Skip to main content

The Regulation of Chromatin by Dynamic SUMO Modifications

  • Protocol
  • First Online:
SUMO

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1475))

Abstract

Protein modification by the small ubiquitin-related modifier (SUMO) protein regulates numerous cellular pathways and mounting evidence reveals a critical role for SUMO in modulating gene expression. Dynamic sumoylation of transcription factors, chromatin-modifying enzymes, histones, and other chromatin-associated factors significantly affects the transcriptional status of the eukaryotic genome. Recent studies have employed high-throughput ChIP-Seq analyses to gain clues regarding the role of the SUMO pathway in regulating chromatin-based transactions. Indeed, the global distribution of SUMO across chromatin reveals an important function for SUMO in controlling transcription, particularly of genes involved in protein synthesis. These newly appreciated patterns of genome-wide sumoylation will inform more directed studies aimed at analyzing how the dynamics of gene expression are controlled by posttranslational SUMO modification.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Flotho A, Melchior F (2013) Sumoylation: a regulatory protein modification in health and disease. Annu Rev Biochem 82:357–385

    Article  CAS  PubMed  Google Scholar 

  2. Gareau JR, Lima CD (2010) The SUMO pathway: emerging mechanisms that shape specificity, conjugation and recognition. Nat Rev Cell Biol 11(12):861–871

    Article  CAS  Google Scholar 

  3. Bylebyl GR, Belichenko I, Johnson ES (2003) The SUMO isopeptidase Ulp2 prevents accumulation of SUMO chains in yeast. J Biol Chem 278(45):44113–44120

    Article  CAS  PubMed  Google Scholar 

  4. Johnson ES, Gupta AA (2001) An E3-like factor that promotes SUMO conjugation to the yeast septins. Cell 106(6):735–744

    Article  CAS  PubMed  Google Scholar 

  5. Bencsath KP, Podgorski MS, Pagala VR, Slaughter CA, Schulman BA (2002) Identification of a multifunctional binding site on Ubc9p required for Smt3p conjugation. J Biol Chem 277(49):47938–47945

    Article  CAS  PubMed  Google Scholar 

  6. Tatham MH et al (2001) Polymeric chains of SUMO-2 and SUMO-3 are conjugated to protein substrates by SAE1/SAE2 and Ubc9. J Biol Chem 276(38):35368–35374

    Article  CAS  PubMed  Google Scholar 

  7. Minty A, Dumont X, Kaghad M, Caput D (2000) Covalent modification of p73alpha by SUMO-1. Two-hybrid screening with p73 identifies novel SUMO-1-interacting proteins and a SUMO-1 interaction motif. J Biol Chem 275(46):36316–36323

    Article  CAS  PubMed  Google Scholar 

  8. Rodriguez MS, Dargemont C, Hay RT (2001) SUMO-1 conjugation in vivo requires both a consensus modification motif and nuclear targeting. J Biol Chem 276(16):12654–12659

    Article  CAS  PubMed  Google Scholar 

  9. Hietakangas V et al (2006) PDSM, a motif for phosphorylation-dependent SUMO modification. Proc Natl Acad Sci U S A 103(1):45–50

    Article  CAS  PubMed  Google Scholar 

  10. Matic I et al (2010) Site-specific identification of SUMO-2 targets in cells reveals an inverted SUMOylation motif and a hydrophobic cluster SUMOylation motif. Mol Cell 39(4):641–652

    Article  CAS  PubMed  Google Scholar 

  11. Mohideen F et al (2009) A molecular basis for phosphorylation-dependent SUMO conjugation by the E2 UBC9. Nat Struct Mol Biol 16(9):945–952

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Hickey CM, Wilson NR, Hochstrasser M (2012) Function and regulation of SUMO proteases. Nat Rev Mol Cell Biol 13(12):755–766

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Li SJ, Hochstrasser M (1999) A new protease required for cell-cycle progression in yeast. Nature 398(6724):246–251

