Key gene regulatory sequences with distinctive ontological signatures associate with differentially endonuclease-accessible mouse sperm chromatin

Reproduction

Volumn 142, Issue 1, 2011, Pages 73-86

  Saida, Myriam ^a   Iles, David ^b   Elnefati, Abdul ^a   Brinkworth, Martin ^c   Miller, David ^a  

^a UNIVERSITY OF LEEDS   (United Kingdom)

^b UNIVERSITY OF LEEDS   (United Kingdom)

^c UNIVERSITY OF BRADFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; ENDONUCLEASE; HISTONE; MICROCOCCAL NUCLEASE; TRANSCRIPTION FACTOR CTCF;

ANIMAL CELL; ANIMAL EXPERIMENT; ARTICLE; CHROMATIN; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTER MODEL; CONTROLLED STUDY; DATA MINING; DENTISTRY; DIGESTION; DISEASE ASSOCIATION; DISSECTION; EXPERIMENTAL STUDY; FLUORESCENCE IN SITU HYBRIDIZATION; GENE CONTROL; GENE SEQUENCE; GENETIC ANALYSIS; HUMAN; METHYLATION; MOUSE; NONHUMAN; PERCEPTION; PRIORITY JOURNAL; PROMOTER REGION; SENSORY DYSFUNCTION; SPERM;

ANIMALS; BACTERIAL PROTEINS; BINDING SITES; CELL NUCLEUS; CHROMATIN; COMPARATIVE GENOMIC HYBRIDIZATION; DATA MINING; DNA METHYLATION; EPIDIDYMIS; HISTONES; HYDROLYSIS; IN SITU HYBRIDIZATION, FLUORESCENCE; MALE; MICE; MICROCOCCAL NUCLEASE; NUCLEOSOMES; POLYNUCLEOTIDES; PROMOTER REGIONS, GENETIC; REPRESSOR PROTEINS; SOLUBILITY; SPERMATOZOA;

EID: 79960449192     PISSN: 14701626     EISSN: 17417899     Source Type: Journal    
DOI: 10.1530/REP-10-0536     Document Type: Article

References (41)

