Nuclear membrane

Ever since Robert Brown's discovery of the nucleus in 1833 it has been known that the nucleus is surrounded by a membranous structure. The nuclear membrane is a lipid bilayer 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 Cell Atlas, 277 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 shows enrichment of terms for biological processes mainly related to structural organization of the nucleus and nucleocytoplasmic transport. About 85% (n=236) of the nuclear membrane proteins localize to other cellular compartments in addition to the nuclear membrane, with 30% (n=82) also localizing to other substructures within the nuclear meta compartment. The most common additional localization except for the nucleoplasm is vesicles.


TPR - A-431

LMNB1 - MCF7

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).

  • 1% (277 proteins) of all human proteins have been experimentally detected in the nuclear membrane by the Human Protein Atlas.
  • 67 proteins in the nuclear membrane are supported by experimental evidence and out of these 17 proteins are enhanced by the Human Protein Atlas.
  • 236 proteins in the nuclear membrane have multiple locations.
  • 41 proteins in the nuclear membrane show a cell to cell variation. Of these 37 show a variation in intensity and 4 a spatial 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 membrane is contiguous with the endoplasmic reticulum (ER), while the innermost membrane 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, 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 associated to membranes, whereas A-type lamins are solubilized and dispersed (Gruenbaum Y et al. (2005); Stuurman N et al. (1998)). 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 containing 2 Nuclear membrane
LMNB1 Lamin B1 Nuclear membrane
TOR1AIP1 Torsin 1A interacting protein 1 Nuclear membrane
LBR Lamin B receptor Nuclear membrane
LMNB2 Lamin B2 Nuclear membrane

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

Gene Description Average NX
TMPO Thymopoietin 27
LMNB2 Lamin B2 22
TPR Translocated promoter region, nuclear basket protein 21
LBR Lamin B receptor 19
NUP153 Nucleoporin 153 18
LMNB1 Lamin B1 18
LEMD2 LEM domain containing 2 18
TOR1AIP1 Torsin 1A interacting protein 1 17
SNUPN Snurportin 1 17
SUN2 Sad1 and UNC84 domain containing 2 16

The space between the inner and the outer membrane is called the perinuclear space. The membranes are connected to each other at 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)). 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 - HEK 293

LBR - U-2 OS

LBR - RH-30

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, U-2 OS and RH-30 cells.


Figure 4. 3D-view of the nuclear membrane in U-2 OS, 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 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 both 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, depolymerization of the nuclear lamina, removal of proteins associated with the inner nuclear membrane. 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 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).

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.

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

Of the nuclear membrane proteins identified in the Cell Atlas, approximately 85% (n=236) also localize to other cellular compartments (Figure 6). 30% (n=82) of all nuclear membrane protein only also localize to other nuclear structures. The network plot shows that the most common locations shared with nuclear membrane are nucleoplasm, cytosol and vesicles, with nucleoplasm and vesicles being overrepresented. 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. Localization to the nuclear membrane and vesicles could reflect the fact that the nuclear membrane is connected to the secretory pathways through its association with the ER and/or highlight proteins involved in nuclear transport. 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 more than one protein and at least 0.5% 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-251 MG

MX1 - U-2 OS

TOR1A - MCF7

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. EMD 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 U-2 OS 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) shows that genes encoding nuclear membrane proteins shows a similar distribution between these classes as do all genes presented in the Cell Atlas.

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 Cell Atlas. 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

Clegg JS., Properties and metabolism of the aqueous cytoplasm and its boundaries. Am J Physiol. (1984)
PubMed: 6364846 

Luby-Phelps K., The physical chemistry of cytoplasm and its influence on cell function: an update. Mol Biol Cell. (2013)
PubMed: 23989722 DOI: 10.1091/mbc.E12-08-0617

Luby-Phelps K., Cytoarchitecture and physical properties of cytoplasm: volume, viscosity, diffusion, intracellular surface area. Int Rev Cytol. (2000)
PubMed: 10553280 

Ellis RJ., Macromolecular crowding: obvious but underappreciated. Trends Biochem Sci. (2001)
PubMed: 11590012 

Bright GR et al., Fluorescence ratio imaging microscopy: temporal and spatial measurements of cytoplasmic pH. J Cell Biol. (1987)
PubMed: 3558476 

Kopito RR., Aggresomes, inclusion bodies and protein aggregation. Trends Cell Biol. (2000)
PubMed: 11121744 

Aizer A et al., Intracellular trafficking and dynamics of P bodies. Prion. (2008)
PubMed: 19242093 

Carcamo WC et al., Molecular cell biology and immunobiology of mammalian rod/ring structures. Int Rev Cell Mol Biol. (2014)
PubMed: 24411169 DOI: 10.1016/B978-0-12-800097-7.00002-6

Lang F., Mechanisms and significance of cell volume regulation. J Am Coll Nutr. (2007)
PubMed: 17921474 

Thul PJ et al., A subcellular map of the human proteome. Science. (2017)
PubMed: 28495876 DOI: 10.1126/science.aal3321

Uhlén M et al., Tissue-based map of the human proteome. Science (2015)
PubMed: 25613900 DOI: 10.1126/science.1260419

Boisvert FM et al., The multifunctional nucleolus. Nat Rev Mol Cell Biol. (2007)
PubMed: 17519961 DOI: 10.1038/nrm2184

Scheer U et al., Structure and function of the nucleolus. Curr Opin Cell Biol. (1999)
PubMed: 10395554 DOI: 10.1016/S0955-0674(99)80054-4

Németh A et al., Genome organization in and around the nucleolus. Trends Genet. (2011)
PubMed: 21295884 DOI: 10.1016/j.tig.2011.01.002

