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Series GSE13328 Query DataSets for GSE13328
Status Public on Feb 10, 2009
Title Chromatin structure marks cell-type and gender specific replication of the Drosophila genome
Organism Drosophila melanogaster
Experiment type Expression profiling by array
Genome binding/occupancy profiling by genome tiling array
Summary Duplication of eukaryotic genomes during S phase is coordinated in space and time. In order to identify zones of initiation and cell-type as well as gender-specific plasticity of DNA replication, we profiled replication timing, histone acetylation and transcription throughout the Drosophila genome. We observed two waves of replication initiation with many distinct zones firing in early and multiple, less defined peaks at the end of S phase, suggesting that initiation becomes more promiscuous at the end of S phase. A comparison of different cell types revealed widespread plasticity of replication timing on autosomes. Most occur in large regions but only half coincide with local differences in transcription. In contrast to confined autosomal differences, a global shift in replication timing occurs throughout the single male X chromosome. Unlike in females, the dosage compensated X chromosome replicates almost exclusively early. This difference occurs at sites which are not transcriptionally hyperactivated, but show increased acetylation of lysine 16 of histone H4. This suggests a transcription-independent, yet chromosome-wide process related to chromatin. Importantly, H4K16ac is also enriched at initiation zones as well as early replicating regions on autosomes during S phase. Together, our data reveal novel organizational principles of DNA replication of the Drosophila genome and imply chromatin structure as a determinant of replication timing locally and chromosome-wide.

Keywords: cell type comparison, chip-chip, replication timing
 
Overall design RNA was isolated from Kc and Cl8 cells (5 replicates each) and hybridized to gene expression arrays. RNA was isolated from kc ane Cl8 cells (2 replciates each) and hybridised to tiling arrays. Early and late replicating DNA was isolated from Kc (5 replicates), Cl8 (2 replicates) and S2 (2 replicates) cells and hybridized to tiling arrays. Replicating DNA from four S phase fractions ( 2 replicates each) was isolated from Kc cells and hybridized to tiling arrays, with genomic DNA (2 replicates) from Kc cells as a control. Nascent DNA was isolated from Kc cells and hybridized to tiling arrays, with genomic DNA as a control (3 replicates each). ChIP-chip was perfomred for RNA Polymerase II in Kc (2 replicates) and Cl8 (3 replicates) cells. ChIP-chip was performed for H4K16ac in Kc (3 replicates) and Cl8 (4 replicates) cells. ChIP-chip for H4K16ac was performed in early and late S phase Kc cells (2 replicates each).
 
Contributor(s) Schwaiger M, Stadler MB, Bell O, Kohler H, Oakeley EJ, Schübeler D
Citation(s) 19270159
Submission date Oct 23, 2008
Last update date Aug 28, 2018
Contact name Michaela Schwaiger
E-mail(s) michaela.schwaiger@univie.ac.at
Organization name University of Vienna
Lab Technau
Street address Althanstr. 14
City Vienna
ZIP/Postal code 1090
Country Austria
 
Platforms (3)
GPL1322 [Drosophila_2] Affymetrix Drosophila Genome 2.0 Array
GPL5919 [Dm35b_MR] Affymetrix Drosophila Tiling 1.0R Array
GPL6629 [DM_tiling2_MR] Affymetrix Drosophila Tiling 2.0R Array
Samples (25)
GSM336351 Kc-RNA-1
GSM336352 Kc-RNA-2
GSM336353 Kc-RNA-3
Relations
BioProject PRJNA109923

HMM based differentially replicating regions Kc-Cl8 header descriptions
chromosome GSM336362 minus GSM336363 was used as input for Hidden Markov Model segmentation to define those regions which are marked by the chromosomal coordinates.
start GSM336362 minus GSM336363 was used as input for Hidden Markov Model segmentation to define those regions which are marked by the chromosomal coordinates.
end GSM336362 minus GSM336363 was used as input for Hidden Markov Model segmentation to define those regions which are marked by the chromosomal coordinates.
Cl8-Kc transcription GSM336365
HMM switch.type GSM336362 minus GSM336363 was used as input for Hidden Markov Model segmentation to define the replciation switch chracteristics of those regions which are marked by the chromosomal coordinates.
Kc replication timing GSM336362
Cl8 replication timing GSM336363
Kc-Cl8 replication timing GSM336362 - GSM336363
H4K16.Kc GSM336366
H4K16.Cl8 GSM336367
Kc.Pol2 GSM336368
Cl8.Pol2 GSM336369
significant replication timing switch Columns B,C,E,H

