y., Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation Genome Biology 2009 10 4, article R41
33. Tang C., Shi X., Wang W., Global analysis of in vivo EGR1-binding sites in erythroleukemia cell using chromatin immunoprecipitation and massively parallel sequencing. Electrophoresis. In press
34. Tu K., Yu H., Hua Y.-J., Li Y.-Y., Liu L., Xie L., Li Y.-X., Combinatorial network of primary and secondary microRNA-driven regulatory mechanisms Nucleic Acids Research 2009 37 18 5969 5980
35. Landgraf P., Rusu M., Sheridan R., Sewer A., Iovino N., Aravin A., Pfeffer S., Rice A., Kamphorst A. O., Landthaler M., Lin C., Socci N. D., Hermida L., Fulci V., Chiaretti S., Fo R., Schliwka J., Fuchs U., Novosel A., Mller R.-U., Schermer B., Bissels U., Inman J., Phan Q., Chien M., Weir D. B., Choksi R., De Vita G., Frezzetti D., Trompeter H.-I., Hornung V., Teng G., Hartmann G., Palkovits M., Di Lauro R., Wernet P., Macino G., Rogler C. E., Nagle J. W., Ju J., Papavasiliou F. N., Benzing T., Lichter P., Tam W., Brownstein M. J., Bosio A., Borkhardt A., Russo J. J., Sander C., Zavolan M., Tuschl T., A mammalian microRNA expression atlas based on small RNA library sequencing Cell 2007 129 7 1401 1414
36. Jiang C. Z., Pugh B. F., Nucleosome positioning and gene regulation: advances through genomics Nature Reviews Genetics 2009 10 3 161 172
37. Hobert O., Gene regulation by transcription factors and MicroRNAs Science 2008 319 5871 1785 1786