The Inner Nuclear Membrane Protein Lamin B Receptor Forms Distinct Microdomains and Links Epigenetically Marked Chromatin to the Nuclear Envelope

Abstract

Using heterochromatin-enriched fractions, we have detected specific binding of mononucleosomes to the N-terminal domain of the inner nuclear membrane protein lamin B receptor. Mass spectrometric analysis reveals that LBR-associated particles contain complex patterns of methylated/acetylated histones and are devoid of "euchromatic" epigenetic marks. LBR binds heterochromatin as a higher oligomer and forms distinct nuclear envelope microdomains in vivo. The organization of these membrane assemblies is affected significantly in heterozygous ic (ichthyosis) mutants, resulting in a variety of structural abnormalities and nuclear defects.A significant proportion of heterochromatin is localized in the periphery of the cell nucleus and maintains a close spatial association with the inner nuclear membrane (1-5). This spatial association reflects a multiplicity of interactions between chromatin components and integral or peripheral proteins of the nuclear envelope (NE) 1 (6, 7).Because chromatin is extensively and differentially modified (8, 9), it is tempting to think that certain epigenetic marks or factors associated with histone modifying enzymes provide binding sites for NE proteins. However, it is equally possible that transcriptionally active, noncondensed chromatin is subjected to silencing and "heterochromatinization" upon contact to the NE. Both of these hypotheses receive experimental support: chromatin that is silenced through binding to SIRs can tether itself to the NE (10), whereas targeting of marker genes to the inner nuclear membrane suppresses their expression (11).One of the factors that have been implicated in chromatin anchorage to the NE is the lamin B receptor (12). LBR is a polytopic inner nuclear membrane protein consisting of a long, N-terminal domain, seven or eight hydrophobic transmembrane regions, and a C-terminal tail (13). The N-terminal part of the molecule protrudes to the nucleoplasm and contains multiple serine-arginine motifs that are phosphorylated by the SRPK1 and the cdc2 kinases (14, 15); the hydrophobic region represents, instead, a (functional) form of sterol reductase and is involved in cholesterol metabolism (16).Immunodepletion of LBR from detergent-solubilized NE vesicles results in proteoliposomes with a diminished ability to bind chromatin. Furthermore, direct binding of electrophoretically purified LBR to metaphase chromosomes can be demonstrated by in vitro assays (17). Corroborating these observations, anti-LBR antibodies block nuclear assembly in sea urchin egg extracts (18), whereas direct (19) and indirect (20) interactions with heterochromatin protein 1 (HP1) have been claimed in the literature.Two critical parameters in LBR-chromatin interactions are the physical state of LBR and the molecular features of LBRassociated chromatin. To address these issues, we have isolated fragments of peripheral heterochromatin attached to the inner nuclear membrane. These subcellular fractions were utilized to affinity select mononucleosomes that associate with LBR and investigate L...

Histone H3 variants and their potential role in indexing mammalian genomes: The “H3 barcode hypothesis”

“…2C). LBR has been shown to bind distinct heterochromatin-enriched fractions (39). Moreover, Makatsori and coworkers (23) found that LBR-associated purified fractions contain histone H3 enriched in PTMs associated with transcriptional silencing similar to those that we have observed on H3.1.…”

Granulocytic nuclear differentiation of lamin B receptor–deficient mouse EPRO cells

“…This association could be promoted indirectly by LBR-HP1 interactions [49] and/or by direct binding between LBR and methyl lysine-modified nucleosomes. [50] In parallel to the repositioning of these regions, the apparent number of pericentric "spots" per nucleus (confocal slice) declines slightly and their size increases. For example, the percentage estimate of spots (>1.5 µm diameter) per nucleus in ATRA-treated cells is: +/+, 1%; +/ic, 2%; ic/ic, 32%.…”

Dynamics and interplay of nuclear architecture, genome organization, and gene expression

“…In addition, Man1 can interact with Smads and ␤-catenin, antagonizing signaling by TGF␤ and Wnt proteins, respectively (Pan et al 2005;Markiewicz et al 2006). Moreover, the lamin B receptor (LBR) has been implicated in heterochromatin regulation via interaction with HP1, which binds to histone H3K9-trimethyl marks (Makatsori et al 2001;Polioudaki et al 2001). Finally, the SUN-Nesprin complex links the perinuclear skeleton with the cytoplasmic filament system (for detailed review, see Schirmer and Foisner 2007).…”