Single-cell epigenomics reveals mechanisms of human cortical development

During mammalian development, differences in chromatin state coincide with cellular differentiation and reflect changes in the gene regulatory landscape1. In the developing brain, cell fate specification and topographic identity are important for defining cell identity2 and confer selective vulnerabilities to neurodevelopmental disorders3. Here, to identify cell-type-specific chromatin accessibility patterns in the developing human brain, we used a single-cell assay for transposase accessibility by sequencing (scATAC-seq) in primary tissue samples from the human forebrain. We applied unbiased analyses to identify genomic loci that undergo extensive cell-type- and brain-region-specific changes in accessibility during neurogenesis, and an integrative analysis to predict cell-type-specific candidate regulatory elements. We found that cerebral organoids recapitulate most putative cell-type-specific enhancer accessibility patterns but lack many cell-type-specific open chromatin regions that are found in vivo. Systematic comparison of chromatin accessibility across brain regions revealed unexpected diversity among neural progenitor cells in the cerebral cortex and implicated retinoic acid signalling in the specification of neuronal lineage identity in the prefrontal cortex. Together, our results reveal the important contribution of chromatin state to the emerging patterns of cell type diversity and cell fate specification and provide a blueprint for evaluating the fidelity and robustness of cerebral organoids as a model for cortical development.

Murine in vivo total body nitrogen by photoactivation

A facility to measure total body nitrogen (TBN) by photoactivation analysis in rats, using the 14N(gamma, n)13N reaction, was designed, calibrated and evaluated. TBN provides a quantitative estimate of nutritional status. TBN in humans can be measured by neutron activation, however the small absolute amount of nitrogen in rats causes difficulties with this technique. Photoactivation analysis involved irradiating the specimen with high energy photons from an 18 MV Medical Linear Accelerator to a dose of approximately 2 Gy. The technique was calibrated using urea solution rat phantoms with 2.0-3.0% nitrogen content. By analysing the measured decay curve, the initial nitrogen count rate of 0.51 MeV photons was determined and the initial oxygen count rate, being an interfering source of 0.51 MeV photons, was shown to be constant. Within the range of nitrogen concentrations studied, the response is linear (r2 = 0.9) with a CV of 3.5%. Thus, photoactivation provides a relatively simple, in vivo technique for determining total body nitrogen in rats.