Theoretical analysis of the role of chromatin interactions in long-range action of enhancers and insulators

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 50, 2011, Pages 19919-19924

  Mukhopadhyay, Swagatam ^a   Schedl, Paul ^b   Studitsky, Vasily M ^c,d   Sengupta, Anirvan M ^e  

^a Cold Spring Harbor Laboratory ^*  (United States)

^b PRINCETON UNIVERSITY   (United States)

^c RUTGERS ROBERT WOOD JOHNSON MEDICAL SCHOOL   (United States)

^d MOSCOW STATE UNIVERSITY   (Russian Federation)

^e RUTGERS UNIVERSITY   (United States)

Author keywords

Chromatin polymer model; Enhancer promoter; Long range gene regulation

Indexed keywords

DNA; POLYMER;

ARTICLE; CHROMATIN LOOP; CHROMATIN STRUCTURE; ENHANCER REGION; EUCHROMATIN; GENE EXPRESSION; GENETIC REGULATION; HETEROCHROMATIN; INSULATOR ELEMENT; MOLECULAR INTERACTION; MOLECULAR MODEL; NUCLEOSOME; PRIORITY JOURNAL; PROMOTER REGION; SIMULATION;

CHROMATIN; ENHANCER ELEMENTS, GENETIC; INSULATOR ELEMENTS; MODELS, BIOLOGICAL; MODELS, MOLECULAR; TIME FACTORS;

EID: 84055200882     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1103845108     Document Type: Article

References (57)

1. Blackwood EM, Kadonaga JT (1998) Going the distance: a current view of enhancer action. Science 281:60-63. (Pubitemid 28354042)
2. Dorsett D (1999) Distant liaisons: long-range enhancer-promoter interactions in drosophila. Curr Opin Genet Dev 9:505-514.
3. Nobrega MA, Ovcharenko I, Afzal V, Rubin EM (2003) Scanning human gene deserts for long-range enhancers. Science 302:413. (Pubitemid 37296259)
4. West AG, Fraser P (2005) Remote control of gene transcription. Hum Mol Genet 14:R101-R111. (Pubitemid 40542626)
5. Bondarenko VA, Liu YV, Jiang YI, Studitsky VM (2003) Communication over a large distance: enhancers and insulators. Biochem Cell Biol 81:241-251. (Pubitemid 37076245)
6. Bushey AM, Dorman ER, Corces VG (2008) Chromatin insulators: regulatory mechanisms and epigenetic inheritance. Mol Cell 32:1-9.
7. Capelson M, Corces VG (2004) Boundary elements and nuclear organization. Biol Cell 96:617-629. (Pubitemid 39562236)
8. Corces VG (1995) Chromatin insulators. keeping enhancers under control. Nature 376:462-463.
9. Gaszner M, Felsenfeld G (2006) Insulators: exploiting transcriptional and epigenetic mechanisms. Nat Rev Genet 7:703-713. (Pubitemid 44260006)
10. Valenzuela L, Kamakaka RT (2006) Chromatin insulators. Annu Rev Genet 40:107-138. (Pubitemid 44956781)
11. Wallace JA, Felsenfeld G (2007)We gather together: insulators and genome organization. Curr Opin Genet Dev 17:400-407. (Pubitemid 350016897)
12. Cuddapah S, et al. (2009) Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Res 19:24-32.
13. Carter D, Chakalova L, Osborne CS, Dai YF, Fraser P (2002) Long-range chromatin regulatory interactions in vivo. Nat Genet 32:623-626. (Pubitemid 35435174)
14. Tolhuis B, Palstra RJ, Splinter E, Grosveld F, de Laat W (2002) Looping and interaction between hypersensitive sites in the active beta-globin locus. Mol Cell 10:1453-1465. (Pubitemid 36050885)
15. Geyer PK, Clark I (2002) Protecting against promiscuity: the regulatory role of insulators. Cell Mol Life Sci 59:2112-2127. (Pubitemid 36140284)
16. Majumder P, Cai HN (2003) The functional analysis of insulator interactions in the drosophila embryo. Proc Nat'l Acad Sci USA 100:5223-5228. (Pubitemid 36542686)
17. Geyer PK (1997) The role of insulator elements in defining domains of gene expression. Curr Opin Genet Dev 7:242-248.
18. Gerasimova TI, Corces VG (2001) Chromatin insulators and boundaries: effects on transcription and nuclear organization. Annu Rev Genet 35:193-208. (Pubitemid 34032975)
19. Gohl D, et al. (2011) Mechanism of boundary action: roadblock, sink or loop? Genetics 187:731-748.
20. Gohl D, Müller M, Pirrotta V, Affolter M, Schedl P (2008) Enhancer blocking and transvection at the drosophila apterous locus. Genetics 178:127-143. (Pubitemid 351398736)
21. Savitskaya E, et al. (2006) Study of long-distance functional interactions between Su (Hw) insulators that can regulate enhancer-promoter communication in Drosophila melanogaster. Mol Cell Biol 26:754-761. (Pubitemid 43146473)
22. Shimada J, Yamakawa H (1984) Ring-closure probabilities for twisted wormlike chains-application to DNA. Macromolecules 17:689-698.
23. Cui Y, Bustamante C (2000) Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure. Proc Natl Acad Sci USA 97:127-132. (Pubitemid 30055795)
24. Dekker J, Rippe K, Dekker M, Kleckner N (2002) Capturing chromosome conformation. Science 295:1306-1311. (Pubitemid 34157624)
25. Tsytsykova AV, et al. (2007) Activation-dependent intrachromosomal interactions formed by the TNF gene promoter and two distal enhancers. Proc Nat'l Acad Sci USA 104:16850-16855. (Pubitemid 350210954)
26. Deschenes J, Bourdeau V, White JH, Mader S (2007) Regulation of GREB1 transcription by estrogen receptor alpha through a multipartite enhancer spread over 20 kb of upstream flanking sequences. J Biol Chem 282:17335-17339. (Pubitemid 47100267)
27. Angelov D, Vitolo JM, Mutskov V, Dimitrov S, Hayes JJ (2001) Preferential interaction of the core histone tail domains with linker DNA. Proc Natl Acad Sci USA 98:6599-6604. (Pubitemid 32538262)
28. Arya G, Schlick T (2009) A tale of tails: how histone tails mediate chromatin compaction in different salt and linker histone environments. J Phys Chem A 113:4045-4059.
29. Arya G, Zhang Q, Schlick T (2006) Flexible histone tails in a new mesoscopic oligonucleosome model. Biophys J 91:133-150. (Pubitemid 44015314)