    Article  CAS  PubMed  Google Scholar 

  14. Li SJ, Hochstrasser M (2000) The yeast ULP2 (SMT4) gene encodes a novel protease specific for the ubiquitin-like Smt3 protein. Mol Cell Biol 20(7):2367–2377

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Nayak A, Muller S (2014) SUMO-specific proteases/isopeptidases: SENPs and beyond. Genome Biol 15(7):422

    Article  PubMed  PubMed Central  Google Scholar 

  16. Mukhopadhyay D, Dasso M (2007) Modification in reverse: the SUMO proteases. Trends Biochem Sci 32(6):286–295

    Article  CAS  PubMed  Google Scholar 

  17. Kerscher O (2007) SUMO junction-what's your function? New insights through SUMO-interacting motifs. EMBO Rep 8(6):550–555

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Song J, Durrin LK, Wilkinson TA, Krontiris TG, Chen Y (2004) Identification of a SUMO-binding motif that recognizes SUMO-modified proteins. Proc Natl Acad Sci U S A 101(40):14373–14378

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Hecker CM, Rabiller M, Haglund K, Bayer P, Dikic I (2006) Specification of SUMO1- and SUMO2-interacting motifs. J Biol Chem 281(23):16117–16127

    Article  CAS  PubMed  Google Scholar 

  20. Psakhye I, Jentsch S (2012) Protein group modification and synergy in the SUMO pathway as exemplified in DNA repair. Cell 151(4):807–820

    Article  CAS  PubMed  Google Scholar 

  21. Gill G (2005) Something about SUMO inhibits transcription. Curr Opin Genet Dev 15(5):536–541

    Article  CAS  PubMed  Google Scholar 

  22. Rosonina E, Duncan SM, Manley JL (2010) SUMO functions in constitutive transcription and during activation of inducible genes in yeast. Genes Dev 24(12):1242–1252

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Rosonina E, Duncan SM, Manley JL (2012) Sumoylation of transcription factor Gcn4 facilitates its Srb10-mediated clearance from promoters in yeast. Genes Dev 26(4):350–355

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Neyret-Kahn H et al (2013) Sumoylation at chromatin governs coordinated repression of a transcriptional program essential for cell growth and proliferation. Genome Res 23(10):1563–1579

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Chymkowitch P et al (2015) Sumoylation of Rap1 mediates the recruitment of TFIID to promote transcription of ribosomal protein genes. Genome Res 25(6):897–906

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Liu HW et al (2012) Chromatin modification by SUMO-1 stimulates the promoters of translation machinery genes. Nucleic Acids Res 40(20):10172–10186

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Cubenas-Potts C, Matunis MJ (2013) SUMO: a multifaceted modifier of chromatin structure and function. Dev Cell 24(1):1–12

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Raman N, Nayak A, Muller S (2013) The SUMO system: a master organizer of nuclear protein assemblies. Chromosoma 122(6):475–485

    Article  CAS  PubMed  Google Scholar 

  29. Garcia-Dominguez M, Reyes JC (2009) SUMO association with repressor complexes, emerging routes for transcriptional control. Biochim Biophys Acta 1789(6–8):451–459

    Article  CAS  PubMed  Google Scholar 

  30. Lyst MJ, Stancheva I (2007) A role for SUMO modification in transcriptional repression and activation. Biochem Soc Trans 35(Pt 6):1389–1392

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Johnston M (1999) Feasting, fasting and fermenting. Glucose sensing in yeast and other cells. Trends Genet 15(1):29–33

    Article  CAS  PubMed  Google Scholar 

  32. Frolova E, Johnston M, Majors J (1999) Binding of the glucose-dependent Mig1p repressor to the GAL1 and GAL4 promoters in vivo: regulationby glucose and chromatin structure. Nucleic Acids Res 27(5):1350–1358

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Treitel MA, Carlson M (1995) Repression by SSN6-TUP1 is directed by MIG1, a repressor/activator protein. Proc Natl Acad Sci U S A 92(8):3132–3136

