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Control of Drosophila endocycles by E2F and CRL4(CDT2).
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PMID:  22037307     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Endocycles are variant cell cycles comprised of DNA synthesis (S)- and gap (G)-phases but lacking mitosis. Such cycles facilitate post-mitotic growth in many invertebrate and plant cells, and are so ubiquitous that they may account for up to half the world's biomass. DNA replication in endocycling Drosophila cells is triggered by cyclin E/cyclin dependent kinase 2 (CYCE/CDK2), but this kinase must be inactivated during each G-phase to allow the assembly of pre-Replication Complexes (preRCs) for the next S-phase. How CYCE/CDK2 is periodically silenced to allow re-replication has not been established. Here, using genetic tests in parallel with computational modelling, we show that the endocycles of Drosophila are driven by a molecular oscillator in which the E2F1 transcription factor promotes CycE expression and S-phase initiation, S-phase then activates the CRL4(CDT2) ubiquitin ligase, and this in turn mediates the destruction of E2F1 (ref. 7). We propose that it is the transient loss of E2F1 during S phases that creates the window of low Cdk activity required for preRC formation. In support of this model overexpressed E2F1 accelerated endocycling, whereas a stabilized variant of E2F1 blocked endocycling by deregulating target genes, including CycE, as well as Cdk1 and mitotic cyclins. Moreover, we find that altering cell growth by changing nutrition or target of rapamycin (TOR) signalling impacts E2F1 translation, thereby making endocycle progression growth-dependent. Many of the regulatory interactions essential to this novel cell cycle oscillator are conserved in animals and plants, indicating that elements of this mechanism act in most growth-dependent cell cycles.
Authors:
Norman Zielke; Kerry J Kim; Vuong Tran; Shusaku T Shibutani; Maria-Jose Bravo; Sabarish Nagarajan; Monique van Straaten; Brigitte Woods; George von Dassow; Carmen Rottig; Christian F Lehner; Savraj S Grewal; Robert J Duronio; Bruce A Edgar
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.     Date:  2011-10-30
Journal Detail:
Title:  Nature     Volume:  480     ISSN:  1476-4687     ISO Abbreviation:  Nature     Publication Date:  2011 Dec 
Date Detail:
Created Date:  2011-12-01     Completed Date:  2012-02-23     Revised Date:  2014-09-16    
Medline Journal Info:
Nlm Unique ID:  0410462     Medline TA:  Nature     Country:  England    
Other Details:
Languages:  eng     Pagination:  123-7     Citation Subset:  IM    
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MeSH Terms
Descriptor/Qualifier:
Animals
Cell Cycle / physiology*
Drosophila Proteins / metabolism*
Drosophila melanogaster / cytology*,  enzymology*,  growth & development,  metabolism
E2F Transcription Factors / metabolism*
Female
Male
S Phase / physiology
Salivary Glands / cytology
Ubiquitin-Protein Ligases / metabolism*
Grant Support
ID/Acronym/Agency:
5 P50GM66050/GM/NIGMS NIH HHS; GM51186/GM/NIGMS NIH HHS; GM57859/GM/NIGMS NIH HHS; MOP-86622//Canadian Institutes of Health Research; R01 GM051186/GM/NIGMS NIH HHS; R01 GM051186-14A1/GM/NIGMS NIH HHS
Chemical
Reg. No./Substance:
0/Drosophila Proteins; 0/E2F Transcription Factors; 0/E2F protein, Drosophila; EC 6.3.2.19/CRL4(Cdt2) protein, Drosophila; EC 6.3.2.19/Ubiquitin-Protein Ligases
Comments/Corrections
Comment In:
Nat Rev Mol Cell Biol. 2011 Dec;12(12):768   [PMID:  22086370 ]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine

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Journal Information
Journal ID (nlm-journal-id): 0410462
Journal ID (pubmed-jr-id): 6011
Journal ID (nlm-ta): Nature
Journal ID (iso-abbrev): Nature
ISSN: 0028-0836
ISSN: 1476-4687
Article Information
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License:
nihms-submitted publication date: Day: 5 Month: 1 Year: 2012
Electronic publication date: Day: 30 Month: 10 Year: 2011
pmc-release publication date: Day: 01 Month: 6 Year: 2012
Volume: 480 Issue: 7375
First Page: 123 Last Page: 127
ID: 3330263
PubMed Id: 22037307
DOI: 10.1038/nature10579
ID: nihpa326672

