Unusual DNA packaging characteristics in endoreduplicated Caenorhabditis elegans oocytes defined by in vivo accessibility to an endogenous nuclease activity

Epigenetics and Chromatin

Volumn 6, Issue 1, 2013, Pages

  Gu, Sam Guoping ^c   Goszczynski, Barbara ^b   McGhee, James D ^b   Fire, Andrew Z ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF CALGARY   (Canada)

^c RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; NUCLEASE;

ANIMAL EXPERIMENT; ARTICLE; CAENORHABDITIS ELEGANS; CELL INTERACTION; CHROMATIN; CONTROLLED STUDY; DNA HELIX; DNA PACKAGING; ENZYME ACTIVITY; FEMALE; IN VIVO STUDY; INTERACTIONS WITH DNA; NONHUMAN; NUCLEOSOME; OOCYTE; OVULATION; PRIORITY JOURNAL;

ANIMALIA; CAENORHABDITIS ELEGANS;

EID: 84886738495     PISSN: None     EISSN: 17568935     Source Type: Journal    
DOI: 10.1186/1756-8935-6-37     Document Type: Article

References (48)

1. Germline chromatin. Schaner CE, Kelly WG, WormBook 2006 1 14
2. Specification of the germ line. Strome S, WormBook 2005 1 10
3. Development of the reproductive system of Caenorhabditis elegans. Hirsh D, Oppenheim D, Klass M, Dev Biol 1976 49 200 219 10.1016/0012-1606(76)90267-0 943344
4. Control of oocyte meiotic maturation and fertilization. Greenstein D, WormBook 2005 1 12
5. On the control of oocyte meiotic maturation and ovulation in Caenorhabditis elegans. McCarter J, Bartlett B, Dang T, Schedl T, Dev Biol 1999 205 111 128 10.1006/dbio.1998.9109 9882501 (Pubitemid 29042662)
6. A sperm cytoskeletal protein that signals oocyte meiotic maturation and ovulation. Miller MA, Nguyen VQ, Lee MH, Kosinski M, Schedl T, Caprioli RM, Greenstein D, Science 2001 291 2144 2147 10.1126/science.1057586 11251118 (Pubitemid 32224444)
7. DNA-protein interactions in the Caenorhabditis elegans embryo: oocyte and embryonic factors that bind to the promoter of the gut-specific ges-1 gene. Stroeher VL, Kennedy BP, Millen KJ, Schroeder DF, Hawkins MG, Goszczynski B, McGhee JD, Dev Biol 1994 163 367 380 10.1006/dbio.1994.1155 8200477 (Pubitemid 24221621)
8. Gene expression profiling of cells, tissues, and developmental stages of the nematode C elegans. McKay SJ, Johnsen R, Khattra J, Asano J, Baillie DL, Chan S, Dube N, Fang L, Goszczynski B, Ha E, Halfnight E, Hollebakken R, Huang P, Hung K, Jensen V, Jones SJ, Kai H, Li D, Mah A, Marra M, McGhee J, Newbury R, Pouzyrev A, Riddle DL, Sonnhammer E, Tian H, Tu D, Tyson JR, Vatcher G, Warner A, et al. Cold Spring Harb Symp Quant Biol 2003 68 159 169 10.1101/sqb.2003.68. 159 15338614 (Pubitemid 38955563)
9. Proteome of the Caenorhabditis elegans oocyte. Chik JK, Schriemer DC, Childs SJ, McGhee JD, J Proteome Res 2011 10 2300 2305 10.1021/pr101124f 21452892
10. Small DNA pieces in C elegans are intermediates of DNA fragmentation during apoptosis. Aruscavage PJ, Hellwig S, Bass BL, PLoS One 2010 5 11217 10.1371/journal.pone.0011217 20585459
11. Developmental genetics of chromosome I spermatogenesis-defective mutants in the nematode Caenorhabditis elegans. L'Hernault SW, Shakes DC, Ward S, Genetics 1988 120 435 452 3197956
12. The C elegans spe-9 gene encodes a sperm transmembrane protein that contains EGF-like repeats and is required for fertilization. Singson A, Mercer KB, L'Hernault SW, Cell 1998 93 71 79 10.1016/S0092-8674(00)81147-2 9546393 (Pubitemid 28173553)
13. The Caenorhabditis elegans spe-26 gene is necessary to form spermatids and encodes a protein similar to the actin-associated proteins kelch and scruin. Varkey JP, Muhlrad PJ, Minniti AN, Do B, Ward S, Genes Dev 1995 9 1074 1086 10.1101/gad.9.9.1074 7744249