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Texari L et al (2013) The nuclear pore regulates GAL1 gene transcription by controlling the localization of the SUMO protease Ulp1. Mol Cell 51(6):807–818

    Article  CAS  PubMed  Google Scholar 

  35. Ng CH et al (2015) Sumoylation controls the timing of Tup1-mediated transcriptional deactivation. Nat Commun 6:6610

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Liu HW, Banerjee T, Guan X, Freitas MA, Parvin JD (2015) The chromatin scaffold protein SAFB1 localizes SUMO-1 to the promoters of ribosomal protein genes to facilitate transcription initiation and splicing. Nucleic Acids Res 43(7):3605–3613

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Niskanen EA et al (2015) Global SUMOylation on active chromatin is an acute heat stress response restricting transcription. Genome Biol 16:153

    Article  PubMed  PubMed Central  Google Scholar 

  38. Seifert A, Schofield P, Barton GJ, Hay RT (2015) Proteotoxic stress reprograms the chromatin landscape of SUMO modification. Sci Signal 8(384):rs7

    Article  PubMed  Google Scholar 

  39. Saitoh H, Hinchey J (2000) Functional heterogeneity of small ubiquitin-related protein modifiers SUMO-1 versus SUMO-2/3. J Biol Chem 275(9):6252–6258

    Article  CAS  PubMed  Google Scholar 

  40. Tatham MH, Matic I, Mann M, Hay RT (2011) Comparative proteomic analysis identifies a role for SUMO in protein quality control. Sci Signal 4(178):rs4

    Article  CAS  PubMed  Google Scholar 

  41. Golebiowski F et al (2009) System-wide changes to SUMO modifications in response to heat shock. Science signaling 2(72):ra24

    Article  PubMed  Google Scholar 

  42. Miller MJ et al (2013) Quantitative proteomics reveals factors regulating RNA biology as dynamic targets of stress-induced SUMOylation in Arabidopsis. Mol Cell Proteom 12(2):449–463

    Article  CAS  Google Scholar 

  43. Kurepa J et al (2003) The small ubiquitin-like modifier (SUMO) protein modification system in Arabidopsis. Accumulation of SUMO1 and -2 conjugates is increased by stress. J Biol Chem 278(9):6862–6872

    Article  CAS  PubMed  Google Scholar 

  44. Bruderer R et al (2011) Purification and identification of endogenous polySUMO conjugates. EMBO Rep 12(2):142–148

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Lewicki MC, Srikumar T, Johnson E, Raught B (2015) The S. cerevisiae SUMO stress response is a conjugation-deconjugation cycle that targets the transcription machinery. J Proteomics 118:39–48

    Article  CAS  PubMed  Google Scholar 

  46. Hendriks IA et al (2014) Uncovering global SUMOylation signaling networks in a site-specific manner. Nat Struct Mol Biol 21(10):927–936

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Tammsalu T et al (2014) Proteome-wide identification of SUMO2 modification sites. Sci Signal 7(323):rs2

    Article  PubMed  PubMed Central  Google Scholar 

  48. Hong Y et al (2001) Regulation of heat shock transcription factor 1 by stress-induced SUMO-1 modification. J Biol Chem 276(43):40263–40267

    Article  CAS  PubMed  Google Scholar 

  49. Goodson ML et al (2001) Sumo-1 modification regulates the DNA binding activity of heat shock transcription factor 2, a promyelocytic leukemia nuclear body associated transcription factor. J Biol Chem 276(21):18513–18518

    Article  CAS  PubMed  Google Scholar 

  50. Nathan D et al (2006) Histone sumoylation is a negative regulator in Saccharomyces cerevisiae and shows dynamic interplay with positive-acting histone modifications. Genes Dev 20(8):966–976

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Kalocsay M, Hiller NJ, Jentsch S (2009) Chromosome-wide Rad51 spreading and SUMO-H2A.Z-dependent chromosome fixation in response to a persistent DNA double-strand break. Mol Cell 33(3):335–343