Control of Drosophila endocycles by E2F and CRL4Cdt2
Norman Zielke12*
Kerry J. Kim3*
Vuong Tran2*
Shusaku T. Shibutani5
Maria-Jose Bravo2
Sabarish Nagarajan6
Monique van Straaten1
Brigitte Woods2
George von Dassow3
Carmen Rottig4
Christian F. Lehner4
Savraj Grewal6
Robert J. Duronio5
Bruce A. Edgar12
1German Cancer Research Center (DKFZ)-Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
2Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
3Center for Cell Dynamics, Friday Harbor Labs, University of Washington, 620 University Rd., Friday Harbor, WA 98250, USA
4Zoologisches Institut, Universität Zürich, Winterthurerstr. 190, 8057 Zürich, Switzerland
5Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
6Clark H. Smith Brain Tumor Center, Southern Alberta Cancer Research Institute, and Department of Biochemistry and Molecular Biology, University of Calgary, 3330 Hospital Drive, Calgary, Alberta, T2N 4N1, Canada
*These authors contributed equally to this work.

S-phase control in proliferating animal cells depends upon the E3 ubiquitin ligase, APCFzy/Cdc20, which is activated by Cyclin/Cdk1 during mitosis. APCFzy/Cdc20 promotes the degradation of mitotic Cyclins, thereby extinguishing Cdk1 activity following mitosis, and it also promotes the degradation of Geminin (Gem), an inhibitor of the preRC component Cdt1. The combination of low Geminin and low Cyclin/Cdk1 activity during early G1 allows the assembly of preRCs containing origin recognition complex (ORC) proteins, Cdc6, Cdt1/Double-parked (Dup), and MCM2-7 onto replication origins, thus “licensing” the DNA for renewed replication9. Drosophila’s endocycling cells do not express mitotic Cyclin/Cdk1 complexes or APCFzy/Cdc2010,11, and so this mechanism of S-phase regulation cannot apply to them. These endocycles do however employ CycE/Cdk2 to trigger S-phases12,13 (Fig 1, 2), and they also require the G1-specific APC variant, APCFzr/Cdh1, which mediates cyclic degradation of cell cycle factors including Geminin and Orc110,14. Importantly, while over-expressed CycE/Cdk2 is tolerated in mitotic cell cycles15, it blocks endocycling (Fig 2, 3)5,6. This is likely due to CycE/Cdk2’s ability to suppress APCFzr/Cdh1 and drive Geminin accumulation10,14,16, though CycE may also inhibit preRC formation directly by phosphorylating preRC components. The importance of CycE oscillation for endocycling is underscored by the finding that Archipelago (Ago/Cdc4/Fbw7), which promotes CycE degradation as a component of an SCF ubiquitin ligase, is required for the progression of endocycles, but not mitotic cycles (Fig S1)17. Despite its importance the mechanism controlling CycE/Cdk2 periodicity in the endocycle has remained obscure for over a decade.

We addressed this problem in Drosophila’s larval salivary glands, which undergo ~10 asynchronous endocycles from ~7–96 hours after egg deposition (h AED), reaching a final ploidy of ~1350C18. Studies in the fly ovary had suggested that the CycE/Cdk2 inhibitor dacapo (dap) might periodically silence Cdk2 during endocycling19, but our analysis ruled this out for salivary glands (Fig S2)10. Hence we asked whether cyclic CycE/Cdk2 activity might be controlled transcriptionally. CycE transcription is regulated by the E2F1 transcription factor2022, the accumulation of which is periodic in mitotic Drosophila cells7,2325 because it is targeted for degradation during S-phase by the PCNA/replication fork-associated E3 ubiquitin ligase CRL4Cdt27. In the salivary cells, E2f1 mRNA was ubiquitous (Fig 1c) but E2F1 protein was cyclic, being virtually absent in S-phase nuclei (Fig 1d, 2a). Continuously over-expressed E2F1 proteins were also depleted from S-phase nuclei (Fig 2c, 3c), consistent with periodic degradation. This implied that E2F-dependent transcription might also oscillate. Indeed, the mRNAs encoding CycE and two other E2F targets, RnrS and pcna were periodic (Fig 1, 3, S15, see also13). These mRNAs accumulated when E2F1 was over-expressed (Fig 3a) and were reduced in mutants for Dp, E2F1’s obligate dimerization partner (Fig S15). Thus periodic CycE expression is likely due to periodic activity of its regulator, E2F. CycE protein was also cyclic, being present during a bit of each Gap phase and much of each S-phase (Fig 1e)13,26. Based on these and other results10 we determined that E2F1 accumulates during G-phases and is destroyed upon entry into S-phase, whereas its target CycE rises late in G-phases and persists through most of each S-phase.

