Macrophage Activation as a Model System for Understanding Enhancer Transcription and eRNA Function

Chapter

Abstract

Macrophages are innate immune cells that sense the presence of pathogens through conserved pattern recognition receptors, which include TLR4. Activation of TLR4 by bacterial lipopolysaccharide induces the expression of thousands of genes that function to initiate inflammation and coordinate innate and adaptive immune responses. Transcriptional activation of TLR4-responsive genes is mediated by signal-dependent transcription factors, such as NFκB, which bind to DNA regulatory elements termed enhancers. Recent findings indicate that macrophage enhancers are actively transcribed in concert with nearby genes. Similar observations have been reported for other cell types, raising the general question of whether enhancer transcription and/or the resulting enhancer RNAs (eRNAs) are of functional importance. Here, we review the use of macrophage activation as an experimental system for addressing these questions and highlight areas for future research.

Keywords

Macrophage Enhancer Promoter eRNA mRNA Transcription TLR Chromatin Histone methylation Histone acetylation Nucleosome NFkB 
This is a preview of subscription content, log in to check access.

References

  1. Allen MA, Andrysik Z, Dengler VL, Mellert HS, Guarnieri A, Freeman JA, Sullivan KD, Galbraith MD, Luo X, Kraus WL et al (2014) Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms. Elife 3:e02200PubMedCentralPubMedCrossRefGoogle Scholar
  2. Allison KA, Kaikkonen MU, Gaasterland T, Glass CK (2014) Vespucci: a system for building annotated databases of nascent transcripts. Nucleic Acids Res 42:2433–2447PubMedCentralPubMedCrossRefGoogle Scholar
  3. Beutler B (2000) Tlr4: central component of the sole mammalian LPS sensor. Curr Opin Immunol 12:20–26PubMedCrossRefGoogle Scholar
  4. Chao SH, Price DH (2001) Flavopiridol inactivates P-TEFb and blocks most RNA polymerase II transcription in vivo. J Biol Chem 276:31793–31799PubMedCrossRefGoogle Scholar
  5. Chen Z, Zhang C, Wu D, Chen H, Rorick A, Zhang X, Wang Q (2011) Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth. EMBO J 30:2405–2419PubMedCentralPubMedCrossRefGoogle Scholar
  6. Core LJ, Waterfall JJ, Lis JT (2008) Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322:1845–1848PubMedCentralPubMedCrossRefGoogle Scholar
  7. Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA et al (2010) Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A 107:21931–21936PubMedCentralPubMedCrossRefGoogle Scholar
  8. Cristancho AG, Lazar MA (2011) Forming functional fat: a growing understanding of adipocyte differentiation. Nat Rev Mol Cell Biol 12:722–734PubMedCrossRefGoogle Scholar
  9. Dawson MA, Prinjha RK, Dittmann A, Giotopoulos G, Bantscheff M, Chan WI, Robson SC, Chung CW, Hopf C, Savitski MM et al (2011) Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia. Nature 478:529–533PubMedCentralPubMedCrossRefGoogle Scholar
  10. De Santa F, Barozzi I, Mietton F, Ghisletti S, Polletti S, Tusi BK, Muller H, Ragoussis J, Wei CL, Natoli G (2010) A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol 8:e1000384PubMedCentralPubMedCrossRefGoogle Scholar
  11. Escoubet-Lozach L, Benner C, Kaikkonen MU, Lozach J, Heinz S, Spann NJ, Crotti A, Stender J, Ghisletti S, Reichart D et al (2011) Mechanisms establishing TLR4-responsive activation states of inflammatory response genes. PLoS Genet 7:e1002401PubMedCentralPubMedCrossRefGoogle Scholar
  12. Feng R, Desbordes SC, Xie H, Tillo ES, Pixley F, Stanley ER, Graf T (2008) PU.1 and C/EBPalpha/beta convert fibroblasts into macrophage-like cells. Proc Natl Acad Sci U S A 105:6057–6062PubMedCentralPubMedCrossRefGoogle Scholar
  13. Garber M, Yosef N, Goren A, Raychowdhury R, Thielke A, Guttman M, Robinson J, Minie B, Chevrier N, Itzhaki Z et al (2012) A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol Cell 47:810–822PubMedCrossRefGoogle Scholar
  14. Gerber M, Shilatifard A (2003) Transcriptional elongation by RNA polymerase II and histone methylation. J Biol Chem 278:26303–26306PubMedCrossRefGoogle Scholar
