Bovine in vitro blastocysts with distinct morphokinetic patterns show transcriptomic differences at genome activation

Reis, A.; Belghiti, M.; Laffont, L.; Ruffini, S.; Archilla, C.; brusq, N.; Teste, A.; Marquant-Leguienne, B.; Canon, E.; Jouneau, L.; Jaszczyszyn, Y.; Ponter, A.; Cacciarella, M.; Unrug, J.; Stamler, E.; Duranthon, V.; Trubuil, A.

doi:10.64898/2026.06.28.733532

bioRxiv · 10.64898/2026.06.28.733532

Bovine in vitro blastocysts with distinct morphokinetic patterns show transcriptomic differences at genome activation

Reis, A.·Belghiti, M.·Laffont, L.·Ruffini, S.·Archilla, C.·brusq, N.·Teste, A.·Marquant-Leguienne, B.·Canon, E.·Jouneau, L.·Jaszczyszyn, Y.·Ponter, A.·Cacciarella, M.·Unrug, J.·Stamler, E.·Duranthon, V.·Trubuil, A.

View original source ↗Export metadata ↓

Abstract

Bovine embryo in vitro production (IVP) is characterised by low efficiency and variable outcomes. Monitoring early embryonic development by videomicroscopy revealed substantial morphokinetic heterogeneity in the first four embryonic cycles (EC, conventionally referred to as the 2-, 4-, 8- and 16-cell stages). Morphokinetic analysis offers a promising approach to characterize divergent developmental trajectories and provide a better understanding of underlying molecular mechanisms. We developed a Random Forest classification system (Bovine Embryo Analyser based on Morphokinetics: BEAM) to predict embryo phenotype. It is based on morphokinetic variables collected from the 1st to the 4th EC and predicts four blastocyst categories (EHB: Early Hatching Blastocyst, HB: Hatching Blastocyst, SSB: Subtle Developmental Shift Blastocyst, ADB: Arrhythmic Development Blastocyst). Classification performance on an independent dataset was good (F1 score = 0.59; Accuracy = 0.78), indicating that the BEAM can be useful for embryo development studies. The BEAM was further applied to embryos submitted to 4.3 days of culture and having completed the 4th EC (16-32 cells). RNA sequencing was performed on sixteen samples (4 x 8 pooled embryos/category). The ADB category was significantly enriched in transcripts involved in the regulation of transcriptional activity compared to the EHB category. In addition, in the ADB category, 22.7% (n = 185/816) of the upregulated genes were of maternal origin while only 6.2% were of embryonic origin (n = 54/816). In conclusion, despite being at a comparable developmental stage and transcriptionally competent, the ADB category showed delayed maternal transcript degradation suggesting delayed transition to embryonic transcriptional autonomy. Illustrated Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/733532v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@13a0958org.highwire.dtl.DTLVardef@13b88a1org.highwire.dtl.DTLVardef@18707c9org.highwire.dtl.DTLVardef@105759_HPS_FORMAT_FIGEXP M_FIG C_FIG Summary SentenceIn vitro produced bovine embryo morphokinetic patterns allow prediction of four blastocyst categories (up to the 4th embryonic cycle) and are associated with distinct transcriptomic profiles at embryonic genome activation in competent embryos.

Explore related subjects

Developmental Biology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Reis, A., Belghiti, M., Laffont, L., Ruffini, S., Archilla, C., brusq, N., Teste, A., Marquant-Leguienne, B., Canon, E., Jouneau, L., Jaszczyszyn, Y., Ponter, A., Cacciarella, M., Unrug, J., Stamler, E., Duranthon, V., Trubuil, A.. 2026-06-29. Bovine in vitro blastocysts with distinct morphokinetic patterns show transcriptomic differences at genome activation. https://doi.org/10.64898/2026.06.28.733532

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Neural tracking of stressed syllables in Dutch nursery rhymes relates to vocabulary outcomes in a large, longitudinal sample