These observations suggested that endocycles run using a molecular oscillator in which E2F1 promotes CycE transcription, and then CycE/Cdk2 triggers S-phase and the consequent destruction of E2F1 to reset the cycle (Fig 1g). To evaluate this hypothesis we built a computational model that translated known regulatory interactions into a system of delay differential equations describing the concentrations of E2F1, RBF, CycE, Geminin, and Cdt1/Dup, and the activities of APCFzr/Cdh1 and CRL4Cdt2 (Fig 1g, Supplementary Methods, Fig S4, S5). In this model, when CycE was low Gem was degraded by APCFzr/Cdh1, allowing preRC licensing through Cdt1/Dup. High CycE suppressed APCFzr/Cdh1 activity and allowed Gem accumulation, and also triggered phosphorylation of RBF, S-phase initiation, activation of CRL4Cdt2 and the subsequent degradation of E2F1 and Cdt1/Dup. The model’s behavior depended on unmeasured parameters representing biochemical kinetics (Table S1), but Monte-Carlo searches found numerous parameters sets that simulated actual endocycles (Fig 1h, i). The model robustly produced oscillations of its components despite quantitative parameter variation (Fig S6–9) and did not require exquisitely tuned kinetics to reproduce oscillations like those observed in vivo (Supplementary Discussion).

We tested the computational model by challenging it to reproduce the results of genetic experiments performed in parallel. The model reproduced nearly all observed mutant and gene over-expression phenotypes (Fig 2, S10). Notably, it predicted that increasing E2F1 should accelerate endocycling and lead to hyper-polyploidy, as subsequently observed experimentally (Fig 2, 3, S11). As predicted, we observed increased relative DNA amounts in E2f1+/+ cells generated in an E2f1+/− background, and found that E2f17172 homozygous null mutant cells supported essentially no endocycling (Fig 2b, S13). Thus both loss- and gain-of-function experiments indicated that E2F1 is an essential dose-dependent regulator of endocycle progression.

An important prediction of the computational model was that periodic E2F1 destruction should be essential for endocycling. Drosophila E2F1 is targeted for proteolysis during S-phase via a conserved motif, the PIP box, which binds the replication fork-associated protein, PCNA, and mediates interaction with the CRL4Cdt2 ubiquitin ligase7. Consistent with model predictions, a stabilized but active form of E2F1 lacking the PIP box (GFP-E2F1PIP3A)7 blocked endocycle progression (Fig 2, 3, S11). Likewise RNAi against Cul4, a CRL4Cdt2 component, arrested endocycling (Fig 2b, S11, S12). Levels of E2F1 in cells arrested by GFP-E2F1PIP3A were not higher than in control GFP-E2F1-expressing cells that cycled, suggesting that this arrest was due to inappropriately timed expression of E2F1 rather than its excessive accumulation (Fig 3h, S11). Hence S-phase dependent degradation of E2F1 is essential for endocycling.

One discrepancy between the data and our model was that whereas the model could not readily predict endocycling without E2F (Fig S10), Dp and E2f1 E2f2 mutants support endocycling21,22,26. Our analysis showed that although Dp protein was barely detectable in Dp mutant glands (Fig S15) cells in these mutants nevertheless endocycled slowly and sustained periodic expression of CycE and RnrS, and Geminin oscillation (Fig 2b, S14, S15). One explanation for these apparently discrepant observations is that residual maternal E2F activity persists in these mutants. Consistent with this possibility we found that GFP-E2F1PIP3A was able to block endocycling in Dp mutants (Fig S16). Given this observation, the Dp mutant phenotype cannot be construed as confounding the model (see Supplementary Discussion).

We next asked how stabilized E2F1 arrests endocycling. Consistent with model predictions, cells arrested by GFP-E2F1PIP3A or Cul4-RNAi accumulated CycE and Geminin (Fig 3). In these arrested cells, however, Geminin accumulation occurred following rather than prior to arrest (Fig S12), indicating that it did not initiate the arrest. Interestingly, gem null mutant glands supported rather normal endocycles (Fig S17), but arrest by Rca110,14, an APCFzr/Cdh1 inhibitor, was substantially rescued in the gem mutants (Fig 3e, S18). This demonstrates that the predominant function of APCFzr/Cdh1 in these endocycles is the degradation of Geminin. Importantly, gem mutant cells could be arrested by ectopic CycE10,14 or E2F1PIP3A (Fig 3e, S18, S19). We conclude that while Geminin accumulation might consolidate the arrest caused by excess E2F1, it is neither initiating nor essential for this arrest.

