Allele-Specific Genome-wide Profiling in Human Primary Erythroblasts Reveal Replication Program Organization

PLoS Genetics

Volumn 10, Issue 5, 2014, Pages

  Mukhopadhyay, Rituparna ^a   Lajugie, Julien ^a   Fourel, Nicolas ^a   Selzer, Ari ^a   Schizas, Michael ^a   Bartholdy, Boris ^a   Mar, Jessica ^a   Lin, Chii Mei ^b   Martin, Melvenia M ^b   Ryan, Michael ^b   Aladjem, Mirit I ^b   Bouhassira, Eric E ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GUANINE QUADRUPLEX;

ALLELE; ARTICLE; BASOPHIL; CELL CYCLE S PHASE; CHROMOSOME INACTIVATION; CONTROLLED STUDY; CPG ISLAND; DNA REPLICATION; EPIGENETICS; ERYTHROBLAST; FEMALE; GENE LIBRARY; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOME ANALYSIS; GENOME IMPRINTING; HUMAN; HUMAN CELL; PRIMARY CELL CULTURE; TRANSCRIPTION INITIATION SITE; X CHROMOSOME; CELL CULTURE; GENE EXPRESSION PROFILING; HUMAN GENOME; METABOLISM; X CHROMOSOME INACTIVATION;

ALLELES; CELLS, CULTURED; ERYTHROBLASTS; GENE EXPRESSION PROFILING; GENOME, HUMAN; GENOMIC IMPRINTING; HUMANS; X CHROMOSOME INACTIVATION;

EID: 84901611545     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1004319     Document Type: Article

References (73)