  15. Ghisletti S, Barozzi I, Mietton F, Polletti S, De Santa F, Venturini E, Gregory L, Lonie L, Chew A, Wei C-L et al (2010) Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. Immunity 32:317–328PubMedCrossRefGoogle Scholar
  16. Hadjur S, Williams LM, Ryan NK, Cobb BS, Sexton T, Fraser P, Fisher AG, Merkenschlager M (2009) Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus. Nature 460:410–413PubMedCentralPubMedGoogle Scholar
  17. Hah N, Danko CG, Core L, Waterfall JJ, Siepel A, Lis JT, Kraus WL (2011) A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell 145:622–634PubMedCentralPubMedCrossRefGoogle Scholar
  18. Harismendy O, Notani D, Song X, Rahim NG, Tanasa B, Heintzman N, Ren B, Fu XD, Topol EJ, Rosenfeld MG et al (2011) 9p21 DNA variants associated with coronary artery disease impair interferon-gamma signalling response. Nature 470:264–268PubMedCentralPubMedCrossRefGoogle Scholar
  19. Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA et al (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 39:311–318PubMedCrossRefGoogle Scholar
  20. Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW et al (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459:108–112PubMedCentralPubMedCrossRefGoogle Scholar
  21. Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK (2010) Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 38:576–589PubMedCentralPubMedCrossRefGoogle Scholar
  22. Heinz S, Romanoski CE, Benner C, Allison KA, Kaikkonen MU, Orozco LD, Glass CK (2013) Effect of natural genetic variation on enhancer selection and function. Nature 503(7477):487–492PubMedCentralPubMedCrossRefGoogle Scholar
  23. Herrera R, Ro HS, Robinson GS, Xanthopoulos KG, Spiegelman BM (1989) A direct role for C/EBP and the AP-I-binding site in gene expression linked to adipocyte differentiation. Mol Cell Biol 9:5331–5339PubMedCentralPubMedGoogle Scholar
  24. Hsieh CL, Fei T, Chen Y, Li T, Gao Y, Wang X, Sun T, Sweeney CJ, Lee GS, Chen S et al (2014) Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation. Proc Natl Acad Sci U S A 111:7319–7324PubMedCentralPubMedCrossRefGoogle Scholar
  25. Hughes CM, Rozenblatt-Rosen O, Milne TA, Copeland TD, Levine SS, Lee JC, Hayes DN, Shanmugam KS, Bhattacharjee A, Biondi CA et al (2004) Menin associates with a trithorax family histone methyltransferase complex and with the hoxc8 locus. Mol Cell 13:587–597PubMedCrossRefGoogle Scholar
  26. Kagey MH, Newman JJ, Bilodeau S, Zhan Y, Orlando DA, van Berkum NL, Ebmeier CC, Goossens J, Rahl PB, Levine SS et al (2010) Mediator and cohesin connect gene expression and chromatin architecture. Nature 467:430–435PubMedCentralPubMedCrossRefGoogle Scholar
  27. Kaikkonen MU, Spann NJ, Heinz S, Romanoski CE, Allison KA, Stender JD, Chun HB, Tough DF, Prinjha RK, Benner C et al (2013) Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. Mol Cell 51:310–325PubMedCentralPubMedCrossRefGoogle Scholar
  28. Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, Harmin DA, Laptewicz M, Barbara-Haley K, Kuersten S et al (2010) Widespread transcription at neuronal activity-regulated enhancers. Nature 465:182–187PubMedCentralPubMedCrossRefGoogle Scholar
  29. Klemsz MJ, McKercher SR, Celada A, Van Beveren C, Maki RA (1990) The macrophage and B cell-specific transcription factor PU.1 is related to the ets oncogene. Cell 61:113–124PubMedCrossRefGoogle Scholar
  30. Koch F, Jourquin F, Ferrier P, Andrau JC (2008) Genome-wide RNA polymerase II: not genes only! Trends Biochem Sci 33:265–273PubMedCrossRefGoogle Scholar
  31. Krogan NJ, Kim M, Tong A, Golshani A, Cagney G, Canadien V, Richards DP, Beattie BK, Emili A, Boone C et al (2003) Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol 23:4207–4218PubMedCentralPubMedCrossRefGoogle Scholar
  32. Kwak H, Lis JT (2013) Control of transcriptional elongation. Annu Rev Genet 47:483–508PubMedCentralPubMedCrossRefGoogle Scholar
  33. Lam MT, Cho H, Lesch HP, Gosselin D, Heinz S, Tanaka-Oishi Y, Benner C, Kaikkonen MU, Kim AS, Kosaka M et al (2013) Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription. Nature 498:511–515PubMedCrossRefGoogle Scholar
