Nuclear membrane

Ever since Robert Brown's discovery of the cell nucleus in 1833 it has been known that the nucleus is surrounded by a membranous structure. The nuclear membrane consists of two lipid bilayers enclosing the nucleus and physically isolating it from the rest of the cell, which enables important molecular processes to occur in the nucleus without interference from the cytoplasm. Example images of proteins localized to the nuclear membrane can be seen in Figure 1.

In the subcellular section, 287 genes (1% of all protein-coding human genes) have been shown to encode proteins that localize to the nuclear membrane (Figure 2). A Gene Ontology (GO)-based functional enrichment analysis of the nuclear membrane proteins show enrichment of genes associated with biological processes mainly related to structural organization of the nucleus and nucleocytoplasmic transport. About 89% (n=255) of the nuclear membrane proteins localize to other cellular compartments in addition to the nuclear membrane, of which 27% (n=77) only localize to other substructures within the nuclear meta compartment.


TPR - A-431

LMNB1 - MCF-7

SUN2 - A-431

Figure 1. Examples of proteins localized to the nuclear membrane. TPR is part of the nuclear pore complex required in nuclear trafficking, and is specifically involved in nuclear export of mRNAs (detected in A-431 cells). LMNB1 is a part of the nuclear lamina, and is a type of intermediate filament protein (detected in MCF7 cells). SUN2 is known to be part of the LINC protein complexes that enables connection of the cytoskeleton to the nuclear membrane (detected in A-431 cells).

0%10%20%30%40%50%60%70%80%90%100%% genesNot mappedSecretedOther organellesNuclear membrane

  • 1% (287 proteins) of all human proteins have been experimentally detected in the nuclear membrane by the Human Protein Atlas.
  • 84 proteins in the nuclear membrane are supported by experimental evidence and out of these 14 proteins are enhanced by the Human Protein Atlas.
  • 255 proteins in the nuclear membrane have multiple locations.
  • 43 proteins in the nuclear membrane show single cell variation.

  • Nuclear membrane proteins are mainly involved in organization of the nucleus and nucleocytoplasmic transport.

Figure 2. 1% of all human protein-coding genes encode proteins localized to the nuclear membrane. Each bar is clickable and gives a search result of proteins that belong to the selected category.

The structure of the nuclear membrane

The nuclear membrane, also known as the nuclear envelope, consists of two lipid bilayers. The outermost layer is contiguous with the endoplasmic reticulum (ER). The innermost layer is lined by a fibrillar network consisting of nuclear intermediate filament proteins, known as nuclear lamins. The nuclear lamina provides structural support and acts as an anchoring point for chromatin, thus playing an important role in nuclear organization. It has been suggested that lamins may also participate in DNA repair, as well as regulation of DNA replication and transcription (Dechat T et al. (2008)). Lamins are classified as A- or B-type lamins, and exhibit different biochemical and functional properties in terms of isoelectric points and behavior during mitosis. During the mitotic phase of cell division, B-type lamins will remain membrane-associated, whereas A-type lamins are solubilized and dispersed (Gruenbaum Y et al. (2005); Stuurman N et al. (1998)). The space between the inner and the outer membrane is refehe perinuclear space. The membranes are connected to each other by large protein complexes, known as nuclear pore complexes, forming a large number of channels that allows for transport in and out of the nucleus. Each nuclear pore complex consists of 100-200 proteins that form a characteristic eight-fold ring symmetry (Paine PL et al. (1975); Reichelt R et al. (1990); CALLAN HG et al. (1950)). A selection of proteins suitable as markers for the nuclear lamina and the nuclear membrane can be found in Table 1. A list of highly expressed nuclear membrane proteins, including lamins, are summarized in Table 2.

Table 1. Selection of proteins suitable as markers for the nuclear membrane.

Gene
Description
Substructure
SUN2 Sad1 and UNC84 domain containing 2 Nuclear membrane
TMPO Thymopoietin Nuclear membrane
SUN1 Sad1 and UNC84 domain containing 1 Nuclear membrane
LEMD2 LEM domain nuclear envelope protein 2 Nuclear membrane
LMNB1 Lamin B1 Nuclear membrane
TOR1AIP1 Torsin 1A interacting protein 1 Nuclear membrane
LBR Lamin B receptor Nuclear membrane
Nucleoli fibrillar center
LMNB2 Lamin B2 Nuclear membrane

Table 2. Highly expressed single localized nuclear membrane proteins across different cell lines.

