Stable and dynamic nucleosome states during a meiotic developmental process

Genome Research

Volumn 21, Issue 6, 2011, Pages 875-884

  Zhang, Liye ^a,b   Ma, Hong ^a,b,c   Pugh, B Franklin ^a,b  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

^c FUDAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ANTISENSE OLIGONUCLEOTIDE;

ARTICLE; DNA REPLICATION; GAMETOGENESIS; GENE CONTROL; GENETIC ASSOCIATION; HISTONE ACETYLATION; HISTONE MODIFICATION; IMMUNOBLOTTING; KARYOTYPE; MEIOSIS; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; SACCHAROMYCES; SEQUENCE ANALYSIS; TRANSCRIPTION INITIATION;

BASE SEQUENCE; CHROMATIN; FLOW CYTOMETRY; GAMETOGENESIS; GENOMICS; HISTONES; IMMUNOBLOTTING; IMMUNOPRECIPITATION; MEIOSIS; MOLECULAR SEQUENCE DATA; NUCLEOSOMES; SACCHAROMYCES; SEQUENCE ANALYSIS, DNA;

SACCHAROMYCES;

EID: 79957929301     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.117465.110     Document Type: Article

References (64)

1. Albert I, Mavrich TN, Tomsho LP, Qi J, Zanton SJ, Schuster SC, Pugh BF. 2007. Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 446: 572-576. (Pubitemid 46514724)
2. Albert I, Wachi S, Jiang C, Pugh BF. 2008. GeneTrack - a genomic data processing and visualization framework. Bioinformatics 24: 1305-1306. (Pubitemid 351659629)
3. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. 2007. High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837. (Pubitemid 46802390)
4. Berchowitz LE, Hanlon SE, Lieb JD, Copenhaver GP. 2009. A positive but complex association between meiotic double-strand break hotspots and open chromatin in Saccharomyces cerevisiae. Genome Res 19: 2245-2257.
5. Bernstein BE, Humphrey EL, Erlich RL, Schneider R, Bouman P, Liu JS, Kouzarides T, Schreiber SL. 2002. Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci 99: 8695-8700. (Pubitemid 34693622)
6. Blitzblau HG, Bell GW, Rodriguez J, Bell SP, Hochwagen A. 2007. Mapping of meiotic single-stranded DNA reveals double-stranded-break hotspots near centromeres and telomeres. Curr Biol 17: 2003-2012. (Pubitemid 350180476)
7. Borde V, Wu TC, Lichten M. 1999. Use of a recombination reporter insert to define meiotic recombination domains on chromosome III of Saccharomyces cerevisiae. Mol Cell Biol 19: 4832-4842. (Pubitemid 29289522)
8. Borde V, Robine N, Lin W, Bonfils S, Geli V, Nicolas A. 2009. Histone H3 lysine 4 trimethylation marks meiotic recombination initiation sites. EMBO J 28: 99-111.
9. Bradley PH, Brauer MJ, Rabinowitz JD, Troyanskaya OG. 2009. Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae. PLoS Comput Biol 5: e1000270. doi: 10.1371/journal.pcbi.1000270.
10. Buhler C, Borde V, Lichten M. 2007. Mapping meiotic single-strand DNA reveals a new landscape of DNA double-strand breaks in Saccharomyces cerevisiae. PLoS Biol 5: e324. doi: 10.1371/journal.pbio.0050324.
11. Buttner S, Eisenberg T, Carmona-Gutierrez D, Ruli D, Knauer H, Ruckenstuhl C, Sigrist C, Wissing S, Kollroser M, Frohlich KU, et al. 2007. Endonuclease G regulates budding yeast life and death. Mol Cell 25: 233-246. (Pubitemid 46109611)
12. Camblong J, Iglesias N, Fickentscher C, Dieppois G, Stutz F. 2007. Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae. Cell 131: 706-717. (Pubitemid 350087198)
13. Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I. 1998. The transcriptional program of sporulation in budding yeast. Science 282: 699-705. (Pubitemid 28489376)
14. Cromie GA, Hyppa RW, Cam HP, Farah JA, Grewal SI, Smith GR. 2007. A discrete class of intergenic DNA dictates meiotic DNA break hotspots in fission yeast. PLoS Genet 3: e141. doi: 10.1371/journal.pgen.0030141.
15. David L, Huber W, Granovskaia M, Toedling J, Palm CJ, Bofkin L, Jones T, Davis RW, Steinmetz LM. 2006. A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci 103: 5320-5325.
16. de Massy B, Rocco V, Nicolas A. 1995. The nucleotide mapping of DNA double-strand breaks at the CYS3 initiation site of meiotic recombination in Saccharomyces cerevisiae. EMBO J 14: 4589-4598.
17. Dion MF, Kaplan T, Kim M, Buratowski S, Friedman N, Rando OJ. 2007. Dynamics of replication-independent histone turnover in budding yeast. Science 315: 1405-1408. (Pubitemid 46399548)
18. Fan QQ, Petes TD. 1996. Relationship between nuclease-hypersensitive sites and meiotic recombination hot spot activity at the HIS4 locus of Saccharomyces cerevisiae. Mol Cell Biol 16: 2037-2043. (Pubitemid 26123723)
19. Fan X, Moqtaderi Z, Jin Y, Zhang Y, Liu XS, Struhl K. 2010. Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 39-end formation. Proc Natl Acad Sci 107: 17945-17950.
20. Gerton JL, DeRisi J, Shroff R, Lichten M, Brown PO, Petes TD. 2000. Inaugural article: global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae. Proc Natl Acad Sci 97: 11383-11390.
21. Govin J, Dorsey J, Gaucher J, Rousseaux S, Khochbin S, Berger SL. 2010. Systematic screen reveals new functional dynamics of histones H3 and H4 during gametogenesis. Genes Dev 24: 1772-1786.
22. Granovskaia MV, Jensen LJ, Ritchie ME, Toedling J, Ning Y, Bork P, Huber W, Steinmetz LM. 2010. High-resolution transcription atlas of the mitotic cell cycle in budding yeast. Genome Biol 11: R24. doi: 10.1186/gb-2010-11-3-r24.
23. Hammoud SS, Nix DA, Zhang H, Purwar J, Carrell DT, Cairns BR. 2009. Distinctive chromatin in human sperm packages genes for embryo development. Nature 460: 473-478.
24. Handel MA, Schimenti JC. 2010. Genetics of mammalian meiosis: regulation, dynamics and impact on fertility. Nat Rev Genet 11: 124-136.
25. Hogan GJ, Lee CK, Lieb JD. 2006. Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters. PLoS Genet 2: e158. doi: 10.1371/journal.pgen.0020158.
26. Hongay CF, Grisafi PL, Galitski T, Fink GR. 2006. Antisense transcription controls cell fate in Saccharomyces cerevisiae. Cell 127: 735-745. (Pubitemid 44716254)
27. Jiang C, Pugh BF. 2009. Nucleosome positioning and gene regulation: advances through genomics. Nat Rev Genet 10: 161-172.
28. Jona G, Choder M, Gileadi O. 2000. Glucose starvation induces a drastic reduction in the rates of both transcription and degradation of mRNA in yeast. Biochim Biophys Acta 1491: 37-48. (Pubitemid 30173331)
29. Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, et al. 2009. The DNA encoded nucleosome organization of a eukaryotic genome. Nature 458: 362-366.
30. Kelly TK, Miranda TB, Liang G, Berman BP, Lin JC, Tanay A, Jones PA. 2010. H2A.Z maintenance during mitosis reveals nucleosome shifting on mitotically silenced genes. Mol Cell 39: 901-911.
31. Kleckner N. 1996. Meiosis: how could it work? Proc Natl Acad Sci 93: 8167-8174.
32. Koerber RT, Rhee HS, Jiang C, Pugh BF. 2009. Interaction of transcriptional regulators with specific nucleosomes across the Saccharomyces genome. Mol Cell 35: 889-902.
33. Krishnamoorthy T, Chen X, Govin J, Cheung WL, Dorsey J, Schindler K, Winter E, Allis CD, Guacci V, Khochbin S, et al. 2006. Phosphorylation of histone H4 Ser1 regulates sporulation in yeast and is conserved in fly and mouse spermatogenesis. Genes Dev 20: 2580-2592. (Pubitemid 44396842)
34. 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: 4207-4218. (Pubitemid 36666424)
35. Kurdistani SK, Tavazoie S, Grunstein M. 2004. Mapping global histone acetylation patterns to gene expression. Cell 117: 721-733. (Pubitemid 38748889)
36. Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C. 2007. A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet 39: 1235-1244. (Pubitemid 47482684)
37. Liu CL, Kaplan T, Kim M, Buratowski S, Schreiber SL, Friedman N, Rando OJ. 2005. Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol 3: e328. doi: 10.1371/journal.pbio.0030328.
38. Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, Schuster SC, Albert I, Pugh BF. 2008. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res 18: 1073-1083. (Pubitemid 351931158)
39. Miura F, Kawaguchi N, Sese J, Toyoda A, Hattori M, Morishita S, Ito T. 2006. A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc Natl Acad Sci 103: 17846-17851. (Pubitemid 44852248)
40. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. 2008. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344-1349. (Pubitemid 351929471)
41. 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: 709-719. (Pubitemid 36385124)
42. Ohta K, Shibata T, Nicolas A. 1994. Changes in chromatin structure at recombination initiation sites during yeast meiosis. EMBO J 13: 5754-5763. (Pubitemid 24363043)
43. Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A. 2009. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 37: e123. doi: 10.1093/nar/gkp596.
44. Pokholok DK, Harbison CT, Levine S, Cole M, Hannett NM, Lee TI, Bell GW, Walker K, Rolfe PA, Herbolsheimer E, et al. 2005. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122: 517-527. (Pubitemid 41191151)
45. Primig M, Williams RM, Winzeler EA, Tevzadze GG, Conway AR, Hwang SY, Davis RW, Esposito RE. 2000. The core meiotic transcriptome in budding yeasts. Nat Genet 26: 415-423.
46. Raithatha SA, Stuart DT. 2005. Meiosis-specific regulation of the Saccharomyces cerevisiae S-phase cyclin CLB5 is dependent on MluI cell cycle box (MCB) elements in its promoter but is independent of MCBbinding factor activity. Genetics 169: 1329-1342. (Pubitemid 40547446)
47. Routh A, Sandin S, Rhodes D. 2008. Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure. Proc Natl Acad Sci 105: 8872-8877.
48. Rufiange A, Jacques PE, Bhat W, Robert F, Nourani A. 2007. Genome-wide replication-independent histone H3 exchange occurs predominantly at promoters and implicates H3 K56 acetylation and Asf1. Mol Cell 27: 393-405. (Pubitemid 47135636)
49. Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, Brudno M. 2009. SHRiMP: accurate mapping of short color-space reads. PLoS Comput Biol 5: e1000386. doi: 10.1371/journal.pcbi.1000386.
50. Santos-Rosa H, Schneider R, Bannister AJ, Sherriff J, Bernstein BE, Emre NC, Schreiber SL, Mellor J, Kouzarides T. 2002. Active genes are trimethylated at K4 of histone H3. Nature 419: 407-411.
51. Santos-Rosa H, Kirmizis A, Nelson C, Bartke T, Saksouk N, Cote J, Kouzarides T. 2009. Histone H3 tail clipping regulates gene expression. Nat Struct Mol Biol 16: 17-22.
52. Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K. 2008. Dynamic regulation of nucleosome positioning in the human genome. Cell 132: 887-898. (Pubitemid 351312809)
53. Segal E, Widom J. 2009. What controls nucleosome positions? Trends Genet 25: 335-343.
54. Shilatifard A. 2006. Chromatin modifications by methylation and ubiquitination: implications in the regulation of gene expression. Annu Rev Biochem 75: 243-269. (Pubitemid 44118033)
55. Shilatifard A. 2008. Molecular implementation and physiological roles for histone H3 lysine 4 (H3K4) methylation. Curr Opin Cell Biol 20: 341-348.
56. Shivaswamy S, Bhinge A, Zhao Y, Jones S, Hirst M, Iyer VR. 2008. Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. PLoS Biol 6: e65. doi: 10.1371/journal.pgen. 0060065.
57. Tirosh I, Sigal N, Barkai N. 2010. Widespread remodeling of mid-coding sequence nucleosomes by Isw1. Genome Biol 11: R49. doi: 10.1186/gb-2010-11-5- r49.
58. Venkatasubrahmanyam S, Hwang WW, Meneghini MD, Tong AH, Madhani HD. 2007. Genome-wide, as opposed to local, antisilencing is mediated redundantly by the euchromatic factors Set1 and H2A.Z. Proc Natl Acad Sci 104: 16609-16614. (Pubitemid 350211064)
59. Whitehouse I, Rando OJ, Delrow J, Tsukiyama T. 2007. Chromatin remodelling at promoters suppresses antisense transcription. Nature 450: 1031-1035. (Pubitemid 350273613)
60. Williams RM, Primig M, Washburn BK, Winzeler EA, Bellis M, Sarrauste de Menthiere C, Davis RW, Esposito RE. 2002. The Ume6 regulon coordinates metabolic and meiotic gene expression in yeast. Proc Natl Acad Sci 99: 13431-13436. (Pubitemid 35215398)
61. Wu TC, Lichten M. 1994. Meiosis-induced double-strand break sites determined by yeast chromatin structure. Science 263: 515-518. (Pubitemid 24082749)
62. Xu Z, Wei W, Gagneur J, Perocchi F, Clauder-Munster S, Camblong J, Guffanti E, Stutz F, Huber W, Steinmetz LM. 2009. Bidirectional promoters generate pervasive transcription in yeast. Nature 457: 1033-1037.
63. Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ. 2005. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309: 626-630. (Pubitemid 41033649)
64. Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K. 2009. Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol 16: 847-852.