Comparative Analysis of DNA Replication Timing Reveals Conserved Large-Scale Chromosomal Architecture

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Recent evidence suggests that the timing of DNA replication is coordinated across megabase-scale domains in metazoan genomes, yet the importance of this aspect of genome organization is unclear. Here we show that replication timing is remarkably conserved between human and mouse, uncovering large regions that may have been governed by similar replication dynamics since these species have diverged. This conservation is both tissue-specific and independent of the genomic G+C content conservation. Moreover, we show that time of replication is globally conserved despite numerous large-scale genome rearrangements. We systematically identify rearrangement fusion points and demonstrate that replication time can be locally diverged at these loci. Conversely, rearrangements are shown to be correlated with early replication and physical chromosomal proximity. These results suggest that large chromosomal domains of coordinated replication are shuffled by evolution while conserving the large-scale nuclear architecture of the genome.

Vyšlo v časopise: Comparative Analysis of DNA Replication Timing Reveals Conserved Large-Scale Chromosomal Architecture. PLoS Genet 6(7): e32767. doi:10.1371/journal.pgen.1001011
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1001011

Souhrn

Zdroje

1. PaulerFM

SloaneMA

HuangR

ReghaK

KoernerMV

2009 H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome. Genome Res 19 221 233

2. WenB

WuH

ShinkaiY

IrizarryRA

FeinbergAP

2009 Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. Nat Genet 41 246 250

3. MikkelsenTS

KuM

JaffeDB

IssacB

LiebermanE

2007 Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448 553 560

4. BernsteinBE

MikkelsenTS

XieX

KamalM

HuebertDJ

2006 A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125 315 326

5. GilbertN

BoyleS

FieglerH

WoodfineK

CarterNP

2004 Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers. Cell 118 555 566

6. GuelenL

PagieL

BrassetE

MeulemanW

FazaMB

2008 Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453 948 951

7. Farkash-AmarS

LipsonD

PoltenA

GorenA

HelmstetterC

2008 Global organization of replication time zones of the mouse genome. Genome Res

8. HirataniI

RybaT

ItohM

YokochiT

SchwaigerM

2008 Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation. PLoS Biol 6 e245 doi:10.1371/journal.pbio.0060245

9. JeonY

BekiranovS

KarnaniN

KapranovP

GhoshS

2005 Temporal profile of replication of human chromosomes. Proc Natl Acad Sci U S A 102 6419 6424

10. MacAlpineDM

RodriguezHK

BellSP

2004 Coordination of replication and transcription along a Drosophila chromosome. Genes Dev 18 3094 3105

11. SchubelerD

ScalzoD

KooperbergC

van SteenselB

DelrowJ

2002 Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing. Nat Genet 32 438 442

12. WhiteEJ

EmanuelssonO

ScalzoD

RoyceT

KosakS

2004 DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proc Natl Acad Sci U S A 101 17771 17776

13. WoodfineK

BeareDM

IchimuraK

DebernardiS

MungallAJ

2005 Replication timing of human chromosome 6. Cell Cycle 4 172 176

14. WoodfineK

FieglerH

BeareDM

CollinsJE

McCannOT

2004 Replication timing of the human genome. Hum Mol Genet 13 191 202

15. Lieberman-AidenE

van BerkumNL

WilliamsL

ImakaevM

RagoczyT

2009 Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326 289 293

16. HurstLD

PalC

LercherMJ

2004 The evolutionary dynamics of eukaryotic gene order. Nat Rev Genet 5 299 310

17. SankoffD

2003 Rearrangements and chromosomal evolution. Curr Opin Genet Dev 13 583 587

18. BatadaNN

HurstLD

2007 Evolution of chromosome organization driven by selection for reduced gene expression noise. Nat Genet 39 945 949

19. AlekseyevMA

PevznerPA

2007 Are there rearrangement hotspots in the human genome? PLoS Comput Biol 3 e209 doi:10.1371/journal.pcbi.0030209

20. SankoffD

TrinhP

2005 Chromosomal breakpoint reuse in genome sequence rearrangement. J Comput Biol 12 812 821

21. HirataniI

RybaT

ItohM

RathjenJ

KulikM

2010 Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis. Genome Res 20 155 169

22. DespratR

Thierry-MiegD

LaillerN

LajugieJ

SchildkrautC

2009 Predictable dynamic program of timing of DNA replication in human cells. Genome Res 19 2288 2299

23. HansenRS

ThomasS

SandstromR

CanfieldTK

ThurmanRE

2010 Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A 107 139 144

24. Farkash-AmarS

SimonI

2010 Genome-wide analysis of the replication program in mammals. Chromosome Res 18 115 125

25. KuhnRM

KarolchikD

ZweigAS

WangT

SmithKE

2009 The UCSC Genome Browser Database: update 2009. Nucleic Acids Res 37 D755 761

26. ChiaromonteF

YapVB

MillerW

2002 Scoring pairwise genomic sequence alignments. Pac Symp Biocomput 115 126

27. KentWJ

BaertschR

HinrichsA

MillerW

HausslerD

2003 Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A 100 11484 11489

28. SchwartzS

KentWJ

SmitA

ZhangZ

BaertschR

2003 Human-mouse alignments with BLASTZ. Genome Res 13 103 107

29. WaterstonRH

Lindblad-TohK

BirneyE

RogersJ

AbrilJF

2002 Initial sequencing and comparative analysis of the mouse genome. Nature 420 520 562

30. RybaT

HirataniI

LuJ

ItohM

KulikM

2010 Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res

31. JaschekS

TanayA

2009 Spatial Clustering of Multivariate Genomic and Epigenomic Information. Recomb

32. PinkCJ

HurstLD

2010 Timing of replication is a determinant of neutral substitution rates but does not explain slow Y chromosome evolution in rodents. Mol Biol Evol 27 1077 1086

33. ChenCL

RappaillesA

DuquenneL

HuvetM

GuilbaudG

2010 Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes. Genome Res 20 447 457

34. MaJ

ZhangL

SuhBB

RaneyBJ

BurhansRC

2006 Reconstructing contiguous regions of an ancestral genome. Genome Res 16 1557 1565