A large brain-specific chondroitin sulfate proteoglycan, identified with monoclonal antibody 6B4 (6B4 proteoglycan/phosphacan), was isolated from rat brain. Soluble proteoglycans in the phosphate-buffered saline extract from 20-day-old rat whole brain were fractionated by anion exchange chromatography and CsCl density gradient centrifugation. 6B4 proteoglycan was further purified by gel filtration and additional ion exchange chromatography. The molecular mass of 6B4 proteoglycan shifted from 800 to 300 x 10(3) mol. wt after chondroitinase ABC digestion. The core protein was substituted with chondroitin sulfate chains with an average molecular weight of 21,000, keratan sulfate and HNK-1 carbohydrates. Glycosidase digestion of 6B4 proteoglycan with O-glycanase, N-glycanase, endo-beta-galactosidase, or keratanase did not remove the HNK-1 epitopes. The expression of 6B4 proteoglycan was developmentally regulated in the rat cerebral cortex; appearing first at embryonic day 14, peaking at postnatal day 0, and persisting throughout adulthood at a lower level. Immunohistochemical analysis indicated that 6B4 proteoglycan was distributed along the radial glial fibers and on the migrating neurons in the embryonal rar cerebrum. The radial glial fibers were stained intensely all along their length, but the neurons in the cortical plate were not stained in contrast to the moderate staining of the migrating neurons in the intermediate zone and the subplate. From postnatal day 5 to postnatal day 20, 6B4 proteoglycan was present throughout the cortex. After postnatal day 30, staining of the neuropil was weakened, and the expression of 6B4 proteoglycan was restricted around subsets of neurons. The positive neurons were mostly non-pyramidal cells (> 95%) and were relatively concentrated in layers IV and VI of the primary somatosensory cortex. Immunohistochemical analysis of the dissociated cortical neurons indicated that 6B4 proteoglycan was distributed on the cell bodies and neurites. 6B4 proteoglycan strikingly promoted neurite extension of cortical neurons from embryonic day-16 rat embryos when coated on coverslips as a substrate. 6B4 proteoglycan is a brain-specific chondroitin sulfate proteoglycan which carries keratan sulfate and HNK-1 carbohydrates. The spatiotemporal expression profile and effects on the dissociated cerebral neurons suggest that 6B4 proteoglycan plays important roles in the migration and differentiation of neurons in the immature cortex, and also in the maintenance of subsets of neurons in the mature cortex.