1. Allen MJ, Bradbury EM & Balhorn R 1996 The chromatin structure of well-spread demembranated human sperm nuclei revealed by atomic force microscopy. Scanning Microscopy 10 989-994.
2. Arpanahi A, Brinkworth M, Iles D, Krawetz SA, Paradowska A, Platts AE, Saida M, Steger K, Tedder P & Miller D 2009 Endonuclease-sensitive regions of human spermatozoal chromatin are highly enriched in promoter and CTCF binding sequences. Genome Research 19 1338-1349. (doi:10.1101/gr.094953.109)
3. Balhorn R 2007 The protamine family of sperm nuclear proteins. Genome Biology 8 227. (doi:10.1186/gb-2007-8-9-227)
4. Braun RE 2001 Packaging paternal chromosomes with protamine. Nature Genetics 28 10-12. (doi:10.1038/ng0501-10)
5. Breitbart H 2003 Signaling pathways in sperm capacitation and acrosome reaction. Cellular and Molecular Biology 49 321-327.
6. Brewer LR, Corzett M & Balhorn R 1999 Protamine-induced condensation and decondensation of the same DNA molecule. Science 286 120-123. (doi:10.1126/science.286.5437.120)
7. Brewer L, Corzett M, Lau EY & Balhorn R 2003 Dynamics of protamine 1 binding to single DNA molecules. Journal of Biological Chemistry 278 42403-42408. (doi:10.1074/jbc.M303610200)
8. Brykczynska U, Hisano M, Erkek S, Ramos L, Oakeley EJ, Roloff TC, Beisel C, Schubeler D, Stadler MB & Peters AH 2010 Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa. Nature Structural & Molecular Biology 17 679-687. (doi:10.1038/nsmb.1821)
9. Chen HL, Li T, Qiu XW, Wu J, Ling JQ, Sun ZH, Wang W, Chen W, Hou A, Vu TH et al. 2006 Correction of aberrant imprinting of IGF2 in human tumors by nuclear transfer-induced epigenetic reprogramming. EMBO Journal 25 5329-5338. (doi:10.1038/sj.emboj.7601399)
10. Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J et al. 2008 Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133 1106-1117. (doi:10.1016/j.cell.2008.04.043)
11. Chong S, Vickaryous N, Ashe A, Zamudio N, Youngson N, Hemley S, Stopka T, Skoultchi A, Matthews J, Scott HS et al. 2007 Modifiers of epigenetic reprogramming show paternal effects in the mouse. Nature Genetics 39 614-622. (doi:10.1038/ng2031)
12. Collas P & Poccia D 1998 Remodeling the sperm nucleus into a male pronucleus at fertilization. Theriogenology 49 67-81. (doi:10.1016/S0093- 691X(97)00403-2)
13. Crasto C, Marenco L, Miller P & Shepherd G 2002 Olfactory receptor database: a metadata-driven automated population from sources of gene and protein sequences. Nucleic Acids Research 30 354-360. (doi:10.1093/nar/30.1.354)
14. Farthing CR, Ficz G, Ng RK, Chan CF, Andrews S, Dean W, Hemberger M & Reik W 2008 Global mapping of DNA methylation in mouse promoters reveals epigenetic reprogramming of pluripotency genes. PLoS Genetics 4 e1000116. (doi:10.1371/journal.pgen.1000116)
15. Gardiner-Garden M, Ballesteros M, Gordon M & Tam PP 1998 Histone-and protamine-DNA association: conservation of different patterns within the beta-globin domain in human sperm. Molecular and Cellular Biology 18 3350-3356. (Pubitemid 28240507)
16. Gatewood JM, Cook GR, Balhorn R, Bradbury EM & Schmid CW 1987 Sequence-specific packaging of DNA in human sperm chromatin. Science 236 962-964. (doi:10.1126/science.3576213)
17. Gatewood JM, Cook GR, Balhorn R, Schmid CW & Bradbury EM 1990 Isolation of 4 core histones from human sperm chromatin representing a minor subset of somatic histones. Journal of Biological Chemistry 265 20662-20666.
18. Govin J, Escoffier E, Rousseaux S, Kuhn L, Ferro M, Thevenon J, Catena R, Davidson I, Garin J, Khochbin S et al. 2007 Pericentric heterochromatin reprogramming by new histone variants during mouse spermiogenesis. Journal of Cell Biology 176 283-294. (doi:10.1083/jcb.200604141)
19. 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. (doi:10.1038/nature08162)
20. Hazzouri M, Rousseaux S, Mongelard F, Usson Y, Pelletier R, Faure AK, Vourc'h C & Sele B 2000 Genome organization in the human sperm nucleus studied by FISH and confocal microscopy. Molecular Reproduction and Development 55 307-315. (doi:10.1002/(SICI)1098-2795 (200003)55:3!307::AID-MRD9O3.0.CO;2-P)
