Chromatin-associated phospholipids are well recognized. A report that catalytically active endonuclear CTP:choline-phosphate cytidylyltransferase ␣ is necessary for cell survival questions whether endonuclear, CDP-choline pathway phosphatidylcholine synthesis may occur in situ. We report that chromatin from human IMR-32 neuroblastoma cells possesses such a biosynthetic pathway. First, membrane-free nuclei retain all three CDP-choline pathway enzymes in proportions comparable with the content of chromatin-associated phosphatidylcholine. Second, following supplementation of cells with deuterated choline and using electrospray ionization mass spectrometry, both the time course and molecular species labeling pattern of newly synthesized endonuclear and whole cell phosphatidylcholine revealed the operation of spatially separate, compositionally distinct biosynthetic routes. Specifically, endogenous and newly synthesized endonuclear phosphatidylcholine species are both characterized by a high degree of diacyl/alkylacyl chain saturation. This unusual species content and synthetic pattern (evident within 10 min of supplementation) are maintained through cell growth arrest by serum depletion and when proliferation is restored, suggesting that endonuclear disaturated phosphatidylcholine enrichment is essential and closely regulated. We propose that endonuclear phosphatidylcholine synthesis may regulate periodic nuclear accumulations of phosphatidylcholine-derived lipid second messengers. Furthermore, our estimates of saturated phosphatidylcholine nuclear volume occupancy of around 10% may imply a significant additional role in regulating chromatin structure.Considerable evidence supports the existence of an endonuclear pool of phospholipid, in association with the nuclear matrix and distinct from the nuclear envelope (1-4). This endonuclear phospholipid is remarkable for several reasons. Although all the major membrane phospholipids, predominantly phosphatidylcholine (PtdCho), 1 phosphatidylethanolamine (PtdEtn), phosphatidylserine, and phosphatidylinositol (PtdIns), may be present typically at 4 -10% of total cell content (2), transmission electron microscopy has failed to reveal endonuclear membranous systems (5). Hence the molecular organization of endonuclear phospholipids in eukaryotic cells is still unclear. Extensive histochemical and cytochemical studies suggest that their spatial distributions overlap that of decondensed chromatin domains (3, 4). A number of in vitro studies suggest a functional relationship between various endonuclear phospholipids and gene expression/transcription (6 -10). Moreover, cell studies have shown that the amounts of endonuclear phospholipids change during progression through the cell cycle (4). The potential physiological importance of intranuclear phospholipid has recently been highlighted by the recognition that the ␣ isoform (CCT␣) of CTP:choline-phosphate cytidylyltransferase, the principal regulatory enzyme of PtdCho biosynthesis (11), is confined to the nucleus throughout the ce...