Cuylen S et al., Ki-67 acts as a biological surfactant to disperse mitotic chromosomes. Nature. (2016)
PubMed: 27362226 DOI: 10.1038/nature18610

Stenström L et al., Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder. Mol Syst Biol. (2020)
PubMed: 32744794 DOI: 10.15252/msb.20209469

Derenzini M et al., Nucleolar size indicates the rapidity of cell proliferation in cancer tissues. J Pathol. (2000)
PubMed: 10861579 DOI: 10.1002/(SICI)1096-9896(200006)191:2<181::AID-PATH607>3.0.CO;2-V

Visintin R et al., The nucleolus: the magician's hat for cell cycle tricks. Curr Opin Cell Biol. (2000)
PubMed: 10801456 

Marciniak RA et al., Nucleolar localization of the Werner syndrome protein in human cells. Proc Natl Acad Sci U S A. (1998)
PubMed: 9618508 

Tamanini F et al., The fragile X-related proteins FXR1P and FXR2P contain a functional nucleolar-targeting signal equivalent to the HIV-1 regulatory proteins. Hum Mol Genet. (2000)
PubMed: 10888599 

Willemsen R et al., Association of FMRP with ribosomal precursor particles in the nucleolus. Biochem Biophys Res Commun. (1996)
PubMed: 8769090 DOI: 10.1006/bbrc.1996.1126

Isaac C et al., Characterization of the nucleolar gene product, treacle, in Treacher Collins syndrome. Mol Biol Cell. (2000)
PubMed: 10982400 

Drygin D et al., The RNA polymerase I transcription machinery: an emerging target for the treatment of cancer. Annu Rev Pharmacol Toxicol. (2010)
PubMed: 20055700 DOI: 10.1146/annurev.pharmtox.010909.105844

Parikh K et al., Colonic epithelial cell diversity in health and inflammatory bowel disease. Nature. (2019)
PubMed: 30814735 DOI: 10.1038/s41586-019-0992-y

Menon M et al., Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration. Nat Commun. (2019)
PubMed: 31653841 DOI: 10.1038/s41467-019-12780-8

Wang L et al., Single-cell reconstruction of the adult human heart during heart failure and recovery reveals the cellular landscape underlying cardiac function. Nat Cell Biol. (2020)
PubMed: 31915373 DOI: 10.1038/s41556-019-0446-7

Wang Y et al., Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine. J Exp Med. (2020)
PubMed: 31753849 DOI: 10.1084/jem.20191130

Liao J et al., Single-cell RNA sequencing of human kidney. Sci Data. (2020)
PubMed: 31896769 DOI: 10.1038/s41597-019-0351-8

MacParland SA et al., Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations. Nat Commun. (2018)
PubMed: 30348985 DOI: 10.1038/s41467-018-06318-7

Vieira Braga FA et al., A cellular census of human lungs identifies novel cell states in health and in asthma. Nat Med. (2019)
PubMed: 31209336 DOI: 10.1038/s41591-019-0468-5

Vento-Tormo R et al., Single-cell reconstruction of the early maternal-fetal interface in humans. Nature. (2018)
PubMed: 30429548 DOI: 10.1038/s41586-018-0698-6

Qadir MMF et al., Single-cell resolution analysis of the human pancreatic ductal progenitor cell niche. Proc Natl Acad Sci U S A. (2020)
PubMed: 32354994 DOI: 10.1073/pnas.1918314117

Solé-Boldo L et al., Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming. Commun Biol. (2020)
PubMed: 32327715 DOI: 10.1038/s42003-020-0922-4

Henry GH et al., A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra. Cell Rep. (2018)
PubMed: 30566875 DOI: 10.1016/j.celrep.2018.11.086

Chen J et al., PBMC fixation and processing for Chromium single-cell RNA sequencing. J Transl Med. (2018)
PubMed: 30016977 DOI: 10.1186/s12967-018-1578-4

Guo J et al., The adult human testis transcriptional cell atlas. Cell Res. (2018)
PubMed: 30315278 DOI: 10.1038/s41422-018-0099-2

Kircher M et al., Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. (2012)
PubMed: 22021376 DOI: 10.1093/nar/gkr771

Barbe L et al., Toward a confocal subcellular atlas of the human proteome. Mol Cell Proteomics. (2008)
PubMed: 18029348 DOI: 10.1074/mcp.M700325-MCP200

Stadler C et al., A single fixation protocol for proteome-wide immunofluorescence localization studies. J Proteomics. (2010)
PubMed: 19896565 DOI: 10.1016/j.jprot.2009.10.012

Takahashi H et al., 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Nat Protoc. (2012)
PubMed: 22362160 DOI: 10.1038/nprot.2012.005

Lein ES et al., Genome-wide atlas of gene expression in the adult mouse brain. Nature. (2007)
PubMed: 17151600 DOI: 10.1038/nature05453

Uhlen M et al., A proposal for validation of antibodies. Nat Methods. (2016)
PubMed: 27595404 DOI: 10.1038/nmeth.3995

Stadler C et al., Systematic validation of antibody binding and protein subcellular localization using siRNA and confocal microscopy. J Proteomics. (2012)
PubMed: 22361696 DOI: 10.1016/j.jprot.2012.01.030

Poser I et al., BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals. Nat Methods. (2008)
PubMed: 18391959 DOI: 10.1038/nmeth.1199

Skogs M et al., Antibody Validation in Bioimaging Applications Based on Endogenous Expression of Tagged Proteins. J Proteome Res. (2017)
PubMed: 27723985 DOI: 10.1021/acs.jproteome.6b00821

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