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Fungal Morphology, Iron Homeostasis, and Lipid Metabolism Regulated by a GATA Transcription Factor in Blastomyces dermatitidis

DOI: 10.1371/journal.ppat.1004959

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Abstract:

In response to temperature, Blastomyces dermatitidis converts between yeast and mold forms. Knowledge of the mechanism(s) underlying this response to temperature remains limited. In B. dermatitidis, we identified a GATA transcription factor, SREB, important for the transition to mold. Null mutants (SREBΔ) fail to fully complete the conversion to mold and cannot properly regulate siderophore biosynthesis. To capture the transcriptional response regulated by SREB early in the phase transition (0–48 hours), gene expression microarrays were used to compare SREB? to an isogenic wild type isolate. Analysis of the time course microarray data demonstrated SREB functioned as a transcriptional regulator at 37°C and 22°C. Bioinformatic and biochemical analyses indicated SREB was involved in diverse biological processes including iron homeostasis, biosynthesis of triacylglycerol and ergosterol, and lipid droplet formation. Integration of microarray data, bioinformatics, and chromatin immunoprecipitation identified a subset of genes directly bound and regulated by SREB in vivo in yeast (37°C) and during the phase transition to mold (22°C). This included genes involved with siderophore biosynthesis and uptake, iron homeostasis, and genes unrelated to iron assimilation. Functional analysis suggested that lipid droplets were actively metabolized during the phase transition and lipid metabolism may contribute to filamentous growth at 22°C. Chromatin immunoprecipitation, RNA interference, and overexpression analyses suggested that SREB was in a negative regulatory circuit with the bZIP transcription factor encoded by HAPX. Both SREB and HAPX affected morphogenesis at 22°C; however, large changes in transcript abundance by gene deletion for SREB or strong overexpression for HAPX were required to alter the phase transition.

References

[1]  Gauthier GM & Klein BS. Insights into fungal morphogenesis and immune evasion. Microbe. 2008; 3: 416–423. pmid:20628478
[2]  Nemecek JC, Wüthrich M, Klein BS. Global control of dimorphism and virulence in fungi. Science. 2006;312: 583–588. pmid:16645097 doi: 10.1126/science.1124105
[3]  Finkel-Jimenez B, Wüthrich M, Klein BS. BAD1, an essential virulence factor of Blastomyces dermatitidis, suppresses host TNF-alpha production through TGF-beta-dependent and–independent mechanisms. J Immunol. 2002;168: 5746–5755. pmid:12023375 doi: 10.4049/jimmunol.168.11.5746
[4]  Chapman SW, Dismukes WE, Proia LA, Bradsher RW, Pappas PG, et al. Clinical practice guidelines for the management of blastomycosis: 2008 update by the Infectious Diseases Society of America. Clin Infect Dis 2008;46: 1801–1812. doi: 10.1086/588300. pmid:18462107
[5]  Gauthier GM, Safdar N, Klein BS, Andes DR. Blastomycosis in solid organ transplant recipients. Transpl Infect Dis. 2007;9: 310–317. pmid:17428278 doi: 10.1111/j.1399-3062.2007.00227.x
[6]  Fisher MC, Koenig GL, White TL, San-Blas G, Negroni R, et al. Biogeographic range expansion into South America by Coccidioides immitis mirrors New World patterns of human migration. Proc Natl Acad Sci USA. 2001;98: 4558–4562. pmid:11287648 doi: 10.1073/pnas.071406098
[7]  Nguyen VQ and Sil A. Temperature-induced switch to the pathogenic yeast form of Histoplasma capsulatum requires Ryp1, a conserved transcriptional regulator. Proc Natl Acad Sci USA 2008;105: 4880–4885. doi: 10.1073/pnas.0710448105. pmid:18339808
[8]  Mahvi TA. A comparative study of the yeast and mycelial phases of Histoplasma capsulatum. I. pathways of carbohydrate dissimilation. J Infect Dis. 1965;115: 226–232. pmid:14331704 doi: 10.1093/infdis/115.3.226
[9]  Kanetsuna F, and Carbonell LM. Enzymes in glycolysis and the citric acid cycle in the yeast and mycelial forms of Paracoccidioides brasiliensis. J Bacteriol. 1966;92: 1315–1320. pmid:5924267
[10]  Arraes EF, Benoliel B, Burtet RT, Costa PL, Galdino AS, et al. General metabolism of the dimorphic and pathogenic fungus Paracoccidioides brasiliensis. Gen Mol Res. 2005;4: 290–308.
