Nuclear compartment-associated genome organization

The very long life of the neuronal nucleus and genome


For decades, neurons in the adult human brain need to maintain their genome in a state that enables the specialized gene expression underlying our ability to think, remember, and move.  

In the nucleus, specific regions of the genome physically interact with distinct membraneless compartments that harbor specialized functions for gene regulation.  This aspect of three-dimensional (3D) genome architecture plays key roles in chromatin biology, transcription, and RNA processing.  

While most cell types are periodically replaced through a process that involves cell division, neurons do not globally “reset” their genome architecture through DNA replication and mitosis.

Thus, in neurons, the structural-spatial organization of the genome is of particular importance.  

The lamina, pores, nucleoli, and speckles are nuclear compartments with gene regulatory functions.  Specific regions of the genome (LADs, NADs, and SPADs) interact with these compartments.  

A new, easy-to-use tool for mapping nuclear compartments


 Click here for cartoon of GO-CaRT in action! 


Because of technical limitations, nuclear compartment-associated genome organization in brain cells had been unknown.  

We recently developed GO-CaRT (Genome Organization using Cut and Run Technology) to map such genomic interactions in mouse and human brain cells.  In GO-CaRT, protein A fused Micrococcal nuclease (pA-MNase) is localized to genomic DNA that is in close proximity to a nuclear compartment as defined by specific antibodies, and the cleaved DNA fragments are identified by paired end sequencing.  GO-CaRT requires relatively few cells (~50,000 cells) and is simple to perform (takes only about 1 day).  To learn more, click here for a JRNLclub presentation.  


Some ongoing research...