Experience-independent transformation of single-cell 3D genome structure and transcriptome during postnatal development of the mammalian brain

Abstract

After birth, the mammalian brain undergoes numerous molecular changes that underlie cognitive plasticity and maturation. However, little is known about the dynamics of three-dimensional (3D) genome structure during this period. Here we generated a 3D genome atlas of 1,954 single cells from the developing mouse cortex and hippocampus, using our diploid chromatin conformation capture (Dip-C) method. In adult tissues, genome structure alone delineates major cell types such as cortical excitatory and inhibitory neurons, and hippocampal granule cells. During development, a major transformation was observed between the first and fourth week after birth-coincident with synaptogenesis and de novo DNA methylation, leading to 3D reorganization across multiple genomic scales. Using reciprocal crosses, we systematically examined allele-specific structure of imprinted genes, revealing chromosome-wide difference at the Prader-Willi/Angelman syndrome locus. These findings thus uncover a previously unknown dimension of postnatal brain development.

Cerebellar Granule Cells Develop Non-neuronal 3D Genome Architecture over the Lifespan

“…3D). Similar to our previous studies in the mouse forebrain (5) and in other systems (2,3), this new single-cell chromatin A/B compartment (scA/B) analysis revealed 3D genome structure types corresponding to diverse cerebellar cell types-including granule cells, astrocytes, oligodendrocytes, and microglia in both species, as well as MLIs and Purkinje cells in mouse. These 3D genome measurements were highly robust, in that replicates (e.g., multiple tissue dissections, multiple Dip-C/Pop-C batches) of the same donors yielded consistent scA/B patterns (Fig.…”

“…Using Pop-C and vDip-C, we solved the initial 3D genome structures of single cerebellar cells, and created a high-resolution atlas for human and mouse spanning both development and aging. We found that although born with a 3D genome structure type similar to forebrain neurons (5), cerebellar granule cells unexpectedly transformed into a highly distinct structural type with specific inter-chromosomal contacts as well as ultra-long-range (10-100 Mb) intra-chromosomal contacts that had been thought to be exclusive to non-neuronal cells (e.g., microglia). In contrast to initial development, this 3D maturation proceeded continuously over lifespan like an aging clock, and was found to be highly robust in exhibiting resistance to functional perturbations including clinically-relevant heterozygous deletion of autism-implicated chromatin remodelers Chd8 and Arid1b, and granule cell-specific deletion of Chd4 (15).…”

“…In mouse, cerebellar granule cells (the vast majority of cerebellar neurons) are generated between postnatal days (P) 0-21; during this period, granule cell progenitors divide, mature, and migrate from the external granular layer (EGL) to the internal granular layer (IGL) of the cerebellar cortex, expanding >100-fold in number. In human beings, granule cells are generated between the third trimester of pregnancy and the age of ~1 year after birth, in stark contrast with the cerebral cortex where neurons are generated well before birth (5); the cerebellum also exhibits a uniquely slow epigenetic aging clock based on bulk DNA methylation assays (19). To explore the genomic underpinnings of this unique timeline of cerebellar development and aging, we created the initial 3D genome atlas extending across the human and mouse lifespan, alongside a combined transcriptome and chromatin-accessibility atlas focused on human postnatal development (Fig.…”

“…Previously, using our high-resolution single-cell 3D genome assay (diploid chromosome conformation capture, or Dip-C) (2-4), we found that cells in the mouse forebrain (cerebral cortex and hippocampus) undergo profound, cell type-specific transformation in transcriptome and genome architecture during the first month of life-providing a structural foundation for functional maturation (5). However, it was unclear if this approach could generalize for comparison across brain regions, species (including human), and lifespan-a major set of goals that for quantitative and statistical accuracy would require new technology to profile many samples and donors in parallel in a single reaction, as well as new technology to isolate rare cell types that contribute to the differential cellular composition of neural circuits across region, species, and age.…”

“…Here we show that the mammalian cerebellum undergoes an extraordinary, life-long 3D genome transformation that is conserved between human and mouse and far greater in magnitude than any corresponding processes observed in the forebrain (5). We first created a multi-ome atlas of the developing human by simultaneously measuring transcriptome and chromatin accessibility within the same cell.…”