Abstract

It is well established that the nuclear envelope has many distinct direct connections to chromatin that contribute to genome organization. The functional consequences of genome organization on gene regulation are less clear. Even less understood is how interactions of lamins and nuclear envelope transmembrane proteins (NETs) with chromatin can produce anchoring tethers that can withstand the physical forces of and on the genome. Chromosomes are the largest molecules in the cell, making megadalton protein structures like the nuclear pore complexes and ribosomes seem small by comparison. Thus to withstand strong forces from chromosome dynamics an anchoring tether is likely to be much more complex than a single protein-protein or protein-DNA interaction. Here we will briefly review known NE-genome interactions that likely contribute to spatial genome organization, postulate in the context of experimental data how these anchoring tethers contribute to gene regulation, and posit several hypotheses for the physical nature of these tethers that need to be investigated experimentally. Significantly, disruption of these anchoring tethers and the subsequent consequences for gene regulation could explain how mutations in nuclear envelope proteins cause diseases ranging from muscular dystrophy to lipodystrophy to premature aging progeroid syndromes. The two favored hypotheses for nuclear envelope protein involvement in disease are (1) weakening nuclear and cellular mechanical stability, and (2) disrupting genome organization and gene regulation. Considerable experimental support has been obtained for both. The integration of both mechanical and gene expression defects in the disruption of anchoring tethers could provide a unifying hypothesis consistent with both.

Highlights

  • It has been 130 years since Rabl (1885) used the ability to readily visualize chromosomes in salamander larvae to observe that genome organization is not random, noting that centromeres were located at the nuclear periphery

  • Fluorescence recovery after photobleaching (FRAP) and photoactivation experiments on nuclear envelope transmembrane proteins (NETs) involved in chromosome repositioning revealed that one population of these NETs is extremely dynamic while another population is not (Zuleger et al, 2011, 2013)

  • Tissue-specific NETs likely function in complexes together with other NETs, the lamin polymer and luminal proteins that generate anchoring tethers that bind to specific proteins on genes requiring tighter regulation

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Summary

INTRODUCTION

It has been 130 years since Rabl (1885) used the ability to readily visualize chromosomes in salamander larvae to observe that genome organization is not random, noting that centromeres were located at the nuclear periphery. The NE lumen is mostly unexplored territory, but some luminal proteins such as Torsin A are known to interact with INM NETs (Goodchild and Dauer, 2005) This incredibly complex structure disassembles and reassembles in each mitosis of higher organisms (Schellhaus et al, 2015). Important questions before us are: how are these patterns established and maintained? How does spatial genome organization contribute to genome regulation? Do disease pathologies reflect disruption of specific critical genes or of random collections of genes altered by global mechanical disruption of NE-genome connections?

GENOME INTERACTIONS AT THE NE
General Chromosomal DNA
Boundary Elements
Chromosome and Gene Positioning
Steric Factors
Adoption of Epigenetic Marks Once at the Periphery
Localized Concentration of Transcriptional Regulators
Gene Activation at the NE
Affinity Tethering
Force Distribution Through the Lamina
The Dynamic Scaffold
CONCLUSION

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