1. Aladjem MI, (2007) Replication in context: dynamic regulation of DNA replication patterns in metazoans. Nat Rev Genet 8: 588-600.
2. Masai H, Matsumoto S, You Z, Yoshizawa-Sugata N, Oda M, (2010) Eukaryotic chromosome DNA replication: where, when, and how? Annu Rev Biochem 79: 89-130.
3. Leonard AC, Mechali M, (2013) DNA replication origins. Cold Spring Harb Perspect Biol 5: a010116.
4. Mechali M, (2010) Eukaryotic DNA replication origins: many choices for appropriate answers. Nat Rev Mol Cell Biol 11: 728-738.
5. Mechali M, (2001) DNA replication origins: from sequence specificity to epigenetics. Nat Rev Genet 2: 640-645.
6. Wu JR, Gilbert DM, (1996) A distinct G1 step required to specify the Chinese hamster DHFR replication origin. Science 271: 1270-1272.
7. Courbet S, Gay S, Arnoult N, Wronka G, Anglana M, et al. (2008) Replication fork movement sets chromatin loop size and origin choice in mammalian cells. Nature 455: 557-560.
8. Abdurashidova G, Radulescu S, Sandoval O, Zahariev S, Danailov MB, et al. (2007) Functional interactions of DNA topoisomerases with a human replication origin. EMBO J 26: 998-1009.
9. Lemaitre JM, Danis E, Pasero P, Vassetzky Y, Mechali M, (2005) Mitotic remodeling of the replicon and chromosome structure. Cell 123: 787-801.
10. Cayrou C, Coulombe P, Puy A, Rialle S, Kaplan N, et al. (2012) New insights into replication origin characteristics in metazoans. Cell Cycle 11: 658-667.
11. Bechhoefer J, Rhind N, (2012) Replication timing and its emergence from stochastic processes. Trends Genet 28: 374-381.
12. Guilbaud G, Rappailles A, Baker A, Chen CL, Arneodo A, et al. (2011) Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome. PLoS Comput Biol 7: e1002322.
13. Shaw A, Olivares-Chauvet P, Maya-Mendoza A, Jackson DA, (2010) S-phase progression in mammalian cells: modelling the influence of nuclear organization. Chromosome Res 18: 163-178.
14. Demczuk A, Gauthier MG, Veras I, Kosiyatrakul S, Schildkraut CL, et al. (2012) Regulation of DNA replication within the immunoglobulin heavy-chain locus during B cell commitment. PLoS Biol 10: e1001360.
15. Yamazaki S, Ishii A, Kanoh Y, Oda M, Nishito Y, et al. (2012) Rif1 regulates the replication timing domains on the human genome. EMBO J 31: 3667-3677.
16. Cornacchia D, Dileep V, Quivy JP, Foti R, Tili F, et al. (2012) Mouse Rif1 is a key regulator of the replication-timing programme in mammalian cells. EMBO J 31: 3678-3690.
17. Donley N, Stoffregen EP, Smith L, Montagna C, Thayer MJ, (2013) Asynchronous replication, mono-allelic expression, and long range Cis-effects of ASAR6. PLoS Genet 9: e1003423.
18. Pope BD, Gilbert DM, (2013) The Replication Domain Model: Regulating Replicon Firing in the Context of Large-Scale Chromosome Architecture. J Mol Biol.
19. Delgado S, Gomez M, Bird A, Antequera F, (1998) Initiation of DNA replication at CpG islands in mammalian chromosomes. EMBO J 17: 2426-2435.
20. Cadoret JC, Meisch F, Hassan-Zadeh V, Luyten I, Guillet C, et al. (2008) Genome-wide studies highlight indirect links between human replication origins and gene regulation. Proc Natl Acad Sci U S A 105: 15837-15842.
21. Sequeira-Mendes J, Diaz-Uriarte R, Apedaile A, Huntley D, Brockdorff N, et al. (2009) Transcription initiation activity sets replication origin efficiency in mammalian cells. PLoS Genet 5: e1000446.
22. Cayrou C, Coulombe P, Vigneron A, Stanojcic S, Ganier O, et al. (2011) Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features. Genome Res 21: 1438-1449.
23. Martin MM, Ryan M, Kim R, Zakas AL, Fu H, et al. (2011) Genome-wide depletion of replication initiation events in highly transcribed regions. Genome Res 21: 1822-1832.
24. Besnard E, Babled A, Lapasset L, Milhavet O, Parrinello H, et al. (2012) Unraveling cell type-specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs. Nat Struct Mol Biol 19: 837-844.
25. Mesner LD, Valsakumar V, Cieslik M, Pickin R, Hamlin JL, et al. (2013) Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early- and late-firing origins. Genome Res.
26. Aladjem MI, Rodewald LW, Kolman JL, Wahl GM, (1998) Genetic dissection of a mammalian replicator in the human beta-globin locus. Science 281: 1005-1009.
27. Paixao S, Colaluca IN, Cubells M, Peverali FA, Destro A, et al. (2004) Modular structure of the human lamin B2 replicator. Mol Cell Biol 24: 2958-2967.
28. Malott M, Leffak M, (1999) Activity of the c-myc replicator at an ectopic chromosomal location. Mol Cell Biol 19: 5685-5695.
29. Altman AL, Fanning E, (2001) The Chinese hamster dihydrofolate reductase replication origin beta is active at multiple ectopic chromosomal locations and requires specific DNA sequence elements for activity. Mol Cell Biol 21: 1098-1110.
30. Gilbert DM, (2002) Replication timing and transcriptional control: beyond cause and effect. Curr Opin Cell Biol 14: 377-383.
31. Gondor A, Ohlsson R, (2009) Replication timing and epigenetic reprogramming of gene expression: a two-way relationship? Nat Rev Genet 10: 269-276.
32. Koren A, McCarroll SA, (2013) Random replication of the inactive X chromosome. Genome Res.
33. Woodfine K, Fiegler H, Beare DM, Collins JE, McCann OT, et al. (2004) Replication timing of the human genome. Hum Mol Genet 13: 191-202.
34. Desprat R, Thierry-Mieg D, Lailler N, Lajugie J, Schildkraut C, et al. (2009) Predictable dynamic program of timing of DNA replication in human cells. Genome Res 19: 2288-2299.
35. Roach JC, Glusman G, Smit AF, Huff CD, Hubley R, et al. (2010) Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328: 636-639.
36. Lajugie J, Mukhopadhyay R, Schizas M, Lailler N, Fourel N, et al. (2013) Complete genome phasing of family quartet by combination of genetic, physical and population-based phasing analysis. PLoS One 8: e64571.
37. Olivier EQ, C; Bouhassira EE, (2012) Novel, High-yield RBC Production Methods from Cells derived from Human ES, Yolk Sac, Fetal Liver, Cord and Peripheral Blood. Stem Cell Translational Medicine 1: 604-614.