30. Moore SC, Ausio J (1997) Major role of the histones H3-H4 in the folding of the chromatin fiber. Biochem Bioph Res Co 230:136-139. (Pubitemid 27210259)
31. Zheng C, Hayes JJ (2003) Structures and interactions of the core histone tail domains. Biopolymers 68:539-546. (Pubitemid 36432066)
32. Chodaparambil JV, et al. (2007) A charged and contoured surface on the nucleosome regulates chromatin compaction. Nat Struct Mol Biol 14:1105-1107. (Pubitemid 350060342)
33. Hizume K, Yoshimura SH, Takeyasu K (2005) Linker histone H1 per se can induce threedimensional folding of chromatin fiber. Biochemistry 44:12978-12989. (Pubitemid 41377278)
34. Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389:251-260. (Pubitemid 27406632)
35. Zhou JS, Fan JY, Rangasamy D, Tremethick DJ (2007) The nucleosome surface regulates chromatin compaction and couples it with transcriptional repression. Nat Struct Mol Biol 14:1070-1076. (Pubitemid 350060339)
36. Bustin M, Catez F, Lim JH (2005) The dynamics of histone H1 function in chromatin. Mol Cell 17:617-620. (Pubitemid 40320912)
37. Grigoryev SA, Correll S, Woodcock CL (2009) Internucleosome interactions in chromatin higher-order fibers. J Biomol Struct Dyn 26:908.
38. Phair RD, et al. (2004) Global nature of dynamic protein-chromatin interactions in vivo: three-dimensional genome scanning and dynamic interaction networks of chromatin proteins. Mol Cell Biol 24:6393-6402. (Pubitemid 38891138)
39. Rochman M, et al. (2009) The interaction of NSBP1/HMGN5 with nucleosomes in euchromatin counteracts linker histone-mediated chromatin compaction and modulates transcription. Mol Cell 35:642-656.
40. Nielsen AL, et al. (2001) Heterochromatin formation in mammalian cells: interaction between histones and HP1 proteins. Mol Cell 7:729-739. (Pubitemid 32436434)
41. Bystricky K, Heun P, Gehlen L, Langowski J, Gasser SM (2004) Long-range compaction and flexibility of interphase chromatin in budding yeast analyzed by high-resolution imaging techniques. Proc Natl Acad Sci USA 101:16495-16500. (Pubitemid 39557741)
42. Langowski J, Heermann DW (2007) Computational modeling of the chromatin fiber. Semin Cell Dev Biol 18:659-667. (Pubitemid 350026435)
43. Nakai T, Hizume K, Yoshimura SH, Takeyasu K, Yoshikawa K (2005) Phase transition in reconstituted chromatin. Europhysics Lett 69:1024-1030. (Pubitemid 40435938)
44. Schiessel H (2003) The physics of chromatin. J Phys-Condens Mat 15:R699-R774.
45. Widom J (1998) Structure, dynamics, and function of chromatin in vitro. Annu Rev Biophys Biom 27:285-327.
46. Hahnfeldt P, Hearst JE, Brenner DJ, Sachs RK, Hlatky LR (1993) Polymer models for interphase chromosomes. Proc Natl Acad Sci USA 90:7854-7858. (Pubitemid 23250049)
47. van den Engh G, Sachs R, Trask BJ (1992) Estimating genomic distance from DNA sequence location in cell nuclei by a random walk model. Science 257:1410-1412.
48. Polikanov YS, Studitsky VM (2009) Analysis of distant communication on defined chromatin templates in vitro. Methods Mol Biol 543:563-576.
49. Goetze S, et al. (2007) The three-dimensional structure of human interphase chromosomes is related to the transcriptome map. Mol Cell Biol 27:4475-4487. (Pubitemid 46906570)
50. Lua R, Borovinskiy AL, Grosberg AY (2004) Fractal and statistical properties of large compact polymers: a computational study. Polymer 45:717-731. (Pubitemid 38082205)
51. Scott KC, Taubman AD, Geyer PK (1999) Enhancer blocking by the drosophila gypsy insulator depends upon insulator anatomy and enhancer strength. Genetics 153:787-798. (Pubitemid 29482335)
52. Kabakcioglu A, Stella AL (2004) Pseudoknots in a homopolymer. Phy Rev E 70:011802-011809.
53. Cremer M, et al. (2008) Multicolor 3D fluorescence in situ hybridization for imaging interphase chromosomes. Methods Mol Biol 463:205-239.
54. Schermelleh L, et al. (2008) Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy. Science 320:1332-1336. (Pubitemid 351929468)
55. Dostie J, et al. (2006) Chromosome conformation capture carbon copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res 16:1299-1309. (Pubitemid 44506963)
56. Simonis M, Kooren J, de Laat W (2007) An evaluation of 3C-based methods to capture DNA interactions. Nat Methods 4:895-901. (Pubitemid 350042374)
57. Binder K (1995) Monte Carlo and Molecular Dynamics Simulations in Polymer Science (Oxford University Press, Oxford).