Data table
chromosome start end Cl8-Kc transcription HMM switch.type Kc replication timing Cl8 replication timing Kc-Cl8 replication timing H4K16.Kc H4K16.Cl8 Kc.Pol2 Cl8.Pol2 significant replication timing switch
chr2L 88 59289 4.093323843 Cl8 early 0.451866192 1.95583274 -1.503966548 0.793620403 0.291880783 0.479523132 -0.003978648 L>E
chr2L 59290 69080 0.853916667 unchanged 2.986703557 2.416798419 0.569905138 0.885680556 0.167833333 0.3179375 0.109597222 no diff
chr2L 69081 73225 0.288018018 Kc early 3.50536 2.67152 0.83384 2.383423423 2.113738739 0.754774775 1.206426426
chr2L 73226 75009 3.132941176 unchanged 3.829046154 2.938307692 0.890738462 2.013333333 1.573284314 0.809411765 1.510326797 no diff
chr2L 75010 80227 1.666853147 Kc early 4.045044586 2.869267516 1.17577707 0.694405594 1.110541958 -0.236083916 -0.07018648
chr2L 80228 94816 0.178897243 unchanged 3.381529126 2.681347087 0.700182039 -0.236875522 -0.038609023 -0.055839599 -0.096424394 no diff
chr2L 94817 137875 -0.979508475 Kc early 4.746492875 3.363537301 1.382955574 1.492319209 1.302432203 0.710728814 0.848570621
chr2L 137876 139255 -0.156842105 unchanged 3.248115385 2.361634615 0.886480769 -0.07745614 -0.635921053 0.277894737 -0.17745614 no diff
chr2L 139256 149855 -0.425670103 Kc early 4.773921311 3.592704918 1.181216393 1.015189003 0.903599656 0.215635739 0.18975945
chr2L 149856 178485 -0.697539474 unchanged 3.335279793 3.043458549 0.291821244 0.973855263 1.320052632 0.604243421 0.830368421 no diff
chr2L 178486 194803 3.061181818 Cl8 early 2.627340807 3.331087444 -0.703746637 0.287598485 1.208534091 0.058659091 -0.008030303
chr2L 194804 216381 2.665387205 unchanged 2.900705107 2.983739703 -0.083034596 1.247861953 1.445147306 0.098636364 0.182205387 no diff
chr2L 216382 288502 0.822900763 Cl8 early 1.003449671 2.294876075 -1.291426404 0.998497031 1.162025445 0.378290076 0.552743003
chr2L 288503 299595 -1.485775578 unchanged 1.34021519 1.489208861 -0.148993671 1.345170517 1.484983498 0.87669967 1.232123212 no diff
chr2L 299596 398354 -0.14000408 Cl8 early -0.271064123 1.108348214 -1.379412338 -0.211984224 -0.144380865 -0.122829457 0.044667483
chr2L 398355 419415 -2.806712803 unchanged 2.631583756 2.477411168 0.154172589 0.900790081 0.698719723 0.251487889 0.414625144 no diff
chr2L 419416 429784 -1.309507042 Kc early 3.692430976 2.652946128 1.039484848 2.291431925 2.138565141 0.991003521 0.933262911
chr2L 429785 455986 -0.981060172 unchanged 3.855099859 3.23757384 0.61752602 0.69469914 0.721278653 0.311074499 0.289226361 no diff
chr2L 455987 466648 0.114261745 Kc early 4.523955128 3.42724359 1.096711538 0.074876957 0.308850671 -0.307315436 -0.094194631
chr2L 466649 467748 0.213548387 unchanged 4.632 3.741931818 0.890068182 -0.334086022 -0.548951613 -0.513548387 -0.239784946 no diff

Total number of rows: 4667

Table truncated, full table size 614 Kbytes.




