Networking in the nucleus: a spotlight on LEM-domain proteins
Introduction
The nuclear lamina is an extensive protein network that lies underneath the inner membrane of the nuclear envelope. This network establishes mechanical support for the nucleus and provides a platform for protein interactions that contribute to gene regulation, DNA replication and genome stability [1, 2, 3]. The major constituents of the nuclear lamina are the A-type and B-type lamins, which scaffold potentially hundreds of proteins [4, 5•] [Schirmer and Worman, this issue] including proteins in the inner nuclear membrane. Multiple human diseases are caused by loss of individual nuclear lamina proteins, highlighting the importance of this network.
The LAP2-emerin-MAN1-domain (LEM-D) protein family has prominent roles within the nuclear lamina. The defining feature of this family is the ∼40 amino acid domain that binds Barrier-to-Autointegration Factor (BAF or BANF1), a metazoan histone-binding and sequence-independent DNA-binding protein [6, 7]. The LEM-D shares sequence similarity with domains that bind DNA including the SAP [SAF/Acinus/PIAS] domain and HeH [helix-extension-helix] domain (reviewed [8, 9]). Indeed, LAP2 carries both a LEM-D and a LEM-like domain that is structurally LEM-related but directly binds DNA [7]. Interestingly, inner nuclear membrane proteins with LEM-related domains are found in unicellular organisms, such as yeast, that lack BAF and lamins. These observations suggest that the LEM-D evolved from an ancestral DNA binding protein involved in bridging chromatin to the nuclear periphery [10•].
Section snippets
Complexity of the LEM-D protein family
LEM-D proteins fall into three groups based on membrane topology and other features (Table 1 and Figure 1 [10•, 11, 12]). Group I LEM-D proteins have amino-terminal LEM-Ds and large nucleoplasmic domains; some are not membrane proteins but most have a single transmembrane domain at their carboxyl-terminus. Representatives of this group include LAP2 and emerin. Group II LEM-D proteins carry amino-terminal LEM-Ds, two internal transmembrane domains, and carboxyl-terminal winged-helix ‘MSC’
Analysis of emerin reveals a dynamic LEM-D protein network at the nuclear lamina
LEM-D proteins interact with proteins of diverse functions. This is best illustrated by studies of emerin [19], a LEM-D protein that interacts with proteins involved in mechanotransduction, cellular architecture, transcriptional regulation, and chromatin tethering [20•]. Emerin also displays self-associations, involving interactions between the amino terminal LEM-D and internal residues that are predicted to form an emerin–emerin network within the nuclear lamina ([21••]; Figure 2). The
LEM-D proteins bridge chromatin at the periphery
LEM-D proteins contribute to the tethering of genomic regions to the nuclear periphery. In yeast, LEM-related proteins recruit repressive subtelomeric domains and ribosomal DNA repeats to the nuclear periphery [26, 27, 28]. In metazoans, LEM-D proteins associate with regions of high repeat density and low gene number that are enriched in repressive epigenetic marks [29•, 30, 31], all features matching those defined for lamin associated domains (LADs) of chromatin [31]. Strikingly, direct
Loss of LEM-D proteins causes tissue-restricted phenotypes
The first LEM-D gene linked to human disease was emerin (STA renamed EMD), the gene responsible for X-linked recessive Emery–Dreifuss muscular dystrophy (EDMD) [39]. Hallmark features of EDMD begin in early childhood with joint contractures and slowly progressive weakness of humeroperoneal muscles, followed by cardiac conductance defects and dilated cardiomyopathy in adulthood. These characteristics suggest emerin is dispensable for muscle development, but needed for muscle maintenance. EDMD is
LEM-D proteins regulate transcription factor function
Altered tissue homeostasis in LEM-D mutants is associated with mis-regulation of signaling pathways (Figure 3). Multiple LEM-D proteins directly interact with signaling effectors [9, 55, 56•]. For example, emerin directly binds and regulates the flux of β-catenin into the nucleus (Figure 3a [57]). In the absence of emerin, levels of nuclear β-catenin increase, resulting in up-regulation of target genes [55, 57]. Similarly, emerin regulates nuclear envelope localization of other transcription
Functional redundancy restricts the impact of individual LEM-D protein loss
LEM-D proteins have overlapping functions. This conclusion is supported by two lines of evidence. First, LEM-D mutants share tissue-specific defects. For example, LAP2α-deficient and emerin-deficient muscles both have higher numbers of satellite stem cells and altered myoblast differentiation associated with mis-regulation of the Rb1/E2F pathway [47, 54]. Second, loss of two LEM-D proteins causes phenotypes significantly more severe than loss of single LEM-D proteins [44, 45, 52••, 60••, 69••].
Concluding remarks
Genetic, cellular and biochemical results from multiple organisms have significantly advanced our understanding of the complex LEM-D protein family. These studies reveal that LEM-D proteins have both shared and unique functions in tissue homeostasis and the maintenance of progenitor cell populations. Interactions with chromatin and signaling effectors predict that LEM-D proteins function as hubs that integrate external signals, which ultimately contribute to the regulation of gene expression.
References and recommended reading
Papers of particular interest, published within the period of review, have been highlighted as:
• of special interest
•• of outstanding interest
Acknowledgements
The authors thank members of the Geyer lab for critical reading of this manuscript. Research in the Geyer lab is supported by National Institutes of Health R01 Grant (GM087341) to P Geyer. AAS is an HHMI Fellow of the Damon Runyon Cancer Research Foundation (DRG-2185-14).
References (74)
- et al.
Broken nuclei — lamins, nuclear mechanics, and disease
Trends Cell Biol
(2014) - et al.
Nuclear lamina at the crossroads of the cytoplasm and nucleus
J Struct Biol
(2012) - et al.
The nuclear membrane proteome: extending the envelope
Trends Biochem Sci
(2005) The carboxyl-terminal nucleoplasmic region of MAN1 exhibits a DNA binding winged helix domain
J Biol Chem
(2006)The endonuclease Ankle1 requires its LEM and GIY-YIG motifs for DNA cleavage in vivo
J Cell Sci
(2012)The molecular basis of emerin–emerin and emerin–BAF interactions
J Cell Sci
(2014)- et al.
Barrier-to-autointegration factor influences specific histone modifications
Nucleus
(2011) Genome-wide analysis links emerin to neuromuscular junction activity in Caenorhabditis elegans
Genome Biol
(2014)- et al.
Nuclear mechanics and mechanotransduction in health and disease
Curr Biol
(2013) MAN1 and emerin have overlapping function(s) essential for chromosome segregation and cell division in Caenorhabditis elegans
Proc Natl Acad Sci U S A
(2003)