38. Hiratani I, Ryba T, Itoh M, Yokochi T, Schwaiger M, et al. (2008) Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol 6: e245.
39. Simon I, Tenzen T, Reubinoff BE, Hillman D, McCarrey JR, et al. (1999) Asynchronous replication of imprinted genes is established in the gametes and maintained during development. Nature 401: 929-932.
40. Aladjem MI, Groudine M, Brody LL, Dieken ES, Fournier RE, et al. (1995) Participation of the human beta-globin locus control region in initiation of DNA replication. Science 270: 815-819.
41. Sharp A, Robinson D, Jacobs P, (2000) Age- and tissue-specific variation of X chromosome inactivation ratios in normal women. Hum Genet 107: 343-349.
42. Mossner M, Nolte F, Hutter G, Reins J, Klaumunzer M, et al. (2013) Skewed X-inactivation patterns in ageing healthy and myelodysplastic haematopoiesis determined by a pyrosequencing based transcriptional clonality assay. J Med Genet 50: 108-117.
43. Beutler E, (1994) G6PD deficiency. Blood 84: 3613-3636.
44. Boggs BA, Chinault AC, (1994) Analysis of replication timing properties of human X-chromosomal loci by fluorescence in situ hybridization. Proc Natl Acad Sci U S A 91: 6083-6087.
45. Lyon MF, (1972) X-chromosome inactivation and developmental patterns in mammals. Biol Rev Camb Philos Soc 47: 1-35.
46. Farkash-Amar S, Lipson D, Polten A, Goren A, Helmstetter C, et al. (2008) Global organization of replication time zones of the mouse genome. Genome Res 18: 1562-1570.
47. Audit B, Baker A, Chen CL, Rappailles A, Guilbaud G, et al. (2013) Multiscale analysis of genome-wide replication timing profiles using a wavelet-based signal-processing algorithm. Nat Protoc 8: 98-110.
48. Ryba T, Hiratani I, Lu J, Itoh M, Kulik M, et al. (2010) Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res 20: 761-770.
49. Koren A, Polak P, Nemesh J, Michaelson JJ, Sebat J, et al. (2012) Differential relationship of DNA replication timing to different forms of human mutation and variation. Am J Hum Genet 91: 1033-1040.
50. Raghuraman MK, Winzeler EA, Collingwood D, Hunt S, Wodicka L, et al. (2001) Replication dynamics of the yeast genome. Science 294: 115-121.
51. Vassilev L, Johnson EM, (1989) Mapping initiation sites of DNA replication in vivo using polymerase chain reaction amplification of nascent strand segments. Nucleic Acids Res 17: 7693-7705.
52. Yoon Y, Sanchez JA, Brun C, Huberman JA, (1995) Mapping of replication initiation sites in human ribosomal DNA by nascent-strand abundance analysis. Mol Cell Biol 15: 2482-2489.
53. Aladjem MI, Rodewald LW, Lin CM, Bowman S, Cimbora DM, et al. (2002) Replication initiation patterns in the beta-globin loci of totipotent and differentiated murine cells: evidence for multiple initiation regions. Mol Cell Biol 22: 442-452.
54. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: R137.
55. Toledo F, Baron B, Fernandez MA, Lachages AM, Mayau V, et al. (1998) oriGNAI3: a narrow zone of preferential replication initiation in mammalian cells identified by 2D gel and competitive PCR replicon mapping techniques. Nucleic Acids Res 26: 2313-2321.
56. Abdurashidova G, Deganuto M, Klima R, Riva S, Biamonti G, et al. (2000) Start sites of bidirectional DNA synthesis at the human lamin B2 origin. Science 287: 2023-2026.
57. Vassilev LT, Burhans WC, DePamphilis ML, (1990) Mapping an origin of DNA replication at a single-copy locus in exponentially proliferating mammalian cells. Mol Cell Biol 10: 4685-4689.
58. Ladenburger EM, Keller C, Knippers R, (2002) Identification of a binding region for human origin recognition complex proteins 1 and 2 that coincides with an origin of DNA replication. Mol Cell Biol 22: 1036-1048.
59. DePamphilis ML, (1999) Replication origins in metazoan chromosomes: fact or fiction? Bioessays 21: 5-16.
60. Costantini M, Bernardi G, (2008) Replication timing, chromosomal bands, and isochores. Proc Natl Acad Sci U S A 105: 3433-3437.
61. Lopes J, Piazza A, Bermejo R, Kriegsman B, Colosio A, et al. (2011) G-quadruplex-induced instability during leading-strand replication. EMBO J 30: 4033-4046.
62. Fu H, Maunakea AK, Martin MM, Huang L, Zhang Y, et al. (2013) Methylation of histone H3 on lysine 79 associates with a group of replication origins and helps limit DNA replication once per cell cycle. PLoS Genet 9: e1003542.
63. Haase SB, Heinzel SS, Calos MP, (1994) Transcription inhibits the replication of autonomously replicating plasmids in human cells. Mol Cell Biol 14: 2516-2524.
64. Mesner LD, Hamlin JL, (2005) Specific signals at the 3′ end of the DHFR gene define one boundary of the downstream origin of replication. Genes Dev 19: 1053-1066.
65. Sasaki T, Ramanathan S, Okuno Y, Kumagai C, Shaikh SS, et al. (2006) The Chinese hamster dihydrofolate reductase replication origin decision point follows activation of transcription and suppresses initiation of replication within transcription units. Mol Cell Biol 26: 1051-1062.
66. Ermakova OV, Nguyen LH, Little RD, Chevillard C, Riblet R, et al. (1999) Evidence that a single replication fork proceeds from early to late replicating domains in the IgH locus in a non-B cell line. Mol Cell 3: 321-330.
67. Norio P, Kosiyatrakul S, Yang Q, Guan Z, Brown NM, et al. (2005) Progressive activation of DNA replication initiation in large domains of the immunoglobulin heavy chain locus during B cell development. Mol Cell 20: 575-587.
68. Dimitrova DS, Gilbert DM, (1998) Regulation of mammalian replication origin usage in Xenopus egg extract. J Cell Sci 111 (Pt 19):: 2989-2998.
69. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
70. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20: 1297-1303.
71. Lajugie J, Bouhassira EE, (2011) GenPlay, a multipurpose genome analyzer and browser. Bioinformatics 27: 1889-1893.
72. Zang C, Schones DE, Zeng C, Cui K, Zhao K, et al. (2009) A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 25: 1952-1958.
73. Huppert JL, Balasubramanian S, (2005) Prevalence of quadruplexes in the human genome. Nucleic Acids Res 33: 2908-2916.