The inner nuclear membrane protein Lem2 coordinates RNA degradation at the nuclear periphery

Abstract

Transcriptionally silent chromatin often localizes to the nuclear periphery. However, whether the nuclear envelope (NE) is a site for post-transcriptional gene repression is not well understood. Here we demonstrate that Schizosaccharomycespombe Lem2, an NE protein, regulates nuclear-exosome-mediated RNA degradation. Lem2 deletion causes accumulation of RNA precursors and meiotic transcripts and de-localization of an engineered exosome substrate from the nuclear periphery. Lem2 does not directly bind RNA but instead interacts with the exosome-targeting MTREC complex and its human homolog PAXT to promote RNA recruitment. This pathway acts largely independently of nuclear bodies where exosome factors assemble. Nutrient availability modulates Lem2 regulation of meiotic transcripts, implying that this pathway is environmentally responsive. Our work reveals that multiple spatially distinct degradation pathways exist. Among these, Lem2 coordinates RNA surveillance of meiotic transcripts and non-coding RNAs by recruiting exosome co-factors to the nuclear periphery.

SUMOylation regulates Lem2 function in centromere clustering and silencing

“…The mechanism by which Lem2 promotes heterochromatic silencing remains opaque; although there is evidence that Lem2 influences the balance of recruitment of opposing chromatin factors including the HDAC repressor complex SHREC and anti-silencing Epe1, no physical association of Lem2 with these factors has been detected (Banday et al, 2016; Barrales et al, 2016). Interestingly, very recent evidence indicates that Lem2 can also influence post-transcriptional silencing by interacting with RNA surveillance factor Red1 to regulate RNA degradation by the nuclear exosome (Martin Caballero et al, 2022). An intriguing possibility is that this post-transcriptional mechanism might contribute to Lem2-mediated silencing of the centromeric imr:ura4+ reporter; in future it will be interesting to explore whether Lem2 interaction with Red1 is affected by SUMOylation.…”

“…Mammalian Lem2 is critical for embryonic development (Tapia et al, 2015), and mutations in LEM2 have been linked to several human diseases including juvenile cataracts, arrhythmic cardiomyopathy, and a novel nuclear envelopathy with progeria-like symptoms (Boone et al, 2016; Abdelfatah et al, 2019; Marbach et al, 2019), highlighting the potential clinical importance of understanding the regulation of Lem2 mediated pathways. In S. pombe , it has previously been suggested that post-translational modification could account for observed differences in Lem2 function in different nutritional conditions (Martin Caballero et al, 2022); it is an intriguing possibility that changes in Lem2 SUMOylation status may mediate the response to environmental cues.…”

“…Interactions with many different partner proteins are thought to enable Lem2 to localise to distinct subcellular domains and contribute to different pathways. Interestingly, evidence indicates that several of these interactions occur through the same (C-terminal MSC) domain of Lem2 (Gu et al, 2017; Pieper et al, 2020; Martin Caballero et al, 2022), yet how competing interactions are regulated to coordinate distinct functions of Lem2 remains largely unknown. The data presented here suggests that hyper-SUMOylation both impairs Lem2 function in centromere silencing, and simultaneously enhances its function in centromere clustering.…”

“…In addition, we show that Lem2 is a key SUMO substrate in the context of both centromere silencing and clustering, and present a novel model whereby SUMOylation may play an important role in modulating the balance of Lem2 interactions with partner proteins to coordinate its diverse functions. It has previously been suggested that post-translational modification could account for observed differences in Lem2 function in different nutritional conditions (Martin Caballero et al, 2022); it is an intriguing possibility that changes in Lem2 SUMOylation status may mediate the response to environmental cues.…”

“…Interestingly, this role of Lem2 in silencing appears to be independent of its role in tethering centromeres at the nuclear periphery: while the N-terminal HeH/LEM domain of Lem2 associates with centromeric chromatin and is required for chromatin tethering (Barrales et al, 2016; Tange et al, 2016), the C-terminal Man1-Src1p-C-terminal (MSC) domain of Lem2 is sufficient to mediate centromere silencing, possibly via recruitment of repressive chromatin factors (Banday et al, 2016; Barrales et al, 2016). A growing number of partner proteins have been implicated in contributing to the diverse functions of Lem2; for example, binding to the inner nuclear membrane protein Bqt4 helps mobilise Lem2 around the nuclear envelope and mediates telomere-related functions (Ebrahimi et al, 2018; Hirano et al, 2018), whilst interaction of Lem2 with the RNA surveillance factor Red1 was recently found to contribute to regulation of meiotic transcripts (Martin Caballero et al, 2022). However, how Lem2 is differentially targeted for roles in these varied processes is yet to be fully elucidated.…”