Histone lactylation couples cellular metabolism with developmental gene regulatory networks

Embryonic cells exhibit diverse metabolic states. Recent studies have demonstrated that metabolic reprogramming drives changes in cell identity by affecting gene expression. However, the connection between cellular metabolism and gene expression remains poorly understood. Here we report that glycolysis-regulated histone lactylation couples the metabolic state of embryonic cells with chromatin organization and gene regulatory network (GRN) activation. We found that lactylation marks genomic regions of glycolytic embryonic tissues, like the neural crest (NC) and pre-somitic mesoderm. Histone lactylation occurs in the loci of NC genes as these cells upregulate glycolysis. This process promotes the accessibility of active enhancers and the deployment of the NC GRN. Reducing the deposition of the mark by targeting LDHA/B leads to the downregulation of NC genes and the impairment of cell migration. The deposition of lactyl-CoA on histones at NC enhancers is supported by a mechanism that involves transcription factors SOX9 and YAP/TEAD. These findings define an epigenetic mechanism that integrates cellular metabolism with the GRNs that orchestrate embryonic development.


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All studies must disclose on these points even when the disclosure is negative.In experiments that did not involve a paired design such as SOX9 loss-of-function (Figure 3D) and SOX9/TEA1-VPR over-expression (Figure 3I), healthy wild-type embryos were randomly assigned to control or treatment groups.
Blinding was not possible or relevant in our study.GT-Blue Control and FITC-LDHA/B morpholino transfected embryos were subjected to screening for transfection efficiency, thereby reavealing control and treated sides.For flow cytometric measurement of lactylation levels, FITC control and FITC-LDHA/B MO had to be injected on the same respective side in all embryos in order to ensure proper collection of control or treated half embryonic heads for subsequent analysis.Lastly, lactate treated explants were phenotypic upon collection.
All genomics experiments were replicated at least twice (two biological replicates).Replication information for other experimetns can be found in the methods section pertaining to a specific experiment.Due to the design of our study the replicates for all experiments are bioligical relicates.
For the multiple regression analysis with SOX9, YAP1, and PanKla, only PanKla peaks with CPM>0 in each sample/replicate (for all factors) were chosen for analysis.Therefore, 10,448 (out of 10,912) peaks were considered.Rationale for this is provided in the methods section.For the flow cytomtery analysis in Figure 1F, 9 cells (with negative values) were excluded from the HH9 dataset on the basis of being outliers and the square root transformation was performed.Excluded cells made up 0.58% of total cells.
Lactylation antiobodies have been validated by the manufacturer (PTM Biolabs).Furthermore, we have performed pan lactylation levels using flow cytometry upon LDHA/B knock-down and observed a decrease in the population of cells that have high lactylation levels.We have also observed dynamic regulation of lactylation levels at differetn stages of NCC development that are consistent with the metabolic transitions udergone by these cells (see Figure 1F and Supplemental Figure 1).AP2B antibody was validated by Rothstein and Simoes-Costa (Genome Research, 2019).Caspase3, pH3, and SOX9 antibodies exhibit expected staining patterns.
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Sample sizes were not pre-determined and are similar to those reported by other studies using similar approaches(Rothstein et al., Genome Research 2019; Azambuja and Simoes-Costa, Dev Cell 2020).