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The gastrula transition reorganizes replication-origin selection in Caenorhabditis elegans

Nature Structural & Molecular Biology volume 24, pages 290–299 (2017)Cite this article

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Abstract

Although some features underlying replication-origin activation in metazoan cells have been determined, little is known about their regulation during metazoan development. Using the nascent-strand purification method, here we identified replication origins throughout Caenorhabditis elegans embryonic development and found that the origin repertoire is thoroughly reorganized after gastrulation onset. During the pluripotent embryonic stages (pregastrula), potential cruciform structures and open chromatin are determining factors that establish replication origins. The observed enrichment of replication origins in transcription factor–binding sites and their presence in promoters of highly transcribed genes, particularly operons, suggest that transcriptional activity contributes to replication initiation before gastrulation. After the gastrula transition, when embryonic differentiation programs are set, new origins are selected at enhancers, close to CpG-island-like sequences, and at noncoding genes. Our findings suggest that origin selection coordinates replication initiation with transcriptional programs during metazoan development.

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Figure 1: Identification of replication origins in C. elegans embryos.
Figure 2: Association of replication origins with IRs and operons.
Figure 3: Association of replication origins with chromatin marks and transcription features.
Figure 4: Association of replication origins with noncoding genes and enhancers.
Figure 5: Enhancer marks in postgastrula-specific origins.
Figure 6: Association of replication origins with CGIs.

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Acknowledgements

This work was supported by the European Research Council (FP7/2007-2013, grant agreement no. 233339), by the Fondation pour la Recherche Médicale (FRM) and the European Commission Network of Excellence EpiGeneSys (HEALTH-F4-2010-257082 to M.M.). M.R.-M. was supported by the Fondation ARC. We thank S. Galas (CRBM, Montpellier) for advice regarding C. elegans development and for providing the strain used in this study, as well as J. Bacal for help with the 2D gel technique, D. van Essen for support in bioinformatics, and E. Andermarcher and J. Hutchins for critical reading of the manuscript.

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Author notes

  1. Emmanuelle Beyne & Christelle Cayrou

    Present address: Present addresses: Laboratory Genetics of Rare Diseases, INSERM U827, Montpellier, France (E.B.) and Institute for Research on Cancer and Aging, Nice (IRCAN), CNRS UMR 7284, Nice, France (C.C.).,

Authors and Affiliations

  1. Institute of Human Genetics, CNRS, Montpellier, France

    Marta Rodríguez-Martínez, Natalia Pinzón, Emmanuelle Beyne, Hervé Seitz, Christelle Cayrou & Marcel Méchali

  2. Agropolymer Engineering and Emerging Technologies, University of Montpellier, Montpellier, France

    Charles Ghommidh

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Contributions

M.M. proposed the project and supervised its execution. C.C. supervised the project and its experimental design. C.G. and M.R.-M. designed the bioreactor conditions for C. elegans synchronous growth. M.R.-M. and C.C. performed the large-scale embryo preparation. M.R.-M. performed nascent-strand purification from the embryos, embryo imaging, fluorescence-activated cell-sorting analysis, and bubble-trap and 2D gel experiments. E.B., N.P., H.S., C.C. and M.R.-M. performed the computational analyses. M.R.-M., C.C. and M.M. prepared the manuscript.

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Correspondence to Hervé Seitz, Christelle Cayrou or Marcel Méchali.

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Integrated supplementary information

Supplementary Figure 1 Flow cytometry analysis of the mixed and pregastrula embryo populations.

(a) Nascent strand (NS) isolation schematic. 0.3-2 kb NS were isolated from total genomic DNA by denaturation and sucrose gradient centrifugation. NS enriched by lambda-exonuclease digestion were hybridized against total genomic DNA on high-density tiling arrays (see Methods for details). (b) Left panels show the scatter distribution (forward vs. side) of the analyzed events (upper panel, mixed C. elegans embryos; lower panel, pre-gastrula embryos). Middle panels show the cell cycle distribution of the events of the lefts panels. For the mixed embryo population, two windows are shown, large (1) and small (2) cell size, to confirm that both populations contain cells in S-phase. The pre-gastrula embryo middle panels represent the whole scatter distribution. PI, propidium iodide. The right panels show representative images of each embryo population analyzed by cell sorting. Embryos were labeled with EdU (green) and stained with DAPI (blue) (merged images on the right panels).

Supplementary Figure 2 Replicates and validation of C. elegans replication origins.

(a) Correlation of the nascent strand microarray data in two of the three replicates for the pre-gastrula and mixed embryo populations. (b) Heatmap representing a significant set of probes of the three replicates (R1-R3) of nascent strand microarray data for pre-gastrula (left) and mixed embryo (right) origins. Colors indicate the intensity of the microarray probe, from low (green) to red (high). (c) Alignment of three independent nascent strand microarray experiments (R1-R3) along C. elegans chromosome 1. The bottom panels show representative profiles of origins in the chromosome arms and center. The background signal from the L1-arrested larval sample was subtracted from each replicate (-L1). (d) Quantitative PCR validation of C. elegans replication origins detected by microarray analysis of the NS purification (n=3), together with the corresponding controls. The graph shows the microarray normalized log2-ratio data (samples compared with genomic DNA) as well as the position of inverted repeats.

Source data

Supplementary Figure 3 Association of inverted repeats and operons with C. elegans replication origins.