Kc initiation zones header descriptions
chromosome GSM336362
init.start GSM336362
init.end GSM336362
initiation zone transcription GSM336365
initiation zone replication timing GSM336362
repl.start GSM336362
repl.end GSM336362
peaks.smooth GSM336362
peak.rt.smooth GSM336362
p-value GSM336362
adjusted p-value p-value after correction for multipe testing using the Benjamini-Hochberg method
nascent DNA GSM336364
H4K16ac GSM336366
RNA Polymerase II GSM336368

Data table
chromosome init.start init.end initiation zone transcription initiation zone replication timing repl.start repl.end peaks.smooth peak.rt.smooth p-value adjusted p-value nascent DNA H4K16ac RNA Polymerase II
chr2L 14088 23588 -0.508829431 0.567266667 88 35088 18588 0.532621899 2.03E-05 3.77E-05 2.748026756 0.93657748 0.515367893
chr2L 67588 75088 4.450338164 3.630463768 44088 86088 72588 3.849030396 0.002031086 0.002866552 1.742657005 2.340048309 0.665724638
chr2L 121588 127088 7.222039474 5.389333333 86588 139088 124088 5.403278198 3.07E-07 7.95E-07 1.651052632 1.87372807 0.068026316
chr2L 143588 151588 0.49716895 4.54886758 139588 180088 147588 4.641239296 6.37E-06 1.28E-05 0.114748858 1.182907154 0.099908676
chr2L 192588 201088 17.90402542 3.289322034 180588 255088 197588 3.23160269 1.09E-07 3.22E-07 0.338559322 0.675254237 -0.023707627
chr2L 282088 290088 0.652690583 1.660053571 255588 335588 287088 1.594783391 3.58E-07 9.08E-07 0.628878924 1.666741405 0.958923767
chr2L 352588 360088 1.743046875 -0.612484375 336088 373588 356588 -0.441657783 5.04E-10 2.37E-08 1.829375 0.564791667 0.232421875
chr2L 424588 430088 -0.613856209 4.206562092 374088 437088 427588 3.95732137 0.001939703 0.002748273 0.209084967 1.479172113 0.096764706
chr2L 461588 467088 -1.210974026 4.725587097 437588 473588 464588 4.532305954 5.58E-06 1.13E-05 -1.012857143 -0.186428571 -0.345876623
chr2L 485088 493088 1.15 5.689769585 474088 500588 490088 5.349659174 2.74E-08 9.95E-08 1.821336406 0.963072197 0.719470046
chr2L 506588 514588 2.746233184 5.253705357 501088 543088 511588 5.133195869 0.000178275 0.000290154 -0.058789238 -0.257294469 -0.299349776
chr2L 545588 553588 1.170678733 3.976552036 543588 638088 547588 3.934505973 0.000202293 0.000326523 -1.406606335 0.314434389 0.979072398
chr2L 638588 645588 -1.050833333 -2.67590625 638588 648088 643088 -2.711500597 0.008755873 0.011132279 -0.86328125 -0.373923611 -0.154140625
chr2L 655588 661088 -0.572857143 -2.589662162 648588 669088 658088 -2.700490838 0.004361188 0.005824859 -0.07877551 -0.46521542 -0.120646259
chr2L 682588 689588 -0.702704918 -2.350704918 669588 705088 685588 -2.304691007 1.67E-09 2.41E-08 -0.816065574 -0.325 -0.01057377
chr2L 714088 722088 -0.562803738 -2.814971963 710088 739588 718588 -2.934278118 0.000180198 0.000292721 -0.450934579 -0.404205607 -0.149953271
chr2L 750088 758088 -0.666457399 -2.406910714 740088 766088 754088 -2.598342043 2.54E-08 9.39E-08 -1.148609865 -0.375590433 -0.11206278
chr2L 836588 845588 0.385731707 3.580455285 766588 845588 842088 3.563536732 0.003609615 0.004885295 0.240121951 0.892344173 -0.035792683
chr2L 857088 865588 -0.007118644 4.048898305 846088 889088 862588 3.980979294 1.26E-07 3.63E-07 -0.482838983 1.477048023 0.026419492
chr2L 889588 897088 1.632392344 3.29707177 889588 947588 892088 3.219640169 0.0458728 0.052019223 -0.370430622 0.619792663 0.390119617

Total number of rows: 2539

Table truncated, full table size 351 Kbytes.




