Elliot, T. A. | bioRxiv Science

bioRxiv2026

Biological implications of a detailed repeat annotation in Octopus vulgaris

Octopuses are phenotypically distinctive organisms, and recent genomic work raises questions about the contributions of transposable elements (TE) to their genomic architecture. We leveraged a robust repeat annotation pipeline, in combination with manual and automated curatorial techniques, to produce a more comprehensive repeat annotation of Octopus vulgaris. This revealed that [~]66% of the genome are repeats, in contrast to previous estimates of 43-50%. Whereas previous studies of TE expansion in Octopus bimaculoides identified two bursts of activity, 25 and 56 MYA, our re-annotation revealed four such expansions at 18, 25, 33, and 56 MYA. We further identified a landscape of TE hot- and cold spots. This much refined TE timescape and landscape will serve as a useful basis for understanding TE contributions to O. vulgaris evolution, and also for identifying factors contributing to variation in the TE community across genomic space and evolutionary time.

genomics↗

bioRxiv2024

Lag3 and PD-L1 govern T cell receptor signal duration in adaptively tolerised CD4+ T cells

Lag3 and PD-1 are immune checkpoints that regulate T cell responses and are current immunotherapy targets. Yet how they function to control early CD4+ T cell activation remains unclear. Here, we show that the PD-1 and Lag3 pathways exhibit layered control of the early CD4+ T cell activation process, with the effects of Lag3 more pronounced in the presence of PD-1 pathway co-blockade (CB). RNA-sequencing revealed that CB drove an early NFAT-dependent transcriptional profile, including promotion of ICOShi T follicular helper (Tfh) cell differentiation. NFAT pathway inhibition abolished CB-induced upregulation of NFAT-dependent co-receptors ICOS and OX40, whilst unaffecting the NFAT-independent gene Nr4a1. Mechanistically, Lag3 and PD-1 pathways functioned additively to regulate the duration of T cell receptor (TCR) signals during CD4+ T cell re-activation. Our data therefore reveal that PD-1 and Lag3 pathways converge to additively regulate TCR signal duration and NFAT-dependent transcriptional activity during early CD4+ T cell re-activation. HighlightsO_LIPD-1 and Lag3 pathways exhibit layered control of early CD4+ T cell activation C_LIO_LITheir co-blockade enhances NFAT-dependent TCR transcriptional programmes C_LIO_LIInhibition of NFAT signalling reverses the functional effects of PD-1 and Lag3 co-blockade C_LIO_LIMechanistically, PD-1 and Lag3 function to additively regulate TCR signal duration during re-activation of CD4+ T cells C_LI

immunology↗