Further investigations revealed that Cyclin A, Cyclin B3 and Cdk1 accumulated in E2F1PIP3A-arrested cells (Fig 3i, S20). These G2/M regulators are not normally expressed in endocycling cells8,10. Large inductions of the mRNAs encoding these factors were observed (Fig 3h), suggesting transcriptional de-repression. Consistent with this notion these factors were also induced in cells mutant for E2f2, Drosophila’s repressor E2F (Fig 3i, j). This suggests that, as in mitotic cells27, excess E2F1 may displace E2F2 and thereby de-repress its targets. In this context E2F2 appears to act as a selectivity factor that represses mitotic targets in endoreplicating cells. Given that Cdk1 is a potent suppressor of PreRCs that can arrest endocycle progression6, its derepression probably contributed to endocycle arrest by E2F1PIP3A.

Altogether our results indicate that periodic E2F1 degradation is necessary for endocycling for three reasons: 1) it creates a window of low CycE/Cdk2 activity; 2) it promotes high APCFzr/Cdh1 activity and thereby suppresses Geminin accumulation; and 3) it allows E2F2 to maintain repression of Cdk1 and its Cyclins. Each of these conditions is required for preRC assembly and endocycle progression. This cell cycle mechanism (Fig 1g, S4) is fundamentally different from that used in mitotic cycles, wherein destruction of the M-phase Cyclins by APCCdc20/Fzy, rather than of E2F1 by the CRL4Cdt2, throws the switch that allows preRC assembly9. Indeed it is noteworthy that the periodic degradation of E2F1 and depletion of CycE are not required for mitotic cell cycles in Drosophila7,12. CRL4Cdt2 is required for endocycling in plants8, suggesting that this element of the endocycle oscillator is conserved.

Finally, we asked what factors control E2F production to regulate endocycle rates. Endocycle speed and number can be manipulated by altering cell growth through changes in dietary protein28 or growth-regulatory genes including dMyc1 and Insulin/PI3K/TOR signaling components29. Hence we starved larvae of protein to suppress insulin/TOR signaling, reduce protein synthesis, and block cell growth. Starvation arrested the salivary endocycles within 24h and strongly depleted E2F1 (Fig 4a,b). E2f1 and Dp mRNA levels were not affected, but the E2F targets CycE, pcna, and rnrS were reduced (Fig 4c, not shown). To test whether this was responsible for starvation-induced endocycle arrest we overexpressed E2F1 in the salivary glands of starved animals. Although these glands failed to grow their nuclei incorporated BrdU and accrued ~7-fold more DNA than controls (Fig 4a). Over-expression of Rheb, which activates the Target of Rapamycin (TOR) kinase and increases ribosome biogenesis and cap-dependent translation, also restored cell growth, E2F1 protein, and endocycle progression in starved animals (Fig 4a). Thus E2F1 appears to act as a “growth sensor” that couples rates of endocycle progression to rates of cell growth. A likely mechanism for this, corroborated by modeling (Fig 4e, S8), involves increased translation of E2F1 in rapidly growing cells. Indeed, we found that the association of E2F1 mRNA with polyribosomes was greatly reduced in protein-starved animals (Fig 4d). Translational control of E2F is an attractive mechanism for coupling growth to G1/S progression not only in endocycling cells, but also in growth-dependent mitotic cells with extended G1 periods.


METHODS SUMMARY

Larvae were raised at 25°C in uncrowded conditions, and salivary glands dissected and analyzed using standard Drosophila genetics and molecular biology methods. DNA quantifications were done using DAPI fluorescence from CCD images. Computational modeling used delay differential equations tracking the concentrations of mRNAs and proteins, and numerically solved in Mathematica 5.2 (Wolfram Research). Full descriptions of experimental and computational methods, genotypes, and reagents is included in the Online Methods section and Supplementary Information.


METHODS
Genetics

To express genes in salivary glands ptc-Gal4, 43B-Gal4 or hey-Gal4 females were crossed to males carrying UAS transgenes. E2f17172/ E2f17172 mutant salivary gland cells were generated by heat shocking hs-Flp; FRT82B E2f17172/FRT82B ub-GPF-nls embryos to 37°C from 2–4h AED. Cdk2 mutant glands were generated using the genotype: F4-Gal4 UAS-GFP/+; Cdk2FRT Cdk23/Cdk22 or F4-Gal4 UAS-GFP/UAS-Flp; Cdk2FRT Cdk23/Cdk22, where Cdk2FRT is a transgene encoding an Flp-excisable Cdk2.

