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Chromatin-localized central metabolism regulating gene expression and cell identity

Periodic Reporting for period 4 - CHROMABOLISM (Chromatin-localized central metabolism regulating gene expression and cell identity)

Berichtszeitraum: 2022-11-01 bis 2023-04-30

Epigenetics research has revealed that in the nucleus of mammalian cells the localization of almost all biomolecules – DNA, RNAs, proteins, protein posttranslational modifications – is tightly regulated to ensure they occupy distinct nuclear territories and specific sites in the genome. In contrast, small molecules and cellular metabolites are generally considered to passively enter the nucleus and lack locus-specific roles due to their fast diffusion. In the CHROMABOLISM project we tested the hypothesis that phase separation, proximity to the nuclear pore and recruitment of metabolic enzymes to chromatin can result in localized roles for at least some metabolites.

A better understanding of the interplay between cellular metabolism, chromatin structure and gene regulation can have important societal implications, particularly for the characterization, prevention and treatment of human diseases. Through the close link between chromatin structure, gene expression and cell identify, our research uncovered novel opportunities to establish desirable cell identify for regenerative medicine and to interfere with aberrant identity of cancer cells.

Overall, we generated comprehensive maps of chromatin-bound metabolic enzymes and nuclear metabolomes in representative leukemia cell lines, developed technology to perturb these nuclear metabolite patterns, and modeling the effects of cellular metabolites on cancer cell identity to identify novel therapeutic targets in leukemia. We uncovered a tight link between folate metabolism and gene expression, and thereby significantly expanded our understanding of nuclear metabolism in control of gene expression and cellular identity.
For mapping nuclear metabolic enzymes and metabolites we have developed and optimized protocols for the rapid isolation of nuclei and of chromatin. In selected leukemia cell lines, we then performed mass-spectrometry based proteomics and metabolomics analyses to determine the cell-type variation of nuclear metabolic enzymes and metabolites in steady state. In parallel, we developed a novel complementary method for microscopy-based live-cell imaging of hundreds of metabolic enzymes in parallel. In short, insertion of a fluorescent tag as a synthetic exon into introns of metabolic enzymes allows the generation of a cell pool, for which in each cell a different enzyme is tagged. The responses of these cells to drugs and other perturbations can then be monitored by live-cell microscopy. Finally, we use in situ sequencing to identify which enzyme is tagged in which cell.

In addition to these untargeted approaches, we conducted detailed characterization of two metabolic enzymes in the nucleus. We systematically studied the BAF complex, a chromatin remodelling ATPase, and identified subunit specific roles and cancer vulnerabilities. Using acute perturbation of the complex we further could show that inhibition of the enzymatic activity of the complex results in rapid changes in chromatin accessibility at at the timescale of minutes. These findings highlight the tight interplay between cellular metabolism, chromatin structure, and gene expression.

In contrast to the classical chromatin protein of the remodeller families, the nuclear role of the second metabolic enzyme we studied, MTHFD1, was unexpected. We had identified MTHFD1 from a genome-scale genetic screen for factors phenocopying inhibition of the histone acetyl-binder BRD4 and could show that the proteins physically interact in the nucleus. We further could show that MTHFD1 links cellular metabolism to purine responses, thereby integrating metabolic signals from the environment, cellular metabolism, and chromatin organization.

In summary, our research has yielded novel insights into basic cell biology, novel therapeutic targets, as well as novel technology for monitoring and controlling subcellular protein localization.
We applied proteomics and metabolomics methods to uncover novel roles of metabolic enzymes and metabolites in the cell’s nucleus. To complement these methods, we established an entirely novel method for pooled tagging of hundreds of metabolic enzymes. We showed that this method can be applied to identify expected and novel effects of small molecule perturbations on the localizations and levels of selected metabolic enzymes. In addition, this method together with a detailed proteomics study, has identified dozens of metabolic enzymes in the nucleus for which such a localization has not been previously studied. We expect our method of pooled intron tagging to have broad application in cell and chemical biology.

In addition to method development, we have uncovered novel roles of the human BAF complex, a chromatin remodelling ATPase in the nucleus. Using systematic knock-out of subunits of this protein complex, we have been able to assign subunit-specific effects on chromatin accessibility and transcription. In addition, we have also uncovered three novel intra-complex synthetic lethalities, that may in the future be exploited as therapeutic targets for the development of therapies for BAF mutant cancers. Studying chromatin remodelling with tight temporal resolution following BAF perturbations allowed us to identify rapid chromatin accessibility changes following BAF complex inhibtion, revealing a tight interplay between nuclear ATP levels, complex activity and gene expression.

Finally, we have uncovered a novel role for MTHFD1 in the nucleus. We identified this folate metabolic enzyme from a genetic screen for genes that when knocked-out phenocopy inhibition of the important chromatin protein BRD4. We have dissected the role of the folate pathway in transcriptional control and to developed chemical probes against selected enzymes of the pathway.

In summary, the CHROMABOLISM project enabled us to significantly advance the knowledge on central metabolic activities in the cell’s nucleus.
CHROMABOLISM project overview