Nuclear structure and scaffolding have been implicated in expression and regulation of the genome (Elcock and Bridger 2010; Fedorova and Zink 2008; Ferrai et al. 2010; Li and Reinberg 2011; Austin and Bellini 2010). Discrete domains of chromatin exist within the nuclear volume, and are suggested to be organized by patterns of gene activity (Zhao, Bodnar, and Spector 2009). The nuclear periphery, which consists of the inner nuclear membrane and associated proteins, forms a sub-nuclear compartment that is mostly associated with transcriptionally repressed chromatin and low gene expression (Guelen et al. 2008). Previous studies from our lab and others have shown that repositioning genes to the nuclear periphery is sufficient to induce transcriptional repression (K L Reddy et al. 2008; Finlan et al. 2008). In addition, a number of studies have provided evidence that many tissue types, including muscle, brain and blood, use the nuclear periphery as a compartment during development to regulate expression of lineage specific genes (Meister et al. 2010; Szczerbal, Foster, and Bridger 2009; Yao et al. 2011; Kosak et al. 2002; Peric-Hupkes et al. 2010). These large regions of chromatin that come in molecular contact with the nuclear periphery are called Lamin Associated Domains (LADs).
The studies described in this dissertation have furthered our understanding of maintenance and establishment of LADs as well as the relationship of LADs with the epigenome and other factors that influence three-dimensional chromatin structure. I provide evidence that LAD patterns from DNA adenine methyltransferase identification (DamID)-derived molecular contact maps are reflective of higher order chromatin structure in both ensemble population measure and single cells. Importantly, this work provides the first in situ visualization of chromosome-wide molecular data in a single cell. These data, showing LAD and nonLAD organization, indicate that there is a speicifc and reproducible organization of sub-chromosomal domains. In addition, this work has furthered our understanding of the influence of chromatin state on both LAD and overall chromosome organization—demonstrating that higher-order chromatin structure and epigenetic signatures are closely linked. This work has contributed to the finding that LAD formation can be sequence driven, which was uncovered by examining variable LADs (vLADs) where LAD patterning differs between cell types. Also, examination of LADs across multiple cell types has uncovered genomic characteristics that can define LADs and may have a functional role in the process of genome organizatio