  • Mutants:
  • w; FRT80B, ago1/TM6B30
  • y,w, hs-FLP1.22; FRT80B P[mini-w], P[ubi-GFP]/TM6B
  • dap4/CyO, act-GFP31
  • dapg36/CyO, act-GFP32
  • w; Dpa1 /CyO, act-GFP21
  • w; Dpa2 /CyO, act-GFP21
  • w; FRT42D, Dpa3 /CyO, act-GFP21,33
  • w; Df(2R)Exel7124 /CyO(act-GFP) (Bloomington Drosophila Stock Center #7872)
  • w; FRT80B, e2f17172/TM6B (e2f17172 is described in 34)
  • w; e2f276Q1, cn, bw/CyO, act-GFP27
  • w; FRT40A, e2f2C03344, dpov/CyO, act-GFP (Gift from Maxim Frolov, University of Illinois, Chicago/USA)
  • w; gemininl(2)k14019,c, px, sp/CyO, act-GFP35
  • w; gemininl(2)k02302,c, px, sp/CyO, act-GFP35
  • w; DF(2R)ST1, Adhn5, pr1, cn*/ CyO, act-GFP35

For mutants, we used the strongest alleles available, which in most cases are null alleles. Details on mutant lesions can be found in the cited papers and FlyBase (http://flybase.org/).

  • Transgenes:
  • ptc-Gal436
  • 43B-Gal45
  • hey-Gal4, Pin/CyO (Gift from Amir Orian, Rappaport Institute, Israel)
  • UASt-Cul4-RNAi (VDRC #44829)
  • UASt-CycE31
  • UASt-CycE-RNAi (Nig-Fly #3938R-3)
  • UASt-Dap31
  • UASp-GFP-E2F17
  • UASp-GFP-E2F1-PIP3A7
  • UASt-E2F115
  • UASt-Rbf137
  • UASt-Rheb38
  • UASt-HA-Rca139

Starvation

At 48h or 72h AED larvae were washed with PBS and transferred to PBS+20% sucrose at 25°C, and maintained on this media until 96h or 120h AED, respectively.

DNA quantification

DNA content in nuclei or whole salivary glands was quantified by DAPI fluorescence. Larvae were raised at 25°C to 96h AED, and fixed glands were dissected and stained, using an internal control (ptc-Gal4 UAS-GFPnls) for each sample. Samples were imaged at 10x with a CCD camera (Spot RT or Roper HQ2). Average cytoplasmic intensity was subtracted, and the integrated DAPI intensity was used to measure DNA content for whole glands (Fig 2) or nuclei (Fig 3). All salivary glands had ~the same number of cells (<10% variability). Controls were set to 1350C according to18.

Quantification of nuclear concentrations

Nuclear BrdU, Cyclin E, E2F1, and GFP-E2F1 concentrations as shown in Fig 1(D-F), S3, and S11 were measured from samples stained with DAPI and the indicated antibodies and imaged by confocal microscopy at 20X. We took image stacks (interval size = 0.65μm; optimal overlap under our conditions) with optimized imaging conditions such that the deviation from linearity was <10%. To measure average nuclear concentrations of E2F1 and CycE, we used ImageJ (NIH) and custom software that searched for nuclei by finding ellipsoidal regions that stained brightly for DNA and had the approximate diameter of a nucleus. About half of all nuclei visually overlapped with their neighbors and were not analyzed. To reproducibly set the boundaries for each nucleus, we restricted our analysis to optical sections in which the average nuclear DNA staining was >90% maximal (typically 2–5 sections). Mean intensity in these regions was measured in other channels to determine nuclear concentrations.

BrdU labeling

Embryos were collected on grape-juice/agar plates for 2h and transferred to regular fly-food 24h after egg deposition. At the indicated time points salivary glands were dissected in Drosophila Ringer’s Solution and incubated for 1h at room temperature with 100μg/ml BrdU in Ringer’s Solution. Afterwards, the samples were fixed for 30min in 4% Paraformaldehyde/PBS and subsequently treated for 30min with 2N HCl. BrdU incorporation was detected with a mouse anti-BrdU antibody (Becton Dickinson) diluted 1:20 in 4% NGS/PBS/0.3% Triton-X100 and goat anti-mouse-Alexa Fluor-568 (Invitrogen) as secondary antibody diluted 1:2000 in 4% NGS/PBS/0.3% Triton-X100.

EdU labeling

EdU incorporation was performed analogous to the procedure for BrdU labeling using the Click-It EdU Alexa Fluor-555 imaging kit from Invitrogen.