Gene
Description
Average nTPM
TMPO Thymopoietin 130
LMNB1 Lamin B1 82
LMNB2 Lamin B2 82
CASC3 CASC3 exon junction complex subunit 53
TPR Translocated promoter region, nuclear basket protein 51
SUN2 Sad1 and UNC84 domain containing 2 49
LEMD2 LEM domain nuclear envelope protein 2 47
SUN1 Sad1 and UNC84 domain containing 1 44
NUP153 Nucleoporin 153 43
TOR1AIP1 Torsin 1A interacting protein 1 38

When imaging an intersection of the cell, the nuclear membrane is visible as a thin circle along the outer rim of the nucleus, which is consistent between cell lines (Figure 3). The membrane is however not perfectly smooth and the membranous cavities can appear as small circles or dots inside the nucleus, not to be confused with nuclear bodies.


LBR - HEK293

LBR - U2OS

LBR - Rh30

Figure 3. Examples of the morphology of nuclear membrane in different cell lines, where the morphology is relatively consistent. The images show immunofluorescent stainings of the protein LBR in HEK 293, U2OS and RH-30 cells.


Figure 4. 3D-view of the nuclear membrane in U2OS, visualized by immunofluorescent staining of LMNB1. The morphology of the nuclear membrane in human induced stem cells can be seen in the Allen Cell Explorer.

The function of the nuclear membrane

The nuclear membrane serves as a barrier between the nucleus and the cytoplasm, separating gene regulation and transcription in the nucleus from translation in the cytoplasm (CALLAN HG et al. (1950); WATSON ML. (1955)). The nuclear pores allow for passive diffusion of small molecules, but also active transport of larger molecules like RNA and proteins, across the nuclear membrane (Paine PL et al. (1975); BAHR GF et al. (1954)). In that sense, the nuclear membrane creates a barrier, but also a linkage, between the nucleus and the rest of the cell. The nuclear membrane is a highly dynamic structure, with a composition that is altered throughout the cell cycle. After replication in S phase, the nuclear membrane expands in G2, but then breaks down upon entry into mitosis to enable connection of the spindle apparatus to the sister chromatids. The breakdown mechanism involves disassembly of the nuclear pore complexes and depolymerization of the nuclear lamina. Reassembly of the nuclear membrane occurs after the completion of mitosis (Terasaki M et al. (2001); Dultz E et al. (2008); Salina D et al. (2002); Beaudouin J et al. (2002); Gerace L et al. (1980); Ellenberg J et al. (1997); Yang L et al. (1997)). Mutations in genes encoding nuclear lamina associated proteins give rise to several human diseases, collectively called laminopathies. One example is the protein emerin that mediates anchoring of the nuclear membrane to the cytoskeleton (Figure 6). Mutations in the EMD gene causes Emery-Dreifuss muscular dystrophy (EDMD); an X chromosome linked disease characterized by contractures and in many cases also cardiomyopathy (Bione S et al. (1994)).

Gene Ontology (GO) analysis of genes encoding proteins mainly localized to the nuclear membrane reveal enrichment of GO terms describing functions that are well in line with known functions of the nuclear membrane. The enriched terms for the GO domain Biological Process are mostly related to molecular transport (Figure 5a). Enrichment analysis of the GO domain Molecular Function gives top hits for terms related to lamins, nuclear pore complexes and nuclear trafficking (Figure 5b).

051015202530354045Fold EnrichmentTRNA export from nucleusTRNA-containing ribonucleopr...Intracellular transport of v...Nuclear migrationMulti-organism localizationMulti-organism transportProtein sumoylationRegulation of cellular respo...Regulation of glycolytic pro...Pore complex assemblyCentrosome localizationMicrotubule organizing cente...Nucleus organizationADP metabolic processRegulation of gene silencing...Glial cell migrationRegulation of small molecule...Show full plot

Figure 5a. Gene Ontology-based enrichment analysis for the nuclear membrane proteome showing the significantly enriched terms for the GO domain Biological Process. Each bar is clickable and gives a search result of proteins that belong to the selected category.

051015202530354045505560Fold EnrichmentLamin bindingStructural constituent of nu...Protein membrane anchorNuclear localization sequenc...Ran GTPase bindingNucleocytoplasmic carrier ac...

Figure 5b. Gene Ontology-based enrichment analysis for the nuclear membrane proteome showing the significantly enriched terms for the GO domain Molecular Function. Each bar is clickable and gives a search result of proteins that belong to the selected category.

Nuclear membrane proteins with multiple locations

Among the nuclear membrane proteins identified in the subcellular section, approximately 89% (n=255) also localize to other cellular compartments (Figure 6). 27% (n=77) of them only localize to other nuclear substructures. The network plot shows that the most common locations shared with nuclear membrane are nucleoplasm and vesicles. Colocalizations of proteins between the nuclear membrane and nucleus are overrepresented, while colocalizations between nuclear memberane and cytosol are underrepresented. Localization to both the nuclear membrane and the nucleoplasm could highlight proteins that localize to the nucleoplasm and are enriched at the inner surface of the nuclear membrane or nuclear lamina, perhaps depending on cell type or state. Examples of multilocalizing proteins within the nuclear membrane proteome can be seen in Figure 7.

