Collagen production is fundamental for the ontogeny and the phylogeny of all multicellular organisms. It depends on hydroxylation of proline residues, a reaction that uses molecular oxygen as a substrate. This dependency is expected to limit collagen production to oxygenated cells. However, during embryogenesis, cells in different tissues that develop under low oxygen levels must produce this essential protein. In this study, using the growth plate of developing bones as a model system, we identify the transcription factor hypoxia-inducible factor 1 α (HIF1α) as a central component in a mechanism that underlies collagen hydroxylation and secretion by hypoxic cells. We show that Hif1a loss of function in growth plate chondrocytes arrests the secretion of extracellular matrix proteins, including collagen type II. Reduced collagen hydroxylation and endoplasmic reticulum stress induction in Hif1a-depleted cells suggests that HIF1α regulates collagen secretion by mediating its hydroxylation and consequently its folding. We demonstrate in vivo the ability of Hif1α to drive the transcription of collagen prolyl 4-hydroxylase, which catalyzes collagen hydroxylation. We also show that, concurrently, HIF1α maintains cellular levels of oxygen, most likely by controlling the expression of pyruvate dehydrogenase kinase 1, an inhibitor of the tricarboxylic acid cycle. Through this two-armed mechanism, HIF1α acts as a central regulator of collagen production that allows chondrocytes to maintain their function as professional secretory cells in the hypoxic growth plate. As hypoxic conditions occur also during pathological conditions such as cancer, our findings may promote the understanding not only of embryogenesis, but also of pathological processes.

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During development, genes are transcribed at specific times, locations and levels. In recent years, the emergence of quantitative tools has significantly advanced our ability to measure transcription with high spatiotemporal resolution in vivo. Here, we highlight recent studies that have used these tools to characterize transcription during development, and discuss the mechanisms that contribute to the precision and accuracy of the timing, location and level of transcription. We attempt to disentangle the discrepancies in how physicists and biologists use the term ‘precision' to facilitate interactions using a common language. We also highlight selected examples in which the coupling of mathematical modeling with experimental approaches has provided important mechanistic insights, and call for a more expansive use of mathematical modeling to exploit the wealth of quantitative data and advance our understanding of animal transcription.

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Pyruvate dehydrogenase kinase family of enzymes (PDK1-4) are central negative regulators of the TCA cycle by phosphorylating the rate-limiting multi-enzyme pyruvate dehydrogenase complex (PDC). Here, we show that the PDK family is dispensable for murine embryonic development and that BCKDK serves as a compensatory mechanism for PDKs by inactivating PDC.To study the role of Pdk family in vivo, we knocked out all four genes one by one.Surprisingly, Pdk total KO mouse embryos developed and were born in the expected ratio.Postnatally, these mice died by day four due to hypoglycemia or ketoacidosis, as confirmed by deep metabolic profiling.Looking for the mechanism that enables development in the absence of Pdk's, we found that PDC site 2 (S300) was phosphorylated in these embryos, suggesting that another kinase compensates for the PDK family. Bioinformatic analysis predicted brunch chain ketoacid dehydrogenase kinase (Bckdk), a key regulator in the catabolism of branched chain amino acids (BCAA), as a candidate. Knockout of both Bckdk and the entire Pdk family led to loss of PDC phosphorylation on S300 and early embryonic lethality which firmly establish the role of BCKDK in the regulation of PDC. Altogether, this work demonstrates a redundancy for the PDK family during development and identifies BCKDK regulation of PDC as a backup mechanism that allows embryonic development. More broadly, BCKDK regulation of PDC reveals a new regulatory crosstalk hardwiring BCAA and glucose catabolic pathways, which feed the TCA cycle.