[11]  Domer JE, and Hamilton JG. The readily extracted lipids of Histoplasma capsulatum and Blastomyces dermatitidis. Biochim Biophys Acta. 1971; 231: 465–478. pmid:5089693 doi: 10.1016/0005-2760(71)90114-7
[12]  Toledo MS, Levery SB, Suzuki E, Straus AH, Takahashi HK. Characterization of cerebrosides from the thermally dimorphic mycopathogen Histoplasma capsulatum: expression of 2-hydroxy fatty N-acyl (E)-Δ3-unsaturation correlates with the yeast-mycelium phase transition. Glycobiology. 2001;11: 113–124. pmid:11287398 doi: 10.1093/glycob/11.2.113
[13]  Kanetsuna F, and Carbonell LM. Cell wall composition of the yeast-like and mycelial forms of Blastomyces dermatitidis. J Bacteriol 1971;106: 946–948. pmid:5557599
[14]  Webster RH and Sil A. Conserved factors Ryp2 and Ryp3 control cell morphology and infectious spore formation in the fungal pathogen Histoplasma capsulatum. Proc Natl Acad Sci USA. 2008;105: 14573–14578. doi: 10.1073/pnas.0806221105. pmid:18791067
[15]  Beyhan S, Gutierrez M, Voorhies M, Sil A. A temperature-responsive network links cell shape and virulence traits in a primary fungal pathogen. PLoS Biol. 2013;11:31001614. doi: 10.1371/journal.pbio.1001614
[16]  Bugeja HE, Hynes MJ, Andrianopoulos A. HgrA is necessary and sufficient to drive hyphal growth in the dimorphic pathogen Penicillium marneffei. Mol Microbiol. 2013;88: 998–1014. doi: 10.1111/mmi.12239. pmid:23656348
[17]  Todd RB, Greenhalgh JR, Hynes MJ, Andrianopoulos A. TupA, the Penicillium marneffei Tup1p homolog, represses both yeast and spore development. Mol Microbiol. 2003;48: 85–94. pmid:12657047 doi: 10.1046/j.1365-2958.2003.03426.x
[18]  Gauthier GM, Sullivan TD, Gallardo SS, Brandhorst TT, Vanden Wymelenberg AJ, et al. SREB, a GATA transcription factor that directs disparate fates in Blastomyces dermatitidis including morphogenesis and siderophore biosynthesis. PLoS Pathog. 2010;6: e1000846. doi: 10.1371/journal.ppat.1000846. pmid:20368971
[19]  Hwang LH, Seth E, Gilmore SA, Sil A. SRE1 regulates iron-dependent and–independent pathways in the fungal pathogen Histoplasma capsulatum. Eukaryot Cell. 2012;11: 16–25. doi: 10.1128/EC.05274-11. pmid:22117028
[20]  Hilty J, Smulian AG, Newman SL. The Histoplasma capsulatum vacuolar ATPase is required for iron homeostasis, intracellular replication in macrophages, and virulence in a murine model of histoplasmosis. Mol Microbiol. 2008;70: 127–139. doi: 10.1111/j.1365-2958.2008.06395.x. pmid:18699866
[21]  Gilmore SA, Naseem S, Konopka JB, Sil A. N-acetylglucosamine (GlcNAc) triggers a rapid, temperature-responsive morphogenetic program in thermally dimorphic fungi. PLoS Genetics. 2013;9: e1003799. doi: 10.1371/journal.pgen.1003799. pmid:24068964
[22]  Chandarlapaty S and Errede B. Ash1, a daughter cell-specific protein, is required for pseudohyphal growth of Saccharomyces cerevisiae. Mol Cell Biol. 1998;18: 2884–2891. pmid:9566907
[23]  Long RM, Singer RH, Meng X, Gonzalez I, Nasmyth K, Jansen RP. Mating type switching in yeast controlled by asymmetric localization of ASH1 mRNA. Science. 1997;277: 383–387. pmid:9219698 doi: 10.1126/science.277.5324.383
[24]  Jung WH, Sham A, White R, Kronstad JW. Iron regulation of the major virulence factors in the AIDS-associated pathogen Cryptococcus neoformans. PLoS Biol. 2006; 4: e410. pmid:17121456 doi: 10.1371/journal.pbio.0040410
[25]  Jung WH and Kronstad JW. The iron-responsive, GATA-type transcription factor cir1 influences mating in Cryptococcus neoformans. Mol Cells. 2011;31: 73–7. doi: 10.1007/s10059-011-0011-0. pmid:21120626