Kc termination zones header descriptions
chromosome GSM336362
termination.start GSM336362
termination.end GSM336362
termination zone transcription GSM336365
termination zone replication timing GSM336362
repl.start GSM336362
repl.end GSM336362
peaks.smooth GSM336362
end.rt.smooth GSM336362
p-value GSM336362
adjusted p-value p-value after correction for multipe testing using the Benjamini-Hochberg method
nascent DNA GSM336364
H4K16ac GSM336366
RNA Polymerase II GSM336368

Data table
chromosome termination.start termination.end termination zone transcription termination zone replication timing repl.start repl.end peaks.smooth end.rt.smooth p-value adjusted p-value nascent DNA H4K16ac RNA Polymerase II
chr2L 29588 47588 -0.629555556 0.383284848 88 35088 18588 0.37738176 2.03E-05 3.77E-05 2.594343434 0.814983165 0.487323232
chr2L 82088 89588 -0.0647343 3.288850242 44088 86088 72588 3.403658762 0.002031086 0.002866552 0.703864734 -0.407713366 0.180603865
chr2L 134088 142088 0.876098655 4.167461883 86588 139088 124088 4.406258773 3.07E-07 7.95E-07 1.127219731 0.653527653 0.404820628
chr2L 175588 184088 5.933554502 2.187018868 139588 180088 147588 2.269183097 6.37E-06 1.28E-05 0.704597156 -0.089099526 0.014739336
chr2L 251088 260588 0.795741445 0.402250951 180588 255088 197588 0.410001732 1.09E-07 3.22E-07 0.303117871 0.697782003 0.314809886
chr2L 330588 343088 0.691498559 -0.860126801 255588 335588 287088 -0.903120933 3.58E-07 9.08E-07 -0.47778098 -0.157463977 -0.216729107
chr2L 369088 377588 -0.78940678 -1.123762712 336088 373588 356588 -1.179759561 5.04E-10 2.37E-08 -0.043305085 -0.486638418 -0.260169492
chr2L 433588 440088 2.030335196 3.333743017 374088 437088 427588 3.690506671 0.001939703 0.002748273 0.382849162 -0.091247672 0.005446927
chr2L 469588 477088 4.71075 4.19245 437588 473588 464588 4.261999799 5.58E-06 1.13E-05 0.2098 0.75605 0.53495
chr2L 498088 503588 1.74755102 4.638612245 474088 500588 490088 4.835497893 2.74E-08 9.95E-08 0.638163265 0.599297052 -0.183095238
chr2L 538588 545088 7.954189944 3.814882682 501088 543088 511588 3.866814673 0.000178275 0.000290154 0.092122905 1.46292365 1.085251397
chr2L 635088 640588 -1.031866667 -2.668622517 543588 638088 547588 -2.781459515 0.000202293 0.000326523 0.3474 -0.412733333 -0.2201
chr2L 643588 651088 -0.893413462 -2.672673077 638588 648088 643088 -2.812481233 0.008755873 0.011132279 -0.328653846 -0.349070513 -0.104399038
chr2L 666588 674088 -1.057251185 -3.440056604 648588 669088 658088 -3.209219189 0.004361188 0.005824859 -0.44521327 -0.354628752 -0.077654028
chr2L 699588 709588 -0.801098901 -2.962622711 669588 705088 685588 -2.98859012 1.67E-09 2.41E-08 0.022967033 -0.480842491 -0.050732601
chr2L 735088 744588 -0.584068441 -3.367704545 710088 739588 718588 -3.294395217 0.000180198 0.000292721 -0.346920152 -0.328111534 -0.174980989
chr2L 763588 770088 -0.877569061 -3.24518232 740088 766088 754088 -3.094093712 2.54E-08 9.39E-08 -1.006022099 -0.55092081 -0.193093923
chr2L 842588 849088 -0.022556818 3.500954545 766588 845588 842088 3.499518738 0.003609615 0.004885295 0.609829545 0.650132576 -0.015056818
chr2L 883588 891588 -0.564009009 3.159396396 846088 889088 862588 3.212464511 1.26E-07 3.63E-07 -1.427252252 -0.352867868 -0.094864865
chr2L 943588 948588 -0.853214286 -2.077328571 889588 947588 892088 -2.01430482 0.0458728 0.052019223 -0.143571429 -0.436166667 -0.03325

Total number of rows: 2539

Table truncated, full table size 354 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE13328_RAW.tar 5.1 Gb (http)(custom) TAR (of CEL, TXT)
Processed data included within Sample table
Processed data provided as supplementary file
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