ChIP-seq analysis of histone H3K9 trimethylation in peripheral blood mononuclear cells of membranous nephropathy patients

Brazilian Journal of Medical and Biological Research

Volumn 47, Issue 1, 2014, Pages 42-49

  Sui, W G ^a   He, H Y ^b   Yan, Q ^a   Chen, J J ^a   Zhang, R H ^b   Dai, Y ^c  

^a Nephrology Department   (China)

^b GUANGXI NORMAL UNIVERSITY   (China)

^c JINAN UNIVERSITY   (China)

Author keywords

ChIP seq; Epigenetics; H3K9me3; Membranous nephropathy

Indexed keywords

BIOLOGICAL MARKER; CREATININE; PROTEIN; UREA; URIC ACID; HISTONE; LYSINE;

ADULT; ARTICLE; BIRC2 GENE; BIRC3 GENE; CHROMATIN IMMUNOPRECIPITATION; CLINICAL ARTICLE; CNTN4 GENE; CONTROLLED STUDY; DGCR6 GENE; FEMALE; FLOW CYTOMETRY; GENE; GENE EXPRESSION; HIGH THROUGHPUT SEQUENCING; HISTONE METHYLATION; HUMAN; HUMAN CELL; MALE; MEMBRANOUS GLOMERULONEPHRITIS; NUCLEOTIDE SEQUENCE; PATHOGENESIS; PERIPHERAL BLOOD MONONUCLEAR CELL; PROTEIN URINE LEVEL; SNX16 GENE; CASE CONTROL STUDY; GENETICS; METABOLISM; METHYLATION; MONONUCLEAR CELL;

ADULT; CASE-CONTROL STUDIES; CHROMATIN IMMUNOPRECIPITATION; FEMALE; GLOMERULONEPHRITIS, MEMBRANOUS; HISTONES; HUMANS; LEUKOCYTES, MONONUCLEAR; LYSINE; MALE; METHYLATION;

EID: 84892986216     PISSN: 0100879X     EISSN: 1414431X     Source Type: Journal    
DOI: 10.1590/1414-431X20132809     Document Type: Article

References (30)