[26]  He Q, Cheng P, Yang Y, Wang L, Garnder KH, Lui Y. (2002) White collar-1, a DNA binding transcription factor and a light sensor. Science 297: 840–843. pmid:12098705 doi: 10.1126/science.1072795
[27]  Todd RB, Fraser JA, Wong KH, Davis MA, Hynes MJ. Nuclear accumulation of GATA factor AreA in response to complete nitrogen starvation by regulation of nuclear export. Eukaryot Cell. 2005;4: 1646–53. pmid:16215172 doi: 10.1128/ec.4.10.1646-1653.2005
[28]  Haas H, Zadra I, Stoffler G, Angermayr K. The Aspergillus nidulans GATA factor SREA is involved in regulation of siderophore biosynthesis and control of iron uptake. J Biol Chem. 1999;274: 4613–9. pmid:9988696 doi: 10.1074/jbc.274.8.4613
[29]  Chao LY, Marletta MA, Rine J. Sre1, an iron-modulated GATA DNA-binding protein of iron-uptake genes in the fungal pathogen Histoplasma capsulatum. Biochemistry. 2008;47: 7274–7283. doi: 10.1021/bi800066s. pmid:18549241
[30]  Smyth GK. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 2004;3: Article 3. doi: 10.2202/1544-6115.1027
[31]  Kendziorski CM, Newton MA, Lan H, Gould MN. On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles. Stat Med. 2003;22: 3899–3914. pmid:14673946 doi: 10.1002/sim.1548
[32]  Kumme J, Dietz M, Wagner C, Schuller HJ. Dimerization of yeast transcription factors Ino2 and Ino4 is regulated by precursors of phospholipid biosynthesis mediated by Opi1 repressor. Curr Genet. 2008;54: 35–45. doi: 10.1007/s00294-008-0197-7. pmid:18542964
[33]  Howard DH. Acquisition, transport, and storage of iron by pathogenic fungi. Clin Microbiol Rev. 1999;23:394–404.
[34]  Giles SS and Czuprynski CJ. Extracellular calcium and magnesium, but not iron, are needed for optimal growth of Blastomyces dermatitidis yeast form cells in vitro. Clin Diagn Lab Immunol. 2004;11: 426–429. pmid:15013999 doi: 10.1128/cdli.11.2.426-429.2004
[35]  Stearman R, Yuan DS, Yamaguchi-Iwai Y, Klausner RD, Dancis A. A permease-oxidase complex involved in high-affinity iron uptake in yeast. Science. 1996;271: 1552–1557. pmid:8599111 doi: 10.1126/science.271.5255.1552
[36]  Jung WH, Sham A, Lian T, Singh A, Kosman DJ, Kronstad JW. Iron source preference and regulation of iron uptake in Cryptococcus neoformans. PLoS Pathog. 2008; 4: e45. doi: 10.1371/journal.ppat.0040045. pmid:18282105
[37]  Knight SA, Vilaire G, Lesulsse E, Dancis A. Iron acquisition from transferrin by Candida albicans depends on the reductive pathway. Infect Immun. 2005;73: 5482–5492. pmid:16113264 doi: 10.1128/iai.73.9.5482-5492.2005
[38]  Schrettl M, Bignell E, Kragl C, Joechl C, Rogers T, et al. Siderophore biosynthesis but not reductive iron assimilation is essential for Aspergillus fumigatus virulence. J Exp Med. 2004;200: 1213–1219. pmid:15504822 doi: 10.1084/jem.20041242
[39]  Labbé S, Khan MG, Jacques JF. Iron uptake and regulation in Schizosaccharomyces pombe. Curr Opin Microbiol. 2013;16: 669–676. doi: 10.1016/j.mib.2013.07.007. pmid:23916750
[40]  Zarnowski R, Cooper KG, Brunold LS, Calaycay J, Woods JP. Histoplasma capsulatum secreted gamma-glutamyltransferase reduces iron by generating an efficient ferric reductant. Mol Microbiol 2008;70: 352–368. doi: 10.1111/j.1365-2958.2008.06410.x. pmid:18761625
[41]  Czabany T, Wagner A, Zweytick D, Lohner K, Leitner E, et al. Structural and biochemical properties of lipid particles from the yeast Saccharomyces cerevisiae. J Biol Chem. 2008;283: 17065–17074. doi: 10.1074/jbc.M800401200. pmid:18430725
