Control of heterochromatin localization and silencing by the nuclear membrane protein Lem2

Abstract

Transcriptionally silent chromatin localizes to the nuclear periphery, which provides a special microenvironment for gene repression. A variety of nuclear membrane proteins interact with repressed chromatin, yet the functional role of these interactions remains poorly understood. Here, we show that, in Schizosaccharomyces pombe, the nuclear membrane protein Lem2 associates with chromatin and mediates silencing and heterochromatin localization. Unexpectedly, we found that these functions can be separated and assigned to different structural domains within Lem2, excluding a simple tethering mechanism. Chromatin association and tethering of centromeres to the periphery are mediated by the N-terminal LEM (LAP2-Emerin-MAN1) domain of Lem2, whereas telomere anchoring and heterochromatin silencing require exclusively its conserved C-terminal MSC (MAN1-Src1 C-terminal) domain. Particularly, silencing by Lem2 is epistatic with the Snf2/HDAC (histone deacetylase) repressor complex SHREC at telomeres, while its necessity can be bypassed by deleting Epe1, a JmjC protein with anti-silencing activity. Furthermore, we found that loss of Lem2 reduces heterochromatin association of SHREC, which is accompanied by increased binding of Epe1. This reveals a critical function of Lem2 in coordinating these antagonistic factors at heterochromatin. The distinct silencing and localization functions mediated by Lem2 suggest that these conserved LEM-containing proteins go beyond simple tethering to play active roles in perinuclear silencing.

Spatial organization of theSchizosaccharomyces pombegenome within the nucleus

“…Lem2 and Man1 share a MAN1/Src1C‐terminal (MSC) domain at their C‐terminal region, which is conserved in eukaryotic Man1 and Lem2 proteins (Mans et al ., ; Brachner and Foisner, ). The Lem2 MSC domain is required for telomere–NE association (Barrales et al ., ) while the role of the Man1 MSC domain in the telomere–NE association has not been reported. It has also been reported that homologues of Lem2 ( S. cerevisiae Heh1/Src1 and C. elegans LEM‐2) associate with telomeric regions (Grund et al ., ; Ikegami et al ., ), and that loss of Heh1 causes defects in the perinuclear positioning of telomeres and the silent rDNA loci in S. cerevisiae (Mekhail et al ., ; Chan et al ., ).…”

“…A conserved HEH/LEM domain INM protein Lem2, which localizes at the nuclear periphery and the SPB (King et al ., ; Hiraoka et al ., ; Gonzalez et al ., ), plays a role similar to Csi1 in stabilizing minichromosomes: lem2 mutant cells show an increased loss of minichromosomes (Tange et al ., ). Despite similar phenotypes of the mutant cells, the roles of Lem2 and Csi1 in centromere–NE association are independent of one another (Barrales et al ., ; Tange et al ., ). Interestingly, loss of minichromosomes in the lem2 mutant is remarkable in a rich medium, suggesting that centromere defects can be changed by environmental conditions, in contrast to the csi1 mutant in which loss of minichromosomes is independent of rich or minimum medium (Tange et al ., ).…”

“…Recent studies indicated that Lem2 plays an important role in heterochromatin formation (Barrales et al ., ; Tange et al ., ). The outer centromeric region is characterized by heterochromatin mark histone H3 lysine 9 di‐methylation (H3K9me2) in S. pombe (Nakayama et al ., ; reviewed in Allshire and Ekwall, ).…”

“…The outer centromeric region is characterized by heterochromatin mark histone H3 lysine 9 di‐methylation (H3K9me2) in S. pombe (Nakayama et al ., ; reviewed in Allshire and Ekwall, ). The level of H3K9me2 at the outer centromere is moderately reduced in the lem2 mutant (Barrales et al ., ; Tange et al ., ). Consistent with this result, deletion of the lem2 gene causes unusual gene expression from outer centromeres (Barrales et al ., ).…”

The 19S proteasome is directly involved in the regulation of heterochromatin spreading in fission yeast

“…Because the proteasome is enriched in NM (33) and both the proteasome and the centromere are localized at the inner nuclear membrane (NM) in fission yeast (53,54), it could be the same nuclear compartment that accounts for the high enrichment of the proteasome at the centromere. In fact, NM proteins are reportedly involved in both regulating heterochromatin and anchoring the proteasome to the NM (55,56). Thus, it may be plausible that NM proteins are involved in recruiting the proteasome to the centromere.…”