1. Makker SP, Tramontano A. Idiopathic membranous nephropathy: an autoimmune disease. Semin Nephrol 2011; 31: 333-340, doi: 10.1016/j.semnephrol.2011.06.004.
2. Elie V, Fakhoury M, Deschenes G, Jacqz-Aigrain E. Physiopathology of idiopathic nephrotic syndrome: lessons from glucocorticoids and epigenetic perspectives. Pediatr Nephrol 2012; 27: 1249-1256, doi: 10.1007/s00467-011-1947-1.
3. Martin C, Zhang Y. The diverse functions of histone lysine methylation. Nat Rev Mol Cell Biol 2005; 6: 838-849, doi: 10.1038/nrm1761.
4. Ciccone DN, Chen T. Histone lysine methylation in genomic imprinting. Epigenetics 2009; 4: 216-220.
5. Park JA, Kim AJ, Kang Y, Jung YJ, Kim HK, Kim KC. Deacetylation and methylation at histone H3 lysine 9 (H3K9) coordinate chromosome condensation during cell cycle progression. Mol Cells 2011; 31: 343-349, doi: 10.1007/s10059-011-0044-4.
6. Shinkai Y, Tachibana M. H3K9 methyltransferase G9a and the related molecule GLP. Genes Dev 2011; 25: 781-788, doi: 10.1101/gad.2027411.
7. Wu CC, Chen JS, Huang CF, Chen CC, Lu KC, Chu P, et al. Approaching biomarkers of membranous nephropathy from a murine model to human disease. J Biomed Biotechnol 2011; 2011: 581928.
8. Raha D, Wang Z, Moqtaderi Z, Wu L, Zhong G, Gerstein M, et al. Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci U S A 2010; 107: 3639-3644, doi: 10.1073/pnas.0911315106.
9. Wacker DA, Kim TH. From sextant to GPS: twenty-five years of mapping the genome with ChIP. J Cell Biochem 2009; 107: 6-10, doi: 10.1002/jcb.22060.
10. Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, et al. Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of arrayand sequencing-based technologies. Genome Res 2007; 17: 898-909, doi: 10.1101/gr.5583007.
11. Cybulsky AV. Membranous nephropathy. Contrib Nephrol 2011; 169: 107-125, doi: 10.1159/000313948.
12. Lin B, Wang J, Hong X, Yan X, Hwang D, Cho JH, et al. Integrated expression profiling and ChIP-seq analyses of the growth inhibition response program of the androgen receptor. PLoS One 2009; 4: e6589, doi: 10.1371/journal.pone.0006589.
13. Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL. Searching for SNPs with cloud computing. Genome Biol 2009; 10: R134, doi: 10.1186/gb-2009-10-11-r134.
14. Feng J, Liu T, Zhang Y. Using MACS to identify peaks from ChIP-Seq data. Curr Protoc Bioinformatics 2011; Chapter 2: Unit 214.
15. Shin JH, Li RW, Gao Y, Baldwin R, Li CJ. Genome-wide ChIP-seq mapping and analysis reveal butyrate-induced acetylation of H3K9 and H3K27 correlated with transcription activity in bovine cells. Funct Integr Genomics 2012; 12: 119-130, doi: 10.1007/s10142-012-0263-6.
16. Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S. AmiGO: online access to ontology and annotation data. Bioinformatics 2009; 25: 288-289, doi: 10.1093/bioinformatics/btn615.
17. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009; 10: R25, doi: 10.1186/gb-2009-10-3-r25.
18. Georgiev S, Boyle AP, Jayasurya K, Ding X, Mukherjee S, Ohler U. Evidence-ranked motif identification. Genome Biol 2010; 11: R19, doi: 10.1186/gb-2010-11-2-r19.
19. Shi J, Dawe RK. Partitioning of the maize epigenome by the number of methyl groups on histone H3 lysines 9 and 27. Genetics 2006; 173: 1571-1583, doi: 10.1534/genetics.106.056853.
20. Pfuhl T, Durr M, Spurk A, Schwalbert B, Nord R, Mysliwietz J, et al. Biochemical characterisation of the proteins encoded by the DiGeorge critical region 6 (DGCR6) genes. Hum Genet 2005; 117: 70-80, doi: 10.1007/s00439-005-1267-2.
21. Seet LF, Hong W. The Phox (PX) domain proteins and membrane traffic. Biochim Biophys Acta 2006; 1761: 878-896, doi: 10.1016/j.bbalip.2006.04.011.
22. Hanson BJ, Hong W. Evidence for a role of SNX16 in regulating traffic between the early and later endosomal compartments. J Biol Chem 2003; 278: 34617-34630, doi: 10.1074/jbc.M300143200.
23. Prunotto M, Carnevali ML, Candiano G, Murtas C, Bruschi M, Corradini E, et al. Autoimmunity in membranous nephropathy targets aldose reductase and SOD2. J Am Soc Nephrol 2010; 21: 507-519, doi: 10.1681/ASN.2008121259.
24. Cottrell CE, Bir N, Varga E, Alvarez CE, Bouyain S, Zernzach R, et al. Contactin 4 as an autism susceptibility locus. Autism Res 2011; 4: 189-199, doi: 10.1002/aur.184.
25. Manderson EN, Birch AH, Shen Z, Mes-Masson AM, Provencher D, Tonin PN. Molecular genetic analysis of a cell adhesion molecule with homology to L1CAM, contactin 6, and contactin 4 candidate chromosome 3p26pter tumor suppressor genes in ovarian cancer. Int J Gynecol Cancer 2009; 19: 513-525, doi: 10.1111/IGC.0b013e3181a3cd38.
26. Fernandez T, Morgan T, Davis N, Klin A, Morris A, Farhi A, et al. Disruption of contactin 4 (CNTN4) results in developmental delay and other features of 3p deletion syndrome. Am J Hum Genet 2004; 74: 1286-1293, doi: 10.1086/421474.
27. Cabal-Hierro L, Lazo PS. Signal transduction by tumor necrosis factor receptors. Cell Signal 2012; 24: 1297-1305, doi: 10.1016/j.cellsig.2012.02.006.
28. Dueber EC, Schoeffler AJ, Lingel A, Elliott JM, Fedorova AV, Giannetti AM, et al. Antagonists induce a conformational change in cIAP1 that promotes autoubiquitination. Science 2011; 334: 376-380, doi: 10.1126/science.1207862.
29. Santoro MM, Samuel T, Mitchell T, Reed JC, Stainier DY. Birc2 (cIap1) regulates endothelial cell integrity and blood vessel homeostasis. Nat Genet 2007; 39: 1397-1402, doi: 10.1038/ng.2007.8.
30. Pradhan M, Baumgarten SC, Bembinster LA, Frasor J. CBP mediates NF-kappaB-dependent histone acetylation and estrogen receptor recruitment to an estrogen response element in the BIRC3 promoter. Mol Cell Biol 2012; 32: 569-575, doi: 10.1128/MCB.05869-11.