Longitudinal assessment of neuronal 3D genomes in mouse prefrontal cortex

• Published in: Nature communications 2016-09, Vol.7 (1), p.12743-12743, Article 12743
• Main Authors: Mitchell, Amanda C., Javidfar, Behnam, Bicks, Lucy K., Neve, Rachael, Garbett, Krassimira, Lander, Sharon S., Mirnics, Karoly, Morishita, Hirofumi, Wood, Marcelo A., Jiang, Yan, Gaisler-Salomon, Inna, Akbarian, Schahram
• Format: Article
• Language: English
• Subjects: 631/208/177; 631/378/2584; Animals; Anxiety; Cell division; Chromosome Aberrations; Cognition; Cognition & reasoning; Dizocilpine Maleate - pharmacology; DNA methylation; Epigenesis, Genetic; Gene Expression Regulation - drug effects; Gene Expression Regulation - physiology; Genome; Genomes; Glutamate Decarboxylase - genetics; Glutamate Decarboxylase - metabolism; Humanities and Social Sciences; Longitudinal Studies; Memory; Mice; multidisciplinary; Neurons - metabolism; Neurosciences; Prefrontal Cortex - cytology; Receptors, N-Methyl-D-Aspartate - antagonists & inhibitors; Science; Science (multidisciplinary); Site-Specific DNA-Methyltransferase (Adenine-Specific); Staining and Labeling; Young adults
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/ncomms12743

Neuronal epigenomes, including chromosomal loopings moving distal cis -regulatory elements into proximity of target genes, could serve as molecular proxy linking present-day-behaviour to past exposures. However, longitudinal assessment of chromatin state is challenging, because conventional chromosome conformation capture assays essentially provide single snapshots at a given time point, thus reflecting genome organization at the time of brain harvest and therefore are non-informative about the past. Here we introduce ‘NeuroDam’ to assess epigenome status retrospectively. Short-term expression of the bacterial DNA adenine methyltransferase Dam, tethered to the Gad1 gene promoter in mouse prefrontal cortex neurons, results in stable G methyl ATC tags at Gad1 -bound chromosomal contacts. We show by NeuroDam that mice with defective cognition 4 months after pharmacological NMDA receptor blockade already were affected by disrupted chromosomal conformations shortly after drug exposure. Retrospective profiling of neuronal epigenomes is likely to illuminate epigenetic determinants of normal and diseased brain development in longitudinal context. Chromosome conformation is a dynamic process, especially in brain. Here, Mitchell and colleagues devise a method they call NeuroDam that can prospectively tag chromosome conformation in the mouse brain in vivo , and longitudinally assess long range chromosome looping weeks and months later.