[42]  Kohlwein SD, Veenhuis M, van der Klei IJ. Lipid droplets and peroxisomes: key players in cellular lipid homeostasis or a matter of–fatstore ‘em up or burn ‘em down. Genetics. 2013;193: 1–50. doi: 10.1534/genetics.112.143362. pmid:23275493
[43]  Radulovic M, Knittelfelder O, Cristobal-Sarramian A, Kolb D, Wolinski H et al. The emergence of lipid droplets in yeast: current status and experimental approaches. Curr Genet. 2013;59: 231–242. doi: 10.1007/s00294-013-0407-9. pmid:24057105
[44]  Manickam E, Sinclair AJ, Cameron-Smith D. Suppressive actions of eicosapentaenoic acid on lipid droplet formation in 3T3-L1 adipocytes. Lipids Health Dis. 2010;9: 57. doi: 10.1186/1476-511X-9-57. pmid:20525346
[45]  Natter K and Kohlwein SD. Yeast and cancer cells–common principles in lipid metabolism. Biochem Biophys Acta. 2013;1831: 314–326. doi: 10.1016/j.bbalip.2012.09.003. pmid:22989772
[46]  Komachi K, Johnson AD. Residues in the WD repeats of Tup1 required for interaction with alpha2. Mol Cell Biol. 1997;17: 6023–6028. pmid:9315661
[47]  DeSilva H, Lee K, Osley MA. Functional dissection of yeast Hir1p, a WD repeat-containing transcriptional corepressor. Genetics. 1998;148: 657–667. pmid:9504914
[48]  Hortschansky P, Eisendle M, Al-Abadallah Q, Schmidt AD, Bergmann S et al. Interaction of HapX with the CCAAT-binding complex—a novel mechanism of gene regulation by iron. EMBO J. 2007;26: 3157–3168. pmid:17568774 doi: 10.1038/sj.emboj.7601752
[49]  Schrettl M, Beckmann N., Varga J., Heinekamp T, Jacobsen ID et al. HapX-mediated adaptation to iron starvation is crucial for virulence of Aspergillus fumigatus. PLoS Pathog. 2010;6: e1001124. doi: 10.1371/journal.ppat.1001124. pmid:20941352
[50]  Chen C, Kalyan P, French SD, Tuch BB, Noble SM. An iron homeostasis regulatory circuit in Candida albicans commensalism and pathogenesis. Cell Host Microbe 2011;10:118–135. doi: 10.1016/j.chom.2011.07.005. pmid:21843869
[51]  Krajaejun T, Gauthier GM, Rappleye CA, Sullivan TD, Klein BS. Development and application of a green fluorescent protein sentinel system for identification of RNA interference in Blastomyces dermatitidis illuminates the role of septin in morphogenesis and sporulation. Eukaryot Cell. 2007;6: 1299–1309. pmid:17496124 doi: 10.1128/ec.00401-06
[52]  Schrettl M, Kim HS, Eisendle M, Kragl C, Nierman WC, et al. SreA-mediated iron regulation in Aspergillus fumigatus. Mol Microbiol. 2008;70: 27–43. doi: 10.1111/j.1365-2958.2008.06376.x. pmid:18721228
[53]  Lan CY, Rodarte G, Murillo LA, Jones T, Davis RW, et al. Regulatory networks affected by iron availability in Candida albicans. Mol Microbiol. 2004;53: 1451–1469. pmid:15387822 doi: 10.1111/j.1365-2958.2004.04214.x
[54]  Roy I and Landau JW. Composition of the alkali resistant cell wall material of dimorphic Blastomyces dermatitidis. Sabouraudia. 1972;10: 107–112. pmid:4557874 doi: 10.1080/00362177285190231
[55]  Kobayashi GS and Guiliacci PL. Cell wall studies of Histoplasma capsulatum. Sabouraudia. 1967;5: 180–188. pmid:6036225 doi: 10.1080/00362176785190371
[56]  Blatzer M, Schrettl M., Sarg B, Lindner HH, Pfaller K, et al. SidL, an Aspergillus fumigatus transacetylase involved in the biosynthesis of the siderophores ferricrocin and hydroxyferricrocin. Appl Environ Microbiol. 2011;77: 4959–4966. doi: 10.1128/AEM.00182-11. pmid:21622789