21. van der Heijden GW, Derijck AA, Ramos L, Giele M, van der Vlag J & de Boer P 2006 Transmission of modified nucleosomes from the mouse male germline to the zygote and subsequent remodeling of paternal chromatin. Developmental Biology 298 458-469. (doi:10.1016/j.ydbio.2006.06.051)
22. van der Heijden GW, Ramos L, Baart EB, van den Berg IM, Derijck AA, van der Vlag J, Martini E & de Boer P 2008 Sperm-derived histones contribute to zygotic chromatin in humans. BMC Developmental Biology 8 34. (doi:10.1186/1471-213X-8-34)
23. Huang DW, Sherman LT & Lempicki RA 2009 Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nature Protocols 4 44-57. (doi:10.1038/nprot.2008.211)
24. Hud NV, Allen MJ, Downing KH, Lee J & Balhorn R 1993 Identification of the elemental packing unit of DNA in mammalian sperm cells by atomic force microscopy. Biochemical and Biophysical Research Communications 193 1347-1354. (doi:10.1006/bbrc.1993.1773)
25. Jirtle RL & Skinner MK 2007 Environmental epigenomics and disease susceptibility. Nature Review Genetics 8 253-262. (doi:10.1038/nrg 2045)
26. Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, Zhang MQ, Lobanenkov VV & Ren B 2007 Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 128 1231-1245. (doi:10.1016/j.cell. 2006.12.048)
27. McLay DW & Clarke HJ 2003 Remodelling the paternal chromatin at fertilization in mammals. Reproduction 125 625-633. (doi:10.1530/rep.0.1250625)
28. Nazarov IB, Shlyakhtenko LS, Lyubchenko YL, Zalenskaya IA & Zalensky AO 2008 Sperm chromatin released by nucleases. Systems Biology in Reproductive Medicine 54 37-46. (doi:10.1080/19396360701876849)
29. Ohlsson R, Renkawitz R & Lobanenkov V 2001 CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease. Trends in Genetics 17 520-527. (doi:10.1016/S0168-9525(01)02366-6)
30. Palmer DK, O'Day K & Margolis RL 1990 The centromere specific histone CENP-A is selectively retained in discrete foci in mammalian sperm nuclei. Chromosoma 100 32-36. (doi:10.1007/BF00337600)
31. Pembrey ME, Bygren LO, Kaati G, Edvinsson S, Northstone K, Sjostrom M & Golding J 2006 Sex-specific, male-line transgenerational responses in humans. European Journal of Human Genetics 14 159-166. (doi:10.1038/sj.ejhg. 5201538)
32. Phillips JE & Corces VG 2009 CTCF: master weaver of the genome. Cell 137 1194-1211. (doi:10.1016/j.cell.2009.06.001)
33. Pittoggi C, Renzi L, Zaccagnini G, Cimini D, Degrassi F, Giordano R, Magnano AR, Lorenzini R, Lavia P & Spadafora C 1999 A fraction of mouse sperm chromatin is organized in nucleosomal hypersensitive domains enriched in retroposon DNA. Journal of Cell Science 112 3537-3548.
34. Powell D, Cran DG, Jennings C & Jones R 1990 Spatial organization of repetitive DNA sequences in the bovine sperm nucleus. Journal of Cell Science 97 185-191. (Pubitemid 120023259)
35. Santos F, Peters AH, Otte AP, Reik W & Dean W 2005 Dynamic chromatin modifications characterise the first cell cycle in mouse embryos. Developmental Biology 280 225-236. (doi:10.1016/j.ydbio.2005. 01.025)
36. Tanphaichitr N, Sobhon P, Taluppeth N & Chalermisarachai P 1978 Basic nuclear proteins in testicular cells and ejaculated spermatozoa in man. Experimental Cell Research 117 347-356. (doi:10.1016/0014-4827(78)90148-9)
37. Ward WS & Coffey DS 1991 DNA packaging and organization in mammalian spermatozoa: comparison with somatic cells. Biology of Reproduction 44 569-574. (doi:10.1095/biolreprod44.4.569)
38. Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, Rebhan M & Schubeler D 2007 Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nature Genetics 39 457-466. (doi:10.1038/ng1990)
39. Wykes SM & Krawetz SA 2003 The structural organization of sperm chromatin. Journal of Biological Chemistry 278 29471-29477. (doi:10.1074/jbc. M304545200)
40. Zalenskaya IA, Bradbury EM & Zalensky AO 2000 Chromatin structure of telomere domain in human sperm. Biochemical and Biophysical Research Communications 279 213-218. (doi:10.1006/bbrc.2000.3917)
41. Zalensky AO, Allen MJ, Kobayashi A, Zalenskaya IA, Balhorn R & Bradbury EM 1995 Well-defined genome architecture in the human sperm nucleus. Chromosoma 103 577-590. (doi:10.1007/BF00357684)