  34. Li W, Notani D, Ma Q, Tanasa B, Nunez E, Chen AY, Merkurjev D, Zhang J, Ohgi K, Song X et al (2013) Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature 498:516–520PubMedCentralPubMedCrossRefGoogle Scholar
  35. MacConaill LE, Hughes CM, Rozenblatt-Rosen O, Nannepaga S, Meyerson M (2006) Phosphorylation of the menin tumor suppressor protein on serine 543 and serine 583. Mol Cancer Res 4:793–801PubMedCrossRefGoogle Scholar
  36. Maurya MR, Gupta S, Li X, Fahy E, Dinasarapu AR, Sud M, Brown HA, Glass CK, Murphy RC, Russell DW et al (2013) Analysis of inflammatory and lipid metabolic networks across RAW264.7 and thioglycolate-elicited macrophages. J Lipid Res 54:2525–2542PubMedCentralPubMedCrossRefGoogle Scholar
  37. Medzhitov R, Horng T (2009) Transcriptional control of the inflammatory response. Nat Rev Immunol 9:692–703PubMedCrossRefGoogle Scholar
  38. Meissner F, Scheltema RA, Mollenkopf HJ, Mann M (2013) Direct proteomic quantification of the secretome of activated immune cells. Science 340:475–478PubMedCrossRefGoogle Scholar
  39. Melo CA, Drost J, Wijchers PJ, van de Werken H, de Wit E, Oude Vrielink JA, Elkon R, Melo SA, Leveille N, Kalluri R et al (2013) eRNAs are required for p53-dependent enhancer activity and gene transcription. Mol Cell 49:524–535PubMedCrossRefGoogle Scholar
  40. Milne TA, Dou Y, Martin ME, Brock HW, Roeder RG, Hess JL (2005) MLL associates specifically with a subset of transcriptionally active target genes. Proc Natl Acad Sci U S A 102:14765–14770PubMedCentralPubMedCrossRefGoogle Scholar
  41. Mousavi K, Zare H, Dell’orso S, Grontved L, Gutierrez-Cruz G, Derfoul A, Hager GL, Sartorelli V (2013) eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci. Mol Cell 51:606–617PubMedCentralPubMedCrossRefGoogle Scholar
  42. Mullen AC, Orlando DA, Newman JJ, Loven J, Kumar RM, Bilodeau S, Reddy J, Guenther MG, DeKoter RP, Young RA (2011) Master transcription factors determine cell-type-specific responses to TGF-beta signaling. Cell 147:565–576PubMedCentralPubMedCrossRefGoogle Scholar
  43. NE II, Heward JA, Roux B, Tsitsiou E, Fenwick PS, Lenzi L, Goodhead I, Hertz-Fowler C, Heger A, Hall N et al (2014) Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes. Nat Commun 5:3979Google Scholar
  44. Ng HH, Robert F, Young RA, Struhl K (2003) Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol Cell 11:709–719PubMedCrossRefGoogle Scholar
  45. Nicodeme E, Jeffrey KL, Schaefer U, Beinke S, Dewell S, Chung CW, Chandwani R, Marazzi I, Wilson P, Coste H et al (2010) Suppression of inflammation by a synthetic histone mimic. Nature 468:1119–1123PubMedCrossRefGoogle Scholar
  46. Ong CT, Corces VG (2011) Enhancer function: new insights into the regulation of tissue-specific gene expression. Nat Rev Genet 12:283–293PubMedCentralPubMedCrossRefGoogle Scholar
  47. Ostuni R, Piccolo V, Barozzi I, Polletti S, Termanini A, Bonifacio S, Curina A, Prosperini E, Ghisletti S, Natoli G (2013) Latent enhancers activated by stimulation in differentiated cells. Cell 152:157–171PubMedCrossRefGoogle Scholar
  48. Pulakanti K, Pinello L, Stelloh C, Blinka S, Allred J, Milanovich S, Kiblawi S, Peterson J, Wang A, Yuan GC et al (2013) Enhancer transcribed RNAs arise from hypomethylated, Tet-occupied genomic regions. Epigenetics 8:1303–1320PubMedCentralPubMedCrossRefGoogle Scholar
  49. Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J (2011) A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470:279–283PubMedCentralPubMedCrossRefGoogle Scholar
  50. Rana R, Surapureddi S, Kam W, Ferguson S, Goldstein JA (2011) Med25 is required for RNA polymerase II recruitment to specific promoters, thus regulating xenobiotic and lipid metabolism in human liver. Mol Cell Biol 31:466–481PubMedCentralPubMedCrossRefGoogle Scholar
  51. Schaukowitch K, Joo JY, Liu X, Watts JK, Martinez C, Kim TK (2014) Enhancer RNA facilitates NELF release from immediate early genes. Mol Cell 56:29–42PubMedCrossRefGoogle Scholar