14. Trashing the genome: the role of nucleases during apoptosis. Samejima K, Earnshaw WC, Nat Rev Mol Cell Biol 2005 6 677 688 10.1038/nrm1715 16103871 (Pubitemid 41748063)
15. NUC-1, a caenorhabditis elegans DNase II homolog, functions in an intermediate step of DNA degradation during apoptosis. Wu YC, Stanfield GM, Horvitz HR, Genes Dev 2000 14 536 548 10716942 (Pubitemid 30159773)
16. Genetic control of programmed cell death in the nematode C elegans. Ellis HM, Horvitz HR, Cell 1986 44 817 829 10.1016/0092-8674(86)90004-8 3955651 (Pubitemid 16045328)
17. Developmental apoptosis in C elegans: a complex CEDnario. Lettre G, Hengartner MO, Nat Rev Mol Cell Biol 2006 7 97 108 10.1038/nrm1836 16493416 (Pubitemid 43278293)
18. A high-resolution, nucleosome position map of C elegans reveals a lack of universal sequence-dictated positioning. Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, Sidow A, Fire A, Johnson SM, Genome Res 2008 18 1051 1063 10.1101/gr.076463.108 18477713 (Pubitemid 351931156)
19. Determinants of nucleosome organization in primary human cells. Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ, Sidow A, Nature 2011 474 516 520 10.1038/nature10002 21602827
20. Partitioning the C elegans genome by nucleosome modification, occupancy, and positioning. Gu SG, Fire A, Chromosoma 2010 119 73 87 10.1007/s00412-009- 0235-3 19705140
21. High-resolution mapping and characterization of open chromatin across the genome. Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE, Cell 2008 132 311 322 10.1016/j.cell.2007.12.014 18243105 (Pubitemid 351172431)
22. Helical repeat of DNA in solution. Wang JC, Proc Natl Acad Sci U S A 1979 76 200 203 10.1073/pnas.76.1.200 284332
23. Nucleosome structure(s) and stability: variations on a theme. Andrews AJ, Luger K, Annu Rev Biophys 2011 40 99 117 10.1146/annurev-biophys-042910-155329 21332355
24. Revisiting higher-order and large-scale chromatin organization. Bian Q, Belmont AS, Curr Opin Cell Biol 2012 24 359 366 10.1016/j.ceb.2012.03.003 22459407
25. Chromatin higher-order structure and dynamics. Woodcock CL, Ghosh RP, Cold Spring Harb Perspect Biol 2010 2 000596 10.1101/cshperspect.a000596 20452954
26. Single-base resolution mapping of H1-nucleosome interactions and 3D organization of the nucleosome. Syed SH, Goutte-Gattat D, Becker N, Meyer S, Shukla MS, Hayes JJ, Everaers R, Angelov D, Bednar J, Dimitrov S, Proc Natl Acad Sci U S A 2010 107 9620 9625 10.1073/pnas.1000309107 20457934
27. A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA. Bishop EP, Rohs R, Parker SC, West SM, Liu P, Mann RS, Honig B, Tullius TD, ACS Chem Biol 2011 6 1314 1320 10.1021/cb200155t 21967305
28. Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. Johnson SM, Tan FJ, McCullough HL, Riordan DP, Fire AZ, Genome Res 2006 16 1505 1516 10.1101/gr.5560806 17038564 (Pubitemid 44878489)
29. Genome-scale identification of nucleosome positions in S. cerevisiae. Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ, Science 2005 309 626 630 10.1126/science.1112178 15961632 (Pubitemid 41033649)
30. A genomic code for nucleosome positioning. Segal E, Fondufe-Mittendorf Y, Chen L, Thastrom A, Field Y, Moore IK, Wang JP, Widom J, Nature 2006 442 772 778 10.1038/nature04979 16862119 (Pubitemid 44258903)
31. Nucleosome organization in the Drosophila genome. Mavrich TN, Jiang C, Ioshikhes IP, Li X, Venters BJ, Zanton SJ, Tomsho LP, Qi J, Glaser RL, Schuster SC, Gilmour DS, Albert I, Pugh BF, Nature 2008 453 358 362 10.1038/nature06929 18408708 (Pubitemid 351693129)