In situ hybridization

Probes for in situ hybridization were generated with the DIG RNA labeling system (Roche). For in vitro transcription with T7/T3 RNA polymerase the following plasmids were used as template: pT7T3-19U-CycE40; pBLu(2)SKM-RnrS41; pBluSKP-E2F142. Salivary glands were dissected from larvae staged to the indicated time points. Small batches of about 30 larvae were fixed overnight in 8% formaldehyde/PBS, pooled in scintillation vials and stored until usage in ethanol at −80°C. The hybridization procedure was performed according to the protocol developed by the Bier-Lab43. For detection samples were probed with the following antibodies: sheep-anti-DIG-AP (1:500, Roche) or mouse anti-DIG-HRP (1:500, Abcam). BCIP/NBT was used as substrate for the AP reaction according to Tautz & Pfeifle44, while the TSA Alexa Fluor-568 Detection Kit (Invitrogen) was used in combination with HRP.

qRT-PCR

At the indicated time points about 50 salivary glands per genotype were dissected in Drosophila Ringer’s Solution and immediately transferred to the lysis-buffer supplied with the RNAeasy mini kit (Qiagen). Samples were stored at −80°C and then processed with the RNAeasy mini kit (Qiagen) according the manufacturers instructions including the optional on-column DNAseI digestion. 100ng of total RNA were used for cDNA synthesis with the Quantitect Reverse Transcription Kit (Qiagen) or the iScript cDNA synthesis kit (Bio-Rad). qRT-PCR data shown in Figure 3 I-K was acquired on a Light Cycler 480 (Roche) using the indicated UPL assays (Roche) and Light Cycler 480 Probes Master (Roche). Relative expression data presented in Figure 4C was acquired on an iQ5 Instrument (Biorad) using QuantiTect Primer Assays (Qiagen) and the iScript one-step RT-PCR SYBR green kit (Bio- Rad). To ensure statistical significance qRT-PCR was performed in quadruplicates from 3–4 independent samples. Relative expression to GAPDH1 and Actin5c was determined with the ΔΔCT method:

[Formula ID: FD1]
ΔCT=CTgene of interest−CTendogenous controlΔΔCT=ΔCTsample−ΔCTcalibratorrelative quantity=2−ΔΔCT

Polysome profiling

Whole larvae were lysed in ice-cold polysome lysis buffer (25mM Tris pH6.8, 10mM MgCl2, 25mM NaCl, 1% Triton-X 100, 0.5% Sodium Deoxycholate, 0.5uM DTT 1ug/ml Cycloheximide, 10ug/ml Heparin, Protease Inhibitor Cocktail (Complete mini, Roche), 2.5 uM PMSF, 5mM Sodium Fluoride, 1mM Sodiumorthovanadate, RNase inhibitor (Ribolock, - Fermentas) using a Dounce Homogenizer. Lysates were then cleared by centrifugation (15,000 rpm, 15 mins, 4C). Equal optical density units (260nM) of cleared lysates were then layered on 15–45% sucrose gradient (prepared in polysome lysis buffer) and centrifuged (37,000 rpm, 2.5 hrs, 4C) in an SW41 Beckman rotor. The gradients were then fractionated using a Brandel BR188 Density Gradient fractionator with continuous OD (254nm) reading and collected into twelve equal fractions. The RNA from each fraction was extracted with Trizol reagent and reversed transcribed using Superscript II (Invitrogen) according to the manufacturers instructions. Quantitative real-time PCR was then performed as described in 45 using a MyIQ PCR machine (BioRad).



Notes

FN2AUTHOR CONTRIBUTIONS

The E2F1-based oscillator was conceived by B.A.E.. N.Z. developed the framework for licensing control and E2F2-mediated repression of mitotic genes. K.J.K. did most of the computational modeling, which was initiated by G.v.D.. Initial experiments were done by V.T., who, with help from B.W. and K.J.K., contributed Fig 1d-f, 2a-b, 4a-b and S13. N.Z. carried out much of the later experimental work with help from M.v.S, and contributed Fig 2b-c, 3c-j, 4c, S1, S3, S11, S12 and S14–20. S.T.S and R.J.D. contributed the GFP-E2F1PIP3A transgenics and controls. M.J.B. contributed Fig 1A-C, 3A-B and S15 G-H. S.N. and S.G. contributed Fig 4D. C.R. and C.F.L. contributed Fig S2 and the cdk2−/− data in Fig 2B. B.A.E. directed the project and wrote the manuscript.