(a) Boxplots showing the percentage of association of inverted repeats (IRs) with pre-gastrula and post-gastrula-specific origins (top graphs) and the reverse correlation (bottom panels), compared with random expectation, in chromosome arms and center (left and right panels respectively). *, P<10-15 (according to the distribution function of the normal distribution); n.s., non-significant difference with random. (b) Boxplots showing the number of pre-gastrula (green) and post-gastrula-specific (orange) origin summits in operons, compared with random data. *, P<10-20 (according to the distribution function of the normal distribution). Data are shown as mean ± s.d. (c) Distribution (%) of pre-gastrula (green) and post-gastrula-specific (orange) replication origins around operon transcription start sites (TSS) (mean percentage ± standard error) in chromosome arms and center.

Source data

Supplementary Figure 4 C. elegans pregastrula origins are localized in open chromatin in transcriptional active regions.

(a) Distribution of the ChIP-Chip signals for the HTZ-1 histone variant and RNA pol II around ±2 kb from pre-gastrula replication origin summits (solid green line) or the centers of random regions (gray line; mean ± 2x s.d. for HTZ-1 and mean ± s.d. for RNA pol II) in chromosome arms (top panels) and centers (lower panels). Only autosomal chromosome were taken in account for HTZ-1 histone variant (b) Numbers of gap regions (left panels) or LEM-2 subdomains (right panels) inside chromosome arms that are overlapped by pre-gastrula origins versus random regions (number ± s.d.). The reverse correlations are also shown (bottom panels). *, P<0.05 (two-sided t-tests); n.s., non-significant differences with random expectation. (c) Mean distributions of pre-gastrula (green) and post-gastrula-specific (orange) origins in each chromosome (origin density/200 kb). Dashed black lines indicate the mean level of gene transcript (dcpm) at each chromosome. (d) Percentage of HOT regions associated with pre- (green) and post-gastrula-specific (orange) replication origins in chromosome arms and centers. * indicates P<10-15 (Chi-squared test); n.s., non-significant difference with random (mean ± s.d.). (e) Replication origin efficiency (total coverage of probes intensity; mean ± s.d.) relative to some genomic features. *, P<10-8; **, P<10-12 (two-sided t-tests) compared with the efficiency in all replication origins.

Source data

Supplementary Figure 5 Distribution of C. elegans origins relative to genes and promoters.

(a) Percentage of pre-gastrula (green) and post-gastrula-specific (orange) replication origins around non-coding TSSs (±3000 bp) in the chromosome arms (left panel) or centers (right panel). Mean random profiles are represented by a full line (± standard error in dashed lines) in a lighter color than the one used for the real data. (b) Box plots showing the percentage of pre-gastrula (green) and post-gastrula-specific (orange) origin summits found in all non-coding gene promoters (total promoters) as well as in non-coding gene promoters in chromosome centers, left and right arms. *, P<10-20 (according to the distribution function of the normal distribution); n.s., non-significant difference with random expectation (mean ± s.d.). (c) ChIP signals for histone H3K4me3 and RNA pol II around ±2 kb from the TSS of non-coding genes overlapped (left panel) or not (right panel) by post-gastrula-specific origins. The y-axis represents the average ChIP signal per 100 bp.

Source data

Supplementary Figure 6 Sequence motifs associated with replication origins.

Scanning for the occurrence of GCTAAAA (a), [AC][GC]GC[CG]C (b) and CG[AC][GC]GCGC (c) motifs in 1-kb regions on both sides of origin summits. The x-axis indicates the position relative to the origin summit, the y-axis the percentage of pre-gastrula origins (green line), post-gastrula-specific origins (orange line) or 100 randoms (gray lines) with at least one occurrence per 100-bp window. Both Watson (sense) and Crick (antisense) chromosomal strands were considered. (d) Box plots showing the total percentage of pre-gastrula (green) and post-gastrula-specific (orange) origin summits overlapping with CGI-like sequences (for origins and random data) (mean ± s.d.) and in (e) chromosome arms and center, separately. *, P<10-8 (according to the distribution function of the normal distribution). (f) Results of bubble trap and 2D gel electrophoresis analysis for a region containing a post-gastrula-specific origin with a CGI-like (positive region; brown box; left panels) and a region without origin and CGI-like (negative region; right panel, same negative region already shown in Figure 2C). The raw data of these regions are on top (combination of three NS microarray replicates), the qPCR validation in the middle, and the 2D gels at the bottom. The black box indicates the position of the probe used for hybridization and the thin pink lines, the Cla1 sites. The results at the bottom are shown for both regions, comparing a mixed embryo sample and a negative control (L1-arrested larval sample). The arrow indicates the position of the signal representing the replication origin.

Source data

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6 and Supplementary Tables 1 and 2 (PDF 1957 kb)

Supplementary Table 3

Significant motifs found in pre- and post-gastrula specific replication origins. Significant n-mers found in post-gastrula specific replication origins. TFs specific n-mer corresponding to the pre-gastrula origin motifs. (XLSX 17 kb)

Supplementary Data Set 1

Uncropped 2D gel (PDF 9837 kb)

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Rodríguez-Martínez, M., Pinzón, N., Ghommidh, C. et al. The gastrula transition reorganizes replication-origin selection in Caenorhabditis elegans. Nat Struct Mol Biol 24, 290–299 (2017). https://doi.org/10.1038/nsmb.3363

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