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ScienceDevelopmental BiologyPeer-reviewed journal article

Species-specific oscillation periods of human and mouse segmentation clocks are due to cell autonomous differences in biochemical reaction parameters

Mitsuhiro MatsudaiD, Hanako Hayashi, Jordi García‐OjalvoiD, Kumiko Yoshioka-Kobayashi, Ryoichiro KageyamaiD, Yoshihiro Yamanaka, Makoto IkeyaiD, Junya ToguchidaiD, Cantas AleviD, Miki EbisuyaiD

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Abstract

While the mechanisms of embryonic development are similar between mouse and human, the tempo is in general slower in human. The cause of interspecies differences in developmental time remains a mystery partly due to lack of an appropriate model system1. Since murine and human embryos differ in their sizes, geometries, and nutrients, we use in vitro differentiation of pluripotent stem cells (PSCs) to compare the same type of cells between the species in similar culture conditions. As an example of well-defined developmental time, we focus on the segmentation clock, oscillatory gene expression that regulates the timing of sequential formation of body segments2-4. In this way we recapitulate the murine and human segmentation clocks in vitro, showing that the species-specific oscillation periods are derived from cell autonomous differences in the speeds of biochemical reactions. Presomitic mesoderm (PSM)-like cells induced from murine and human PSCs displayed the oscillatory expression of HES7, the core gene of the segmentation clock5,6, with oscillation periods of 2-3 hours (mouse PSM) and 5-6 hours (human PSM). Swapping HES7 loci between murine and human genomes did not change the oscillation periods dramatically, denying the possibility that interspecies differences in the sequences of HES7 loci might be the cause of the observed period difference. Instead, we found that the biochemical reactions that determine the oscillation period, such as the degradation of HES7 and delays in its expression, are slower in human PSM compared with those in mouse PSM. With the measured biochemical parameters, our mathematical model successfully accounted for the 2-3-fold period difference between mouse and human. We further demonstrate that the concept of slower biochemical reactions in human cells is generalizable to several other genes, as well as to another cell type. These results collectively indicate that differences in the speeds of biochemical reactions between murine and human cells give rise to the interspecies period difference of the segmentation clock and may contribute to other interspecies differences in developmental time.

In-depth summary

Claude Sonnet 4.6 · xhigh effort · 8 Nov 2026 · from the full text of version 1 (26 May 2019) · CC BY 4.0

Mouse and human segmentation clocks oscillate at 2-3 h and 5-6 h; slower HES7 degradation and longer delays in human cells, not sequence, explain it.

The cause of species differences in developmental tempo is unclear, partly because embryos differ in size, geometry and nutrients. Comparing stem-cell-derived presomitic mesoderm under similar culture conditions isolates cell autonomous causes of the segmentation clock period.

Key results

  1. ShownStem-cell-derived presomitic mesoderm (PSM) recapitulates the species-specific HES7 oscillation period, and the roughly 2-3-fold difference persists in isolated single cells and without NOTCH signaling, so it is cell autonomous.

    Mouse PSM 122 ± 2 min vs human PSM 322 ± 6 min (mean ± sd); sparse cells mouse 160 ± 9 min vs human 376 ± 51 min; DAPT (10 μM) did not significantly change the period in either species. · Main; Figure legends

  2. ShownReplacing the mouse HES7 locus with the human one barely lengthened the mouse period. Knock-out and rescue with mouse or human HES7 constructs gave mouse-like periods in mouse PSM and indistinguishable periods in human PSM, so HES7 sequence does not set the period.

    Homo swap 146 ± 7 min and hetero swap 133 ± 4 min vs wild-type mouse 124 ± 3 min (human PSM 322 min); ex vivo homo swap embryos had ~30 min longer periods than wild type. · Main; Figure legends

  3. ShownHES7 protein and mRNA are degraded more slowly, and transcription/translation and intron delays are longer, in human PSM than in mouse PSM. The repression delay was negligible in both species.

    Protein half-life 21 ± 0.8 min (mouse) vs 40 ± 4 min (human); τTxTl 17 ± 2 vs 30 ± 1 min; mRNA half-life 10 ± 0.3 vs 16 ± 0.3 min; intron delay 13 ± 3 vs 37 ± 3 min. · Main; Figure legends

  4. SuggestedA delay differential equation model driven only by the measured degradation rates and delays reproduces the mouse versus human period gap, and the period is robust to the unmeasured Hill coefficient.

    Simulated periods of ~150 min with murine parameters vs ~300 min with human parameters (Hill coefficient n = 3), compared with the measured 2-3-fold difference; varying the Hill coefficient did not change the period dramatically. · Main; 1. HES7 oscillation model; Figure legends

  5. SuggestedSlower reactions in human cells extend to some other PSM genes and to neural progenitor cells (NPCs), but not to every gene tested.

    Slower protein degradation in human PSM for GBX2, MSGN1, TBX6 but not CDX2, EVX1, Brachyury T; longer delays for TBX6, GBX2, MSGN1 but not EVX1; slower degradation in human NPCs for OTX2, FOXG1, PAX6, SOX1. · Main; Figure legends

Methods, data and reproducibility

Mouse ESCs and human iPSCs were differentiated to PSM and NPCs. HES7 oscillations were tracked with luciferase reporters, and degradation rates and delays were measured with luciferase assays. Fitted parameters fed a delay differential equation model.

  • Mouse ESC (EB5, TT2) and human iPSC (201B7) derived PSM, with HES7 reporter oscillations, locus swaps and knock-out/rescue lines · mouse; human · n = three independent experiments per condition
  • Single-cell HES7 reporter oscillations in sparsely seeded PSM cells · mouse; human · n = eight single cells per species
  • Knock-in mice carrying the human HES7 locus; ex vivo tail bud cultures of E10.5 embryos and micro-CT of 4-week-old mice · mouse · n = two hetero swap ESC clones used for chimeras; embryo count not stated
  • Degradation and expression delay assays for HES7, six other PSM genes and four NPC genes · mouse; human · n = three independent experiments for HES7 assays; not stated for other genes
Methods & tools
HES7 promoter-luciferase reporter, NanoLuc and firefly luciferase assays, Kronos Dio luminometer, CRISPR/Cas9 genome editing, piggyBac transposon vectors, MATLAB dde23, SciPy basin-hopping, R least squares and cross correlation, Two-sided Student's t-test and Dunnett's test
Reagents & environment
MATLAB dde23 (Mathworks) for simulation; Python with SciPy basin-hopping and R for fitting; versions not stated.
Reproducibility gaps
No code or data repository URLs given; model parameter values and constructs are in supplementary tables.
Limitations (5)
  • The authors state that more systematic measurements are needed to establish whether slower biochemical reactions apply across cell types, since only a few genes in PSM and NPCs were tested. · stated by the authors
  • Slower reactions in human cells were not universal: CDX2, EVX1 and Brachyury T degradation, and EVX1 delays, showed no significant species difference. · stated by the authors
  • The molecular mechanism making human cells slower is unresolved; the authors only propose species-specific cellular environments. · stated by the authors
  • The repression Hill coefficient was not measured and can affect the period, so the model varied it only within a realistic range. · stated by the authors
  • Species comparison rests on one mouse ESC line family and one human iPSC line with three experiments per condition, so line-to-line variability and the in vivo human clock are untested. · noted in this summary

Read this if you study developmental tempo, oscillatory gene networks, or want a quantitative stem-cell framework for interspecies timing differences.

Citations
254
FWCI
11.91
Field percentile
top 1%

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