[57]  Labbé S, Pelletier B, Mercier A. Iron homeostasis in the fission yeast Schizosaccharomyces pombe. Biometals. 2007;20: 523–537. pmid:17211681 doi: 10.1007/s10534-006-9056-5
[58]  Zarnowski R and Woods JP. Glutathione-dependent extracellular ferric reductase activities in dimorphic zoopathogenic fungi. Microbiology 2005;151: 2244–2240. doi: 10.1099/mic.0.27918-0
[59]  Di Salvo AF and Denton JF. Lipid content of four strains of Blastomyces dermatitidis of different mouse virulence. J. Bacteriol. 1963;85: 927–931. pmid:14044964
[60]  Kanetsuna F, Carbonell LM, Moreno RE, Rodriguez J. Cell wall composition of the yeast and mycelial forms of Paracoccidioides brasiliensis. J. Bacteriol. 1969;97: 1036–1041. pmid:5776517
[61]  Wilfling F, Wang J, Haas JT, Krahmer N, Gould TJ et al. Triacylglycerol synthesis enzymes mediate lipid droplet growth by relocalizing from ER to lipid droplets. Dev Cell. 2013;24: 384–399. doi: 10.1016/j.devcel.2013.01.013. pmid:23415954
[62]  Oelkers P, Cromley D, Padamsee M, Billheimer JT. The DGA1 gene determines a second triglyceride synthetic pathway in yeast. J Biol Chem 2002;277: 8877–8881. pmid:11751875 doi: 10.1074/jbc.m111646200
[63]  Sorger D, Athenstaedt K, Hrastnik H, Daum G. A yeast strain lacking lipid particles bears a defect in ergosterol formation. J Biol Chem. 2004;279: 31190–31196. pmid:15155725 doi: 10.1074/jbc.m403251200
[64]  Wolinski H, Kolb D, Hermann S, Koning RI, Kohlwein SD. A role for seipin in lipid droplet dynamics and inheritance in yeast. J Cell Sci. 2011;124: 3894–3904. doi: 10.1242/jcs.091454. pmid:22100922
[65]  Maresca B, and Kobayashi G. Changes in membrane fluidity modulate heat shock gene expression and produced attenuated strains in the dimorphic fungus Histoplasma capsulatum. Arch Med Res. 1993;24: 247–249. pmid:8298273
[66]  Carratù L, Franceschelli S, Pardini CL, et al. Membrane lipid perturbation modified the set point of the temperature of heat shock response in yeast. Proc Natl Acad Sci USA. 1996;93: 3870–3875. pmid:8632982 doi: 10.1073/pnas.93.9.3870
[67]  Chen C and Noble SM. Post-transcriptional regulation of the Sef1 transcription factor controls the virulence of Candida albicans in its mammalian host. PLoS Pathog. 2012;8: e1002956. doi: 10.1371/journal.ppat.1002956. pmid:23133381
[68]  Singh RP, Prasad HK, Sinha I, Agarwal N, Ntarajan K. Cap2-HAP complex is a critical transcriptional regulator that has dual but contrasting roles in regulation of iron homeostasis in Candida albicans. J Biol Chem. 2011;286: 25154–25170. doi: 10.1074/jbc.M111.233569. pmid:21592964
[69]  Brandhorst TT, Wüthrich M, Warner T, Klein B. Targeted gene disruption reveals an adhesin indispensable for pathogenicity of Blastomyces dermatitidis. J Exp Med 1999;189: 1207–1216. pmid:10209038 doi: 10.1084/jem.189.8.1207
[70]  Wüthrich M, Filutowicz HI, Warner T, Klein BS. Requisite elements in vaccine immunity to Blastomyces dermatitidis: plasticity uncovers vaccine potential in immune-deficient hosts. J Immunol. 2002;169: 6969–6976. pmid:12471131 doi: 10.4049/jimmunol.169.12.6969
[71]  Harvey RP, Schmid ES, Carrington CC, Stevens DA. Mouse model of pulmonary blastomycosis: utility, simplicity, and quantitative parameters. Am Rev Respir Dis. 1978;117: 695–703 pmid:646221
[72]  Worsham PL and Goldman WE. Quantitative plating of Histoplasma capsulatum without addition of conditioned medium or siderophores. J Med Vet Mycol. 1988;26: 137–143. pmid:3171821 doi: 10.1080/02681218880000211