ACKNOWLEDGEMENTS

Supported by NIH GM51186 to B.A.E., DKFZ, a DAAD fellowship to N.Z., NIGMS 5 P50 GM66050 and NSF MCB0090835 to G.v.D. and K.J.K, DFG LE987/5-1 to C.F.L., CIHR MOP-86622 to S.G., and NIH GM57859 to R.J.D. We thank Yan Liu for help with statistics.


REFERENCES
1. Edgar BA,Orr-Weaver TL. Endoreplication cell cycles: more for lessCellYear: 200110529730611348589
2. Lilly MA,Duronio RJ. New insights into cell cycle control from the Drosophila endocycleOncogeneYear: 2005242765277515838513
3. Sugimoto-Shirasu K,Roberts K. "Big it up": endoreduplication and cell-size control in plantsCurr Opin Plant BiolYear: 2003654455314611952
4. Whitman WB,Coleman DC,Wiebe WJ. Prokaryotes: the unseen majorityProc Natl Acad Sci U S AYear: 199895657865839618454
5. Follette PJ,Duronio RJ,O'Farrell PH. Fluctuations in cyclin E levels are required for multiple rounds of endocycle S phase in DrosophilaCurrent BiologyYear: 199882352389501987
6. Weiss A,Herzig A,Jacobs H,Lehner CF. Continuous Cyclin E expression inhibits progression through endoreduplication cycles in DrosophilaCurrent BiologyYear: 199882392429501988
7. Shibutani ST,et al. Intrinsic negative cell cycle regulation provided by PIP box- and Cul4Cdt2-mediated destruction of E2f1 during S phaseDev CellYear: 20081589090019081076
8. Roodbarkelari F,et al. Cullin 4-ring finger-ligase plays a key role in the control of endoreplication cycles in Arabidopsis trichomesProc Natl Acad Sci U S A107152751528020696906
9. Diffley JF. Regulation of early events in chromosome replicationCurr BiolYear: 200414R778R78615380092
10. Zielke N,Querings S,Rottig C,Lehner C,Sprenger F. The anaphase-promoting complex/cyclosome (APC/C) is required for rereplication control in endoreplication cyclesGenes DevYear: 2008221690170318559483
11. Maqbool SB,et al. Dampened activity of E2F1-DP and Myb-MuvB transcription factors in Drosophila endocycling cellsJ Cell SciYear: 20101234095410621045111
12. Knoblich JA,et al. Cyclin E controls S-phase progression and its down-regulation during Drosophila embryogenesis is required for the arrest of cell proliferationCellYear: 1994771071208156587
13. Lilly MA,Spradling AC. The Drosophila endocycle is controlled by Cyclin E and lacks a checkpoint ensuring S-phase completionGenes & DevelopmentYear: 199610251425268843202
14. Narbonne-Reveau K,et al. APC/CFzr/Cdh1 promotes cell cycle progression during the Drosophila endocycleDevelopmentYear: 20081351451146118321983
15. Neufeld TP,de la Cruz AF,Johnston LA,Edgar BA. Coordination of growth and cell division in the Drosophila wingCellYear: 199893118311939657151
16. Sigrist SJ,Lehner CF. Drosophila fizzy-related down-regulates mitotic cyclins and is required for cell proliferation arrest and entry into endocyclesCellYear: 1997906716819288747
17. Shcherbata HR,Althauser C,Findley SD,Ruohola-Baker H. The mitotic-to-endocycle switch in Drosophila follicle cells is executed by Notch-dependent regulation of G1/S, G2/M and M/G1 cell-cycle transitionsDevelopmentYear: 20041313169318115175253
18. Hammond MP,Laird CD. Control of DNA replication and spatial distribution of defined DNA sequences in salivary gland cells of Drosophila melanogasterChromosomaYear: 1985912792863920018
19. Hong A,et al. The cyclin-dependent kinase inhibitor Dacapo promotes replication licensing during Drosophila endocyclesEmbo JYear: 2007262071208217380129
20. Duronio RJ,O'Farrell PH. Developmental control of the G1 to S transition in Drosophila: cyclin E is a limiting downstream target of E2FGenes and DevelopmentYear: 19959145614687601350
21. Royzman I,Whittaker AJ,Orr-Weaver TL. Mutations in Drosophila DP and E2F distinguish G1-S progression from an associated transcriptional programGenes and DevelopmentYear: 199711199920119271122
22. Duronio RJ,Bonnette PC,O'Farrell PH. Mutations of the Drosophila dDP, dE2F, and cyclin E genes reveal distinct roles for the E2F-DP transcription factor and cyclin E during the S-phase transitionMolecular and Cellular BiologyYear: 1998181411519418862