    Article  CAS  PubMed  Google Scholar 

  52. Shiio Y, Eisenman RN (2003) Histone sumoylation is associated with transcriptional repression. Proc Natl Acad Sci U S A 100(23):13225–13230

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Miller MJ, Barrett-Wilt GA, Hua Z, Vierstra RD (2010) Proteomic analyses identify a diverse array of nuclear processes affected by small ubiquitin-like modifier conjugation in Arabidopsis. Proc Natl Acad Sci U S A 107(38):16512–16517

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Issar N, Roux E, Mattei D, Scherf A (2008) Identification of a novel post-translational modification in Plasmodium falciparum: protein sumoylation in different cellular compartments. Cell Microbiol 10(10):1999–2011

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Kouzarides T (2007) Chromatin modifications and their function. Cell 128(4):693–705

    Article  CAS  PubMed  Google Scholar 

  56. Dhall A et al (2014) Sumoylated human histone H4 prevents chromatin compaction by inhibiting long-range internucleosomal interactions. J Biol Chem 289(49):33827–33837

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Dorigo B, Schalch T, Bystricky K, Richmond TJ (2003) Chromatin fiber folding: requirement for the histone H4 N-terminal tail. J Mol Biol 327(1):85–96

    Article  CAS  PubMed  Google Scholar 

  58. Kirsh O et al (2002) The SUMO E3 ligase RanBP2 promotes modification of the HDAC4 deacetylase. EMBO J 21(11):2682–2691

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Bueno MT, Richard S (2013) SUMOylation negatively modulates target gene occupancy of the KDM5B, a histone lysine demethylase. Epigenetics 8(11):1162–1175

    Article  CAS  PubMed  Google Scholar 

  60. Hendriks IA, Treffers LW, Verlaan-de Vries M, Olsen JV, Vertegaal AC (2015) SUMO-2 orchestrates chromatin modifiers in response to DNA damage. Cell Rep. doi:10.1016/j.celrep.2015.02.033

    PubMed  PubMed Central  Google Scholar 

  61. Yang SH, Sharrocks AD (2004) SUMO promotes HDAC-mediated transcriptional repression. Mol Cell 13(4):611–617

    Article  CAS  PubMed  Google Scholar 

  62. Lindberg MJ, Popko-Scibor AE, Hansson ML, Wallberg AE (2010) SUMO modification regulates the transcriptional activity of MAML1. FASEB J 24(7):2396–2404

    Article  CAS  PubMed  Google Scholar 

  63. Murata T et al (2010) Transcriptional repression by sumoylation of Epstein-Barr virus BZLF1 protein correlates with association of histone deacetylase. J Biol Chem 285(31):23925–23935

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Lyst MJ, Nan X, Stancheva I (2006) Regulation of MBD1-mediated transcriptional repression by SUMO and PIAS proteins. EMBO J 25(22):5317–5328

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Ivanov AV et al (2007) PHD domain-mediated E3 ligase activity directs intramolecular sumoylation of an adjacent bromodomain required for gene silencing. Mol Cell 28(5):823–837

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Nayak A, Viale-Bouroncle S, Morsczeck C, Muller S (2014) The SUMO-specific isopeptidase SENP3 regulates MLL1/MLL2 methyltransferase complexes and controls osteogenic differentiation. Mol Cell 55(1):47–58

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The authors would like to thank Jen Gillies and Jason Berk for their helpful comments on the manuscript. They also acknowledge support from the US National Institutes of Health (R01 GM053756) to M.H. and an NIH Ruth L. Kirschstein National Research Service Award (NRSA) predoctoral fellowship (F31 AG046965) to N.R.W.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Mark Hochstrasser .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer Science+Business Media New York

About this protocol

Cite this protocol

Wilson, N.R., Hochstrasser, M. (2016). The Regulation of Chromatin by Dynamic SUMO Modifications. In: Rodriguez, M. (eds) SUMO. Methods in Molecular Biology, vol 1475. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6358-4_2

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-6358-4_2

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6356-0

  • Online ISBN: 978-1-4939-6358-4

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics