Nanoscale invaginations of the nuclear envelope: Shedding new light on wormholes with elusive function

Abstract

Recent advances in fluorescence microscopy have opened up new possibilities to investigate chromosomal and nuclear 3D organization on the nanoscale. We here discuss their potential for elucidating topographical details of the nuclear lamina. Single molecule localization microscopy (SMLM) in combination with immunostainings of lamina proteins readily reveals tube-like invaginations with a diameter of 100-500 nm. Although these invaginations have been established as a frequent and general feature of interphase nuclei across different cell types, their formation mechanism and function have remained largely elusive. We critically review the current state of research, propose possible connections to lamina associated domains (LADs), and revisit the discussion about the potential role of these invaginations for accelerating mRNA nuclear export. Illustrative studies using 3D super-resolution imaging are shown and will be instrumental to decipher the physiological role of these nanoscale invaginations.

Immunogold FIB‐SEM: Combining Volumetric Ultrastructure Visualization with 3D Biomolecular Analysis to Dissect Cell–Environment Interactions

“…These nanoscale invaginations, commonly referred to as type II nucleoplasmic reticulum (type II NR), [28] are thought to improve access to the nuclear interior, which is typically rich in active genes. [31] Interestingly, volumetric reconstructions revealed that the myotubes frequently exhibited deep inward invaginations in the form of type II NR (13 ± 4 per nucleus section), to a significantly greater level than was observed for myoblasts (3 ± 2) (Figure 4c,d). We next investigated whether NPCs were relocated to sites of nuclear invaginations by quantifying the percentage of NPCs localized at sites of type II NR.…”

“…Mater. 2019, 31,1900488 nuclei remained unaltered (Figure 3c,d). We also counted the number of H3K9me3 immunolabels in each group, measuring a 1.4-fold increase for the nuclei of cells cultured on microgrooves compared to those grown on flat substrates (Figure 3e).…”

“…Mater. 2019, 31,1900488 Having established a specific immunogold FIB-SEM workflow for nuclear antigens, we sought to precisely map the volumetric distribution of the epigenetic mark H3K9me3 within the nucleus of cells subjected to different biophysical cues. Specifically, we compared immunolabeling in neural stem cells cultured for 2 days on either flat polydimethylsiloxane (PDMS) substrates or PDMS surfaces textured with 10 µm wide and 10 µm deep microgrooves (Figure 3a).…”

“…Mater. 2019, 31,1900488 is often associated with gene silencing; [24] however, the reported histone epigenetic modifications that putatively associate with such gene active/inactive regions have never been visualized directly. Using immunogold FIB-SEM imaging and 90 nm thick serial cross sections, we were able to map H3K9me3 distribution in 3D across whole nuclei (Figure 3b).…”

Nucleocytoplasmic Proteomic Analysis Uncovers eRF1 and Nonsense Mediated Decay as Modifiers of ALS C9orf72 Toxicity

“…Tubular invaginations of the nuclear envelope, such as those we describe here, have been observed before in a wide range of cell types and are particularly prominent in dividing cells and cancer tissue 83 . While the mechanistic relevance of these protrusions remains unclear, they have been associated with DNA repair 84 and mRNA transport 85 . These invaginations are not an exclusive feature of patient C9orf72 neurons, nor do they represent an in vitro artifact.…”