32. Dynamic regulation of nucleosome positioning in the human genome. Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K, Cell 2008 132 887 898 10.1016/j.cell.2008.02.022 18329373 (Pubitemid 351312809)
33. New functions for an old variant: no substitute for histone H3.3. Elsaesser SJ, Goldberg AD, Allis CD, Curr Opin Genet Dev 2010 20 110 117 10.1016/j.gde.2010.01.003 20153629
34. Active genes are tri-methylated at K4 of histone H3. Santos-Rosa H, Schneider R, Bannister AJ, Sherriff J, Bernstein BE, Emre NC, Schreiber SL, Mellor J, Kouzarides T, Nature 2002 419 407 411 10.1038/nature01080 12353038
35. ELT-2 is the predominant transcription factor controlling differentiation and function of the C elegans intestine, from embryo to adult. McGhee JD, Fukushige T, Krause MW, Minnema SE, Goszczynski B, Gaudet J, Kohara Y, Bossinger O, Zhao Y, Khattra J, Hirst M, Jones SJ, Marra MA, Ruzanov P, Warner A, Zapf R, Moerman DG, Kalb JM, Dev Biol 2009 327 551 565 10.1016/j.ydbio.2008.11.034 19111532
36. Bending and curvature calculations in B-DNA. Goodsell DS, Dickerson RE, Nucleic Acids Res 1994 22 5497 5503 10.1093/nar/22.24.5497 7816643
37. DNA bending at adenine thymine tracts. Koo HS, Wu HM, Crothers DM, Nature 1986 320 501 506 10.1038/320501a0 3960133 (Pubitemid 16045112)
38. The structure of an oligo(dA).oligo(dT) tract and its biological implications. Nelson HC, Finch JT, Luisi BF, Klug A, Nature 1987 330 221 226 10.1038/330221a0 3670410 (Pubitemid 18006417)
39. Estimation of wedge components in curved DNA. Ulanovsky LE, Trifonov EN, Nature 1987 326 720 722 10.1038/326720a0 3561514 (Pubitemid 17059796)
40. Sequence periodicities in chicken nucleosome core DNA. Satchwell SC, Drew HR, Travers AA, J Mol Biol 1986 191 659 675 10.1016/0022-2836(86)90452-3 3806678 (Pubitemid 17185964)
41. Unusual DNA structures associated with germline genetic activity in Caenorhabditis elegans. Fire A, Alcazar R, Tan F, Genetics 2006 173 1259 1273 10.1534/genetics.106.057364 16648589 (Pubitemid 44127633)
42. Species-specific patterns of DNA bending and sequence. VanWye JD, Bronson EC, Anderson JN, Nucleic Acids Res 1991 19 5253 5261 10.1093/nar/19.19.5253 1923808 (Pubitemid 21912919)
43. Short-range order in two eukaryotic genomes: relation to chromosome structure. Widom J, J Mol Biol 1996 259 579 588 10.1006/jmbi.1996.0341 8683566 (Pubitemid 26226000)
44. Structural analysis of hyperperiodic DNA from Caenorhabditis elegans. Moreno-Herrero F, Seidel R, Johnson SM, Fire A, Dekker NH, Nucleic Acids Res 2006 34 3057 3066 10.1093/nar/gkl397 16738142 (Pubitemid 44540432)
45. Alignment of nucleosomes along DNA and organization of spacer DNA in Drosophila chromatin. Karpov VL, Bavykin SG, Preobrazhenskaya OV, Belyavsky AV, Mirzabekov AD, Nucleic Acids Res 1982 10 4321 4337 10.1093/nar/10.14.4321 6812025
46. A relationship between the helical twist of DNA and the ordered positioning of nucleosomes in all eukaryotic cells. Widom J, Proc Natl Acad Sci U S A 1992 89 1095 1099 10.1073/pnas.89.3.1095 1736292
47. Nascent DNA in nucleosome like structures from chromatin. Levy A, Jakob KM, Cell 1978 14 259 267 10.1016/0092-8674(78)90112-5 667940 (Pubitemid 8369827)
48. A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Parameswaran P, Jalili R, Tao L, Shokralla S, Gharizadeh B, Ronaghi M, Fire AZ, Nucleic Acids Res 2007 35 130 10.1093/nar/gkm760 17932070 (Pubitemid 350111638)