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DNA replication timing.

Rhind N, Gilbert DM.

Cold Spring Harb Perspect Biol. 2013 Aug 1;5(8):a010132. doi: 10.1101/cshperspect.a010132. Review.


Topologically associating domains are stable units of replication-timing regulation.

Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, Vera DL, Wang Y, Hansen RS, Canfield TK, Thurman RE, Cheng Y, Gülsoy G, Dennis JH, Snyder MP, Stamatoyannopoulos JA, Taylor J, Hardison RC, Kahveci T, Ren B, Gilbert DM.

Nature. 2014 Nov 20;515(7527):402-5. doi: 10.1038/nature13986.


Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome.

Guilbaud G, Rappailles A, Baker A, Chen CL, Arneodo A, Goldar A, d'Aubenton-Carafa Y, Thermes C, Audit B, Hyrien O.

PLoS Comput Biol. 2011 Dec;7(12):e1002322. doi: 10.1371/journal.pcbi.1002322. Epub 2011 Dec 29.


Genome-wide identification and characterization of replication origins by deep sequencing.

Xu J, Yanagisawa Y, Tsankov AM, Hart C, Aoki K, Kommajosyula N, Steinmann KE, Bochicchio J, Russ C, Regev A, Rando OJ, Nusbaum C, Niki H, Milos P, Weng Z, Rhind N.

Genome Biol. 2012 Apr 24;13(4):R27. doi: 10.1186/gb-2012-13-4-r27.


Chromatin state marks cell-type- and gender-specific replication of the Drosophila genome.

Schwaiger M, Stadler MB, Bell O, Kohler H, Oakeley EJ, Schübeler D.

Genes Dev. 2009 Mar 1;23(5):589-601. doi: 10.1101/gad.511809.


The replication domain model: regulating replicon firing in the context of large-scale chromosome architecture.

Pope BD, Gilbert DM.

J Mol Biol. 2013 Nov 29;425(23):4690-5. doi: 10.1016/j.jmb.2013.04.014. Epub 2013 Apr 17. Review.


A variable fork rate affects timing of origin firing and S phase dynamics in Saccharomyces cerevisiae.

Supady A, Klipp E, Barberis M.

J Biotechnol. 2013 Oct 20;168(2):174-84. doi: 10.1016/j.jbiotec.2013.06.022. Epub 2013 Jul 9.


Temporal and spatial regulation of eukaryotic DNA replication: from regulated initiation to genome-scale timing program.

Renard-Guillet C, Kanoh Y, Shirahige K, Masai H.

Semin Cell Dev Biol. 2014 Jun;30:110-20. doi: 10.1016/j.semcdb.2014.04.014. Epub 2014 Apr 13. Review.


Chromosome size in diploid eukaryotic species centers on the average length with a conserved boundary.

Li X, Zhu C, Lin Z, Wu Y, Zhang D, Bai G, Song W, Ma J, Muehlbauer GJ, Scanlon MJ, Zhang M, Yu J.

Mol Biol Evol. 2011 Jun;28(6):1901-11. doi: 10.1093/molbev/msr011. Epub 2011 Jan 13.


Eukaryotic gene regulation in three dimensions and its impact on genome evolution.

Babu MM, Janga SC, de Santiago I, Pombo A.

Curr Opin Genet Dev. 2008 Dec;18(6):571-82. doi: 10.1016/j.gde.2008.10.002. Epub 2008 Nov 27.


Late replication domains are evolutionary conserved in the Drosophila genome.

Andreyenkova NG, Kolesnikova TD, Makunin IV, Pokholkova GV, Boldyreva LV, Zykova TY, Zhimulev IF, Belyaeva ES.

PLoS One. 2013 Dec 31;8(12):e83319. doi: 10.1371/journal.pone.0083319. eCollection 2013.


Segmental folding of chromosomes: a basis for structural and regulatory chromosomal neighborhoods?

Nora EP, Dekker J, Heard E.

Bioessays. 2013 Sep;35(9):818-28. doi: 10.1002/bies.201300040. Epub 2013 Jul 5.


A chromatin structure-based model accurately predicts DNA replication timing in human cells.

Gindin Y, Valenzuela MS, Aladjem MI, Meltzer PS, Bilke S.

Mol Syst Biol. 2014 Mar 28;10:722. doi: 10.1002/msb.134859.


Topological domains in mammalian genomes identified by analysis of chromatin interactions.

Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B.

Nature. 2012 Apr 11;485(7398):376-80. doi: 10.1038/nature11082.


Genetic and epigenetic determinants of DNA replication origins, position and activation.

Méchali M, Yoshida K, Coulombe P, Pasero P.

Curr Opin Genet Dev. 2013 Apr;23(2):124-31. doi: 10.1016/j.gde.2013.02.010. Epub 2013 Mar 28. Review.


Space and time in the nucleus: developmental control of replication timing and chromosome architecture.

Gilbert DM, Takebayashi SI, Ryba T, Lu J, Pope BD, Wilson KA, Hiratani I.

Cold Spring Harb Symp Quant Biol. 2010;75:143-53. doi: 10.1101/sqb.2010.75.011. Epub 2010 Dec 7. Review.


Replication timing regulation of eukaryotic replicons: Rif1 as a global regulator of replication timing.

Yamazaki S, Hayano M, Masai H.

Trends Genet. 2013 Aug;29(8):449-60. doi: 10.1016/j.tig.2013.05.001. Epub 2013 Jun 25. Review.


Different nucleosomal architectures at early and late replicating origins in Saccharomyces cerevisiae.

Soriano I, Morafraile EC, Vázquez E, Antequera F, Segurado M.

BMC Genomics. 2014 Sep 13;15:791. doi: 10.1186/1471-2164-15-791.


Control of gene expression and assembly of chromosomal subdomains by chromatin regulators with antagonistic functions.

Lam AL, Pazin DE, Sullivan BA.

Chromosoma. 2005 Sep;114(4):242-51. Epub 2005 Oct 15. Review.


Developmental control of replication timing defines a new breed of chromosomal domains with a novel mechanism of chromatin unfolding.

Takebayashi S, Ryba T, Gilbert DM.

Nucleus. 2012 Nov-Dec;3(6):500-7. doi: 10.4161/nucl.22318. Epub 2012 Sep 28.

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