Sequencing newly replicated DNA reveals widespread plasticity in human replication timing

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

Volumn 107, Issue 1, 2010, Pages 139-144

  Hansen, R Scott ^a   Thomas, Sean ^a   Sandstrom, Richard ^a   Canfield, Theresa K ^a   Thurman, Robert E ^a   Weaver, Molly ^a   Dorschner, Michael O ^a   Gartler, Stanley M ^a   Stamatoyannopoulos, John A ^a  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

Chromatin structure; Gene expression; Tissue specificity

Indexed keywords

DEOXYRIBONUCLEASE I; DNA;

ARTICLE; CELL COMPARTMENTALIZATION; CELL CYCLE; CELL FRACTIONATION; CELL LINEAGE; CELL TYPE; CHROMATIN STRUCTURE; CONTROLLED STUDY; CYTOMETRY; DNA REPLICATION; EPIGENETICS; GENE EXPRESSION; GENE MAPPING; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC VARIABILITY; HUMAN; HUMAN CELL; HUMAN GENOME; PLASTICITY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL;

ANIMALS; CELL LINE; CHROMATIN; DATABASES, GENETIC; DNA; DNA REPLICATION; EPIGENESIS, GENETIC; GENE EXPRESSION PROFILING; GENOME, HUMAN; HUMANS; SEQUENCE ANALYSIS, DNA;

EID: 76349123622     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0912402107     Document Type: Article

References (38)

1. Aladjem MI (2007) Replication in context: Dynamic regulation of DNA replication patterns in metazoans. Nat Rev Genet 8:588-600.
2. Taylor JH, Woods PS, Hughes WL (1957) The organization and duplication of chromosomes as revealed by autoradiographic studies using tritium-labeled thymidinee. Proc Natl Acad Sci USA 43:122-128.
3. Berezney R, Dubey DD, Huberman JA (2000) Heterogeneity of eukaryotic replicons, replicon clusters, and replication foci. Chromosoma 108:471-484.
4. Drouin R, Holmquist GP, Richer CL (1994) High-resolution replication bands compared with morphologic G- and R-bands. Adv Hum Genet 22:47-115.
5. Jackson DA, Pombo A (1998) Replicon clusters are stable units of chromosome structure: Evidence that nuclear organization contributes to the efficient activation and propagation of S phase in human cells. J Cell Biol 140:1285-1295.
6. Watanabe Y, et al. (2002) Chromosome-wide assessment of replication timing for human chromosomes 11q and 21q: Disease-related genes in timing-switch regions. Hum Mol Genet 11:13-21.
7. White EJ, et al. (2004) DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proc Natl Acad Sci USA 101:17771-17776.
8. WoodfineK, etal. (2004)Replication timing of the human genome.Hum Mol Genet 13:191-202.
9. Donaldson AD (2005) Shaping time: Chromatin structure and the DNA replication programme. Trends Genet 21:444-449.
10. Goldman MA, Holmquist GP, Gray MC, Caston LA, Nag A (1984) Replication timing of genes and middle repetitive sequences. Science 224:686-692.
11. Hatton KS, et al. (1988) Replication program of active and inactive multigene families in mammalian cells. Mol Cell Biol 8:2149-2158.
12. Hansen RS, Canfield TK, Fjeld AD, Gartler SM (1996) Role of late replication timing in the silencing of X-linked genes. Hum Mol Genet 5:1345-1353.
13. Hansen RS, et al. (2000) Escape from gene silencing in ICF syndrome: Evidence for advanced replication time as a major determinant. Hum Mol Genet 9:2575-2587.
14. Hiratani I, et al. (2008) Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol 6:e245.
15. Schwaiger M, et al. (2009) Chromatin state marks cell-type- and gender-specific replication of the Drosophila genome. Genes Dev 23:589-601.
16. Cadoret JC, et al. (2008) Genome-wide studies highlight indirect links between human replication origins and gene regulation. Proc Natl Acad Sci USA 105:15837-15842.
17. De Bonis ML, et al. (2006) Maintenance of X- and Y-inactivation of the pseudoautosomal (PAR2) gene SPRY3 is independent from DNA methylation and associated to multiple layers of epigenetic modifications. Hum Mol Genet 15:1123-1132.
18. McNairn AJ, Gilbert DM (2003) Epigenomic replication: Linking epigenetics to DNA replication. Bioessays 25:647-656.
19. Stamatoyannopoulos JA, et al. (2009) Human mutation rate associated with DNA replication timing. Nat Genet 41:393-395.
20. Hansen RS, et al. (1997) A variable domain of delayed replication in FRAXA fragile X chromosomes: X inactivation-like spread of late replication. Proc Natl Acad Sci USA 94: 4587-4592.
21. Hansen RS, Canfield TK, Lamb MM, Gartler SM, Laird CD (1993) Association of fragile X syndrome with delayed replication of the FMR1 gene. Cell 73:1403-1409.
22. Epner E, Forrester WC, Groudine M (1988) Asynchronous DNA replication within the human β-globin gene locus. Proc Natl Acad Sci USA 85:8081-8085.
23. Guelen L, et al. (2008) Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453:948-951.
24. Ermakova OV, 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.
25. Farkash-Amar S, et al. (2008) Global organization of replication time zones of the mouse genome. Genome Res 18:1562-1570.
26. Heard E, Disteche CM (2006) Dosage compensation in mammals: Fine-tuning the expression of the X chromosome. Genes Dev 20:1848-1867.
27. Horsthemke B, Wagstaff J (2008) Mechanisms of imprinting of the Prader-Willi/ Angelman region. Am J Med Genet A 146A:2041-2052.
28. Kawame H, Gartler SM, Hansen RS (1995) Allele-specific replication timing in imprinted domains: Absence of asynchrony at several loci. Hum Mol Genet 4:2287-2293.
29. Rugg-Gunn PJ, Ferguson-Smith AC, Pedersen RA (2007) Status of genomic imprinting in human embryonic stem cells as revealed by a large cohort of independently derived and maintained lines. Hum Mol Genet 16 (Spec no. 2):R243-R251.
30. Wang L, et al. (1999) Allele-specific late replication and fragility of the most active common fragile site, FRA3B. Hum Mol Genet 8:431-437.
31. Francks C, et al. (2007) LRRTM1onchromosome 2p12 is amaternally suppressed gene that is associated paternally withhandednessand schizophrenia. Mol Psychiatry 12:1129-1139.
32. Gimelbrant AA, Ensminger AW, Qi P, Zucker J, Chess A (2005) Monoallelic expression and asynchronous replication of p120 catenin in mouse and human cells. J Biol Chem 280:1354-1359.
33. Ensminger AW, Chess A (2004) Coordinated replication timing of monoallelically expressed genes along human autosomes. Hum Mol Genet 13:651-658.
34. Gimelbrant A, Hutchinson JN, Thompson BR, Chess A (2007) Widespread monoallelic expression on human autosomes. Science 318:1136-1140.
35. Jeon Y, et al. (2005) Temporal profile of replication of human chromosomes. Proc Natl Acad Sci USA 102:6419-6424.
36. Karnani N, Taylor C,Malhotra A, Dutta A (2007) Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas.Genome Res 17:865-876.
37. Sabo PJ, et al. (2006) Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat Methods 3:511-518.
38. Carrel L, Willard HF (2005) X-inactivation profile reveals extensive variability in Xlinked gene expression in females. Nature 434:400-404.