[73]  Sullivan TD, Rooney PJ, Klein BS. Agrobacterium tumefaciens integrates transfer DNA into single chromosomal sites of dimorphic fungi and yields homokaryotic progeny from multinucleate yeast. Eukaryot Cell. 2002;1: 895–905. pmid:12477790 doi: 10.1128/ec.1.6.895-905.2002
[74]  Marty AJ and Gauthier GM. Blastomyces dermatitidis septins CDC3, CDC10, and CDC12 impact the morphology of yeast and hyphae, but are not required for the phase transition. Med Mycol. 2013;51: 93–102. doi: 10.3109/13693786.2012.699685. pmid:22783804
[75]  Jbel M., Mercier A, Pelletier B, Beaudoin J, Labbé S. Iron activates in vivo DNA binding of Schizosaccharomyces pombe transcription factor Fep1 through its amino-terminal region. Eukaryot Cell. 2009;8: 649–664. doi: 10.1128/EC.00001-09. pmid:19252122
[76]  Sambrook J and Russell DW. Molecular cloning: a laboratory manual, 3rd Ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press; 2001. pp. 7.4–7.8.
[77]  Storey JD and Tibshirani R. Statistical significance for genome-wide studies. Proc Natl Acad Sci USA. 2003;100: 9440–9445. pmid:12883005
[78]  Zdobnov EM and Apweiler R. InterProScan—an integration platform for the signature-recognition methods in InterPro. Bioinformatics. 2001;17: 847–848. pmid:11590104 doi: 10.1093/bioinformatics/17.9.847
[79]  Zhang B. and Horvath S. A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol. 2005;4: Article 17. doi: 10.2202/1544-6115.1128
[80]  Langfelder P., Zhang B., Horvath S. Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics. 2008;24: 719–720. pmid:18024473 doi: 10.1093/bioinformatics/btm563
[81]  Hassett R and Kosman DJ. Evidence for Cu(II) reduction as a component of copper uptake by Saccharomyces cerevisiae. J Biol Chem. 1995;270:128–134. pmid:7814363 doi: 10.1074/jbc.270.1.128
[82]  Pelletier B, Beaudoin J, Mukai Y, Labbé S. FEP1, an iron sensor regulating iron transporter gene expression in Schizosaccharomyces pombe. J Biol Chem. 2002;277: 22950–22958. pmid:11956219 doi: 10.1074/jbc.m202682200
[83]  Zarnowski R, Miyazaki M, Dobrzyn A, Ntambi JM, Woods JP. Typing of Histoplasma capsulatum strains by fatty acid profile analysis. J Med Microbiol. 2007;56: 788–797. pmid:17510264 doi: 10.1099/jmm.0.47067-0
[84]  Zarnowski R., Jaromin A., Certik M., Czabany T., Fontaine J., Jakubik T., et al. The oil of Adenanthera pavonina L. seeds and its emulsions. Z Naturforsch C. 2004;59: 321–326. pmid:18998394 doi: 10.1515/znc-2004-5-605
[85]  Mukhopadhyay A, Deplancke B, Walhout AJM, Tissenbaum HA. Chromatin immunoprecipitation by quantitative real-time PCR to study transcription factor binding to DNA in Caenorhabditis elegans. Nat Protocol. 2008;3: 698–709. doi: 10.1038/nprot.2008.38
[86]  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. pmid:19261174
[87]  Kuan P, Chung D, Pan G, Thomson JA, Stewart R, Keles S. A statistical framework for the analysis of ChIP-seq data. J Am Stat Assoc 2011;106: 891–903. doi: 10.1198/jasa.2011.ap09706
[88]  Sun G, Chung D, Liang K, Keles S. Statistical analysis of ChIP-seq data with MOSAiCS. Methods Mol Biol 2013;1038: 193–212. doi: 10.1007/978-1-62703-514-9_12. pmid:23872977
[89]  Landt SG, Marinov GK, Kundaje A et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res 2012; 22: 1813–1831. doi: 10.1101/gr.136184.111. pmid:22955991
[90]  Livak KF, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2-??Ct method. Methods. 2001;25: 402–408. pmid:11846609 doi: 10.1006/meth.2001.1262

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