  52. Schmidt D, Schwalie PC, Ross-Innes CS, Hurtado A, Brown GD, Carroll JS, Flicek P, Odom DT (2010) A CTCF-independent role for cohesin in tissue-specific transcription. Genome Res 20:578–588PubMedCentralPubMedCrossRefGoogle Scholar
  53. Scott EW, Simon MC, Anastasi J, Singh H (1994) Requirement of transcription factor PU.1 in the development of multiple hematopoietic lineages. Science 265:1573–1577PubMedCrossRefGoogle Scholar
  54. Smale ST (2012) Transcriptional regulation in the innate immune system. Curr Opin Immunol 24:51–57PubMedCentralPubMedCrossRefGoogle Scholar
  55. Soufi A, Donahue G, Zaret KS (2012) Facilitators and impediments of the pluripotency reprogramming factors’ initial engagement with the genome. Cell 151:994–1004PubMedCentralPubMedCrossRefGoogle Scholar
  56. Step SE, Lim HW, Marinis JM, Prokesch A, Steger DJ, You SH, Won KJ, Lazar MA (2014) Anti-diabetic rosiglitazone remodels the adipocyte transcriptome by redistributing transcription to PPARgamma-driven enhancers. Genes Dev 28:1018–1028PubMedCentralPubMedCrossRefGoogle Scholar
  57. Szutorisz H, Dillon N, Tora L (2005) The role of enhancers as centres for general transcription factor recruitment. Trends Biochem Sci 30:593–599PubMedCrossRefGoogle Scholar
  58. Takeuchi O, Akira S (2010) Pattern recognition receptors and inflammation. Cell 140:805–820PubMedCrossRefGoogle Scholar
  59. Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B et al (2012) The accessible chromatin landscape of the human genome. Nature 489:75–82PubMedCentralPubMedCrossRefGoogle Scholar
  60. Travers A (1999) Chromatin modification by DNA tracking. Proc Natl Acad Sci U S A 96:13634–13637PubMedCentralPubMedCrossRefGoogle Scholar
  61. Trompouki E, Bowman TV, Lawton LN, Fan ZP, Wu DC, DiBiase A, Martin CS, Cech JN, Sessa AK, Leblanc JL et al (2011) Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration. Cell 147:577–589PubMedCentralPubMedCrossRefGoogle Scholar
  62. Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F et al (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457:854–858PubMedCentralPubMedCrossRefGoogle Scholar
  63. Wang D, Garcia-Bassets I, Benner C, Li W, Su X, Zhou Y, Qiu J, Liu W, Kaikkonen MU, Ohgi KA et al (2011) Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474:390–394PubMedCentralPubMedCrossRefGoogle Scholar
  64. Wood A, Schneider J, Dover J, Johnston M, Shilatifard A (2003) The Paf1 complex is essential for histone monoubiquitination by the Rad6-Bre1 complex, which signals for histone methylation by COMPASS and Dot1p. J Biol Chem 278:34739–34742PubMedCrossRefGoogle Scholar
  65. Wu H, Nord AS, Akiyama JA, Shoukry M, Afzal V, Rubin EM, Pennacchio LA, Visel A (2014) Tissue-specific RNA expression marks distant-acting developmental enhancers. PLoS Genet 10:e1004610PubMedCentralPubMedCrossRefGoogle Scholar
  66. Wynn TA, Chawla A, Pollard JW (2013) Macrophage biology in development, homeostasis and disease. Nature 496:445–455PubMedCentralPubMedCrossRefGoogle Scholar
  67. Xiao T, Hall H, Kizer KO, Shibata Y, Hall MC, Borchers CH, Strahl BD (2003) Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast. Genes Dev 17:654–663PubMedCentralPubMedCrossRefGoogle Scholar
  68. Yin L, Lazar MA (2005) The orphan nuclear receptor Rev-erbalpha recruits the N-CoR/histone deacetylase 3 corepressor to regulate the circadian Bmal1 gene. Mol Endocrinol 19:1452–1459PubMedCrossRefGoogle Scholar
  69. Zamir I, Harding HP, Atkins GB, Horlein A, Glass CK, Rosenfeld MG, Lazar MA (1996) A nuclear hormone receptor corepressor mediates transcriptional silencing by receptors with distinct repression domains. Mol Cell Biol 16:5458–5465PubMedCentralPubMedGoogle Scholar
  70. Zhu Y, Sun L, Chen Z, Whitaker JW, Wang T, Wang W (2013) Predicting enhancer transcription and activity from chromatin modifications. Nucleic Acids Res 41:10032–10043PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer Japan 2015

Authors and Affiliations

  1. 1.Department of Cellular and Molecular Medicine, School of MedicineUniversity of California, San DiegoLa JollaUSA
  2. 2.Department of Medicine, School of MedicineUniversity of California, San DiegoLa JollaUSA

Personalised recommendations