Speech consists of regularities at different timescales. Already during infancy, neural electrophysiological activity aligns to these rhythms. The degree to which infants exhibit neural tracking of speech can be linked to their language development. In this study, we examined how the neural tracking of sung speech develops across age, from infancy to early childhood, and across different frequency bands (i.e., at the stress, syllabic, and phonemic rates), and whether neural tracking at each frequency and age predicts childrens language outcomes. We included 2565 children of the longitudinal YOUth cohort. Children listened to Dutch sung nursery rhymes while EEG was recorded at three measurement waves. After preprocessing the data, we included 955 children at 5 months, 1048 children at 10 months, and 795 children at 2-4 years. The final sample consisted of 750 children who also completed a receptive vocabulary test at 2-4 years. Children from 5 months onwards showed significant neural tracking of stressed syllables, syllables, and phonemes, measured with speech-brain coherence (SBC). Unexpectedly, there were no developmental changes in SBC across different frequency bands from infancy to early childhood. As expected, children with larger receptive vocabularies showed increased SBC in the stressed syllable rate. These findings suggest that stronger tracking of stressed syllables is related to individual differences in language ability.

Developmental Biology↗

bioRxiv2026

FGF Signaling Potentiates Müller Glia for Mammalian Retinal Regeneration

Muller glia possess latent regenerative potential that could be harnessed to restore retinal neurons lost to injury or disease. Although fibroblast growth factor (FGF) signaling is upregulated following retinal damage, its role in mammalian retinal regeneration remains unclear. Here, we investigated the function of FGF signaling in Muller glial reprogramming using genetic, pharmacological, and single-cell transcriptomic approaches. Activation of FGF signaling alone was insufficient to induce Muller glial proliferation in the mouse retina. However, conditional deletion of FGFR1/2 in Muller glia abolished regenerative responses induced by multiple independent pathways, demonstrating that FGF signaling is essential for regenerative competence. Mechanistically, loss of FGF signaling impaired sustained ERK/MAPK activation following injury, while MEK/ERK inhibition phenocopied the regenerative defect. Conversely, constitutive MEK activation induced limited Muller glial proliferation in the absence of injury. Although STAT3/5 inhibition synergized with Activin-A to promote robust proliferation and neurogenic gene expression, it failed to rescue regeneration in FGF-deficient Muller glia. Single-cell RNA sequencing revealed that FGF signaling suppresses multiple anti-regenerative programs, including Hes1, S1pr1, p27, NF-{kappa}B, and p300/CBP activity. Together, these findings identify FGF signaling as a critical permissive regulator of mammalian retinal regeneration that potentiates Muller glia through sustained ERK activation and suppression of transcriptional barriers to regeneration.

Developmental Biology↗

bioRxiv2026

Doublesex- mediated regulation of insulin signaling drives sex-specific body growth

Most animals develop sex-biased body sizes driven by sexually divergent plasticity in nutrient-dependent growth. Prior work in Drosophila, implicated the sex-determination gene transformer (tra) in regulation of sex differences in body size. However, tra does not widely mediate sex determination across insects. Thus, the unifying molecular pathway governing female-biased sexual size dimorphism (SSD) remains poorly established in non-drosophilid insects. The rice stem borer Chilo suppressalis, a devastating lepidopteran crop pest, exhibits a robust SSD, offering an ideal system to dissect underlying mechanisms. We report that female-specific splice forms of the sex-determining gene doublesex (Csdsx) are master regulators of female-biased growth. Disruption of the female-specific Csdsx exon 3 via CRISPR knockout or RNA interference drastically reduces female body size and completely erases the SSD. Csilp2, encoding a key insulin-like peptide (ILP2), is selectively upregulated in late-instar female larvae, and female CsDsx proteins directly bind and activate the Csilp2 promoter to boost transcription. Loss-of-function of Csilp2 eliminates the SSD by suppressing female somatic overgrowth. Our results identify a novel regulatory cascade: female-specific Dsx directly stimulates insulin signaling via Csilp2, bridging core sex-determination circuitry and nutrient-dependent body growth control. SignificanceSexual size dimorphism (SSD), widespread across insects with larger females, strongly shapes reproductive fitness. Yet reports on the molecular connection between sex determination and dimorphic growth are scarce. Using a major agricultural pest, the rice stem borer with a prominent female-biased SSD, we show that female-specific Doublesex (dsx) splice variants directly activate the promoter of Insulin-like peptide 2 in late larvae to trigger increased growth. Knocking out either gene in females abolishes the SSD. Our findings thus establish dsx as a novel link connecting sex-determination, insulin signaling and nutrient-dependent body growth.

Developmental Biology↗