23. Asano M,Nevins JR,Wharton RP. Ectopic E2F expression induces S-phase and apoptosis in Drosophila imaginal discsGenes and DevelopmentYear: 199610142214328647438
24. Reis T,Edgar BA. Negative regulation of dE2F1 by cyclin-dependent kinases controls cell cycle timingCellYear: 200411725326415084262
25. Heriche JK,Ang D,Bier E,O'Farrell PH. Involvement of an SCFSlmb complex in timely elimination of E2F upon initiation of DNA replication in DrosophilaBMC GenetYear: 20034912787468
26. Weng L,Zhu C,Xu J,Du W. Critical role of active repression by E2F and Rb proteins in endoreplication during Drosophila developmentEmbo JYear: 2003223865387512881421
27. Frolov MV,et al. Functional antagonism between E2F family membersGenes & DevelopmentYear: 2001152146216011511545
28. Britton JS,Edgar BA. Environmental control of the cell cycle in Drosophila: nutrition activates mitotic and endoreplicative cells by distinct mechanismsDevelopmentYear: 1998125214921589570778
29. Britton JS,Lockwood WK,Li L,Cohen SM,Edgar BA. Drosophila's insulin/PI3-kinase pathway coordinates cellular metabolism with nutritional conditionsDev CellYear: 2002223924911832249
30. Moberg KH,Mukherjee A,Veraksa A,Artavanis-Tsakonas S,Hariharan IK. The Drosophila F box protein archipelago regulates dMyc protein levels in vivoCurr BiolYear: 20041496597415182669
31. Lane ME,et al. Dacapo, a cyclin-dependent kinase inhibitor, stops cell proliferation during Drosophila developmentCellYear: 199687122512358980229
32. Lane ME,et al. A screen for modifiers of cyclin E function in Drosophila melanogaster identifies Cdk2 mutations, revealing the insignificance of putative phosphorylation sites in Cdk2GeneticsYear: 200015523324410790398
33. Frolov MV,Moon NS,Dyson NJ. dDP is needed for normal cell proliferationMol Cell BiolYear: 2005253027303915798191
34. Duronio RJ,O'Farrell PH,Xie J-E,Brook A,Dyson N. The transcription factor E2F is required for S phase during Drosophila embryogenesisGenes and DevelopmentYear: 19959144514557601349
35. Quinn LM,Herr A,McGarry TJ,Richardson H. The Drosophila Geminin homolog: roles for Geminin in limiting DNA replication, in anaphase and in neurogenesisGenes DevYear: 2001152741275411641279
36. Speicher SA,Thomas U,Hinz U,Knust E. The Serrate locus of Drosophila and its role in morphogenesis of the wing imaginal discs: control of cell proliferationDevelopmentYear: 19941205355448162853
37. Xin S,Weng L,Xu J,Du W. The role of RBF in developmentally regulated cell proliferation in the eye disc and in Cyclin D/Cdk4 induced cellular growthDevelopmentYear: 20021291345135611880344
38. Saucedo LJ,et al. Rheb promotes cell growth as a component of the insulin/TOR signalling networkNat Cell BiolYear: 2003556657112766776
39. Grosskortenhaus R,Sprenger F. Rca1 inhibits APC-Cdh1(Fzr) and is required to prevent cyclin degradation in G2Dev CellYear: 20022294011782312
40. Richardson HE,O'Keefe LV,Reed SI,Saint R. A Drosophila G1-specific cyclin E homolog exhibits different modes of expression during embryogenesisDevelopmentYear: 19931196736908187637
41. Duronio RJ,O'Farrell P. Developmental control of a G1-S transcriptional program in DrosophilaDevelopmentYear: 1994120150315158050359
42. Dynlacht BD,Brook A,Dembski M,Yenush L,Dyson N. DNA-binding and trans-activation properties of Drosophila E2F and DP proteinsProceedings of the National Academy of Sciences USAYear: 19949163596363
43. Kosman D,et al. Multiplex detection of RNA expression in Drosophila embryosScienceYear: 200430584615297669
44. Tautz D,Pfeifle C. A non-radioactive in situ hybridization method for the localization of specific RNAs in Drosophila embryos reveals translational control of the segmentation gene hunchbackChromosomaYear: 19899881852476281
45. Van Gilst MR,Hadjivassiliou H,Yamamoto KR. A Caenorhabditis elegans nutrient response system partially dependent on nuclear receptor NHR-49Proc Natl Acad Sci U S AYear: 2005102134961350116157872

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