Figure 6. Interactive network plot of nuclear membrane proteins with multiple localizations. The numbers in the connecting nodes show the proteins that are localized to the nuclear membrane and to one or more additional locations. Only connecting nodes containing at least 1.0% of proteins in the nuclear membrane proteome are shown. The circle sizes are related to the number of proteins. The cyan colored nodes show combinations that are significantly overrepresented, while magenta colored nodes show combinations that are significantly underrepresented as compared to the probability of observing that combination based on the frequency of each annotation and a hypergeometric test (p≤0.05). Note that this calculation is only done for proteins with dual localizations. Each node is clickable and results in a list of all proteins that are found in the connected organelles.


EMD - U-251MG

MX1 - U2OS

TOR1A - MCF-7

Figure 7. Examples of multilocalizing proteins in the nuclear membrane proteome. The examples show common or overrepresented combinations for multilocalizing proteins in the nuclear membrane proteome. EMD is known to be involved in multiple processes, for example actin formation and stabilization. It is localized to the nuclear membrane and the ER (detected in U-251 cells). MX1 inhibits virus replication by preventing nuclear import of viral compartments, and is a peripheral membrane protein. MX1 is localized to the nuclear membrane and the cytosol (detected in U2OS cells). TOR1A performs a variety of tasks such as protein folding and cell movement control. It is localized to the nuclear membrane and vesicles (detected in MCF7 cells).

Expression levels of nuclear membrane proteins in tissue

Transcriptome analysis and classification of genes into tissue distribution categories (Figure 8) show that genes encoding nuclear membrane proteins have a similar distribution between these classes as do all genes presented in the subcellular resource.

Detected in singleDetected in someDetected in manyDetected in allNot detected0.0102030405060708090100%Nuclear membraneAll localized genes

Figure 8. Bar plot showing the percentage of genes in different tissue distribution categories for nuclear membrane-associated protein-coding genes compared to all genes in the subcellular resource. Asterisk marks a statistically significant deviation (p≤0.05) in the number of genes in a category based on a binomial statistical test. Each bar is clickable and gives a search result of proteins that belong to the selected category.

Relevant links and publications

Dechat T et al., Nuclear lamins: major factors in the structural organization and function of the nucleus and chromatin. Genes Dev. (2008)
PubMed: 18381888 DOI: 10.1101/gad.1652708

Gruenbaum Y et al., The nuclear lamina comes of age. Nat Rev Mol Cell Biol. (2005)
PubMed: 15688064 DOI: 10.1038/nrm1550

Stuurman N et al., Nuclear lamins: their structure, assembly, and interactions. J Struct Biol. (1998)
PubMed: 9724605 DOI: 10.1006/jsbi.1998.3987

Paine PL et al., Nuclear envelope permeability. Nature. (1975)
PubMed: 1117994 

Reichelt R et al., Correlation between structure and mass distribution of the nuclear pore complex and of distinct pore complex components. J Cell Biol. (1990)
PubMed: 2324201 

CALLAN HG et al., Experimental studies on amphibian oocyte nuclei. I. Investigation of the structure of the nuclear membrane by means of the electron microscope. Proc R Soc Lond B Biol Sci. (1950)
PubMed: 14786306 

WATSON ML., The nuclear envelope; its structure and relation to cytoplasmic membranes. J Biophys Biochem Cytol. (1955)
PubMed: 13242591 

BAHR GF et al., The fine structure of the nuclear membrane in the larval salivary gland and midgut of Chironomus. Exp Cell Res. (1954)
PubMed: 13173504 

Terasaki M et al., A new model for nuclear envelope breakdown. Mol Biol Cell. (2001)
PubMed: 11179431 

Dultz E et al., Systematic kinetic analysis of mitotic dis- and reassembly of the nuclear pore in living cells. J Cell Biol. (2008)
PubMed: 18316408 DOI: 10.1083/jcb.200707026

Salina D et al., Cytoplasmic dynein as a facilitator of nuclear envelope breakdown. Cell. (2002)
PubMed: 11792324 

Beaudouin J et al., Nuclear envelope breakdown proceeds by microtubule-induced tearing of the lamina. Cell. (2002)
PubMed: 11792323 

Gerace L et al., The nuclear envelope lamina is reversibly depolymerized during mitosis. Cell. (1980)
PubMed: 7357605 

Ellenberg J et al., Nuclear membrane dynamics and reassembly in living cells: targeting of an inner nuclear membrane protein in interphase and mitosis. J Cell Biol. (1997)
PubMed: 9298976 

Yang L et al., Integral membrane proteins of the nuclear envelope are dispersed throughout the endoplasmic reticulum during mitosis. J Cell Biol. (1997)
PubMed: 9182656 

Bione S et al., Identification of a novel X-linked gene responsible for Emery-Dreifuss muscular dystrophy. Nat Genet. (1994)
PubMed: 7894480 DOI: 10.1038/ng1294-323