Title: Phosphorylated Lamins in Euchromatin: New Clues to Progeria
Abstract: Lamin proteins not only form the nuclear lamina, but some are also found in the nuclear interior. In this issue of Developmental Cell, Ikegami et al. describe that phosphorylated Lamin C in the nuclear interior interacts with enhancer-like elements and link this to deregulated transcription in progeria. Lamin proteins not only form the nuclear lamina, but some are also found in the nuclear interior. In this issue of Developmental Cell, Ikegami et al. describe that phosphorylated Lamin C in the nuclear interior interacts with enhancer-like elements and link this to deregulated transcription in progeria. The inner nuclear membrane of metazoan cells is lined by the nuclear lamina (NL), a meshwork that primarily consists of filament-forming proteins named lamins. Two types of lamins exist: B-type lamins are almost exclusively located at the NL, and A-type lamins are found both at the NL and in the nuclear interior. In mammals, A-type lamins consist of lamins A and C, which are splice variants encoded by one gene. At the NL, all lamins are in close contact with long stretches of chromatin termed Lamina-associated domains (LADs). The thousands of genes that are embedded in LADs are mostly inactive, and the contacts with the NL may contribute to their repression (van Steensel and Belmont, 2017van Steensel B. Belmont A.S. Lamina-Associated Domains: Links with Chromosome Architecture, Heterochromatin, and Gene Repression.Cell. 2017; 169: 780-791Abstract Full Text Full Text PDF PubMed Scopus (502) Google Scholar). While much progress has been made in understanding the properties of lamins at the NL, the presence of A-type lamins in the nuclear interior has remained somewhat of a puzzle (Naetar et al., 2017Naetar N. Ferraioli S. Foisner R. Lamins in the nuclear interior - life outside the lamina.J. Cell Sci. 2017; 130: 2087-2096Crossref PubMed Scopus (101) Google Scholar). What might their function be, and how are they regulated? In this issue of Developmental Cell, Ikegami et al., 2020Ikegami K. Secchia S. Almakki O. Lieb J.D. Moskowitz I.P. Phosphorylated Lamin A/C in the nuclear interior binds active enhancers associated with abnormal transcription in progeria.Dev. Cell. 2020; 52 (this issue): 699-713Abstract Full Text Full Text PDF PubMed Scopus (39) Google Scholar report that a phosphorylated form of Lamin A/C is located in the nuclear interior and specifically interacts with DNA elements that resemble enhancers (Figure 1). This raises the interesting possibility that a pool of A-type lamins regulate gene expression in the nuclear interior, away from LADs and the NL. A-type lamins in the nuclear interior do not form long filaments, and some studies suggested they may interact with chromatin (Naetar et al., 2017Naetar N. Ferraioli S. Foisner R. Lamins in the nuclear interior - life outside the lamina.J. Cell Sci. 2017; 130: 2087-2096Crossref PubMed Scopus (101) Google Scholar). Previous work had indicated that the abundance of this nucleoplasmic pool is controlled by phosphorylation (Kochin et al., 2014Kochin V. Shimi T. Torvaldson E. Adam S.A. Goldman A. Pack C.G. Melo-Cardenas J. Imanishi S.Y. Goldman R.D. Eriksson J.E. Interphase phosphorylation of lamin A.J. Cell Sci. 2014; 127: 2683-2696Crossref PubMed Scopus (105) Google Scholar), which is also known to cause lamin depolymerization during mitosis (Naetar et al., 2017Naetar N. Ferraioli S. Foisner R. Lamins in the nuclear interior - life outside the lamina.J. Cell Sci. 2017; 130: 2087-2096Crossref PubMed Scopus (101) Google Scholar). Importantly, Ikegami and colleagues identified an antibody that specifically recognizes one of the major phosphorylated forms of Lamin A/C that is located in the nuclear interior of interphase cells (Ikegami et al., 2020Ikegami K. Secchia S. Almakki O. Lieb J.D. Moskowitz I.P. Phosphorylated Lamin A/C in the nuclear interior binds active enhancers associated with abnormal transcription in progeria.Dev. Cell. 2020; 52 (this issue): 699-713Abstract Full Text Full Text PDF PubMed Scopus (39) Google Scholar). This provided a unique tool to study the internal pool of Lamin A/C in detail. The key experiments conducted by Ikegami et al., 2020Ikegami K. Secchia S. Almakki O. Lieb J.D. Moskowitz I.P. Phosphorylated Lamin A/C in the nuclear interior binds active enhancers associated with abnormal transcription in progeria.Dev. Cell. 2020; 52 (this issue): 699-713Abstract Full Text Full Text PDF PubMed Scopus (39) Google Scholar consisted of chromatin immunoprecipitation followed by sequencing (ChIP-seq) to map the genome-wide binding pattern of the phosphorylated Lamin A/C. This revealed that the phosphorylated variant associates with thousands of short (∼1 kb) DNA elements that are located in the inter-LAD regions of the genome. Elegant complementation experiments using phospho-mimetic and phospho-deficient mutants established that it is primarily phosphorylated Lamin C, not Lamin A, that exhibits this binding pattern. Moreover, non-phosphorylated Lamin A and Lamin C did not associate with these elements but rather accumulated in LADs. The DNA elements that are preferentially occupied by phospho-Lamin C are generally characterized by highly accessible chromatin and presence of the histone mark H3K27ac, two features that are typically found at active enhancers. Although these features do not conclusively identify functional enhancers (Gasperini et al., 2020Gasperini M. Tome J.M. Shendure J. Towards a comprehensive catalogue of validated and target-linked human enhancers.Nat. Rev. Genet. 2020; (Published online January 27, 2020)https://doi.org/10.1038/s41576-019-0209-0Crossref PubMed Scopus (113) Google Scholar), the sequences occupied by phospho-Lamin C are also enriched for the binding motif of AP-1, a transcription factor that consists of two subunits, c-Fos and c-Jun. Indeed, c-Jun was found to bind to the majority of the phospho-Lamin C target sites. Thus, phosphorylated Lamin C associates with a set of putative enhancers and may work together with AP-1 to regulate nearby genes. The authors then focused on the connection between phospho-Lamin C and gene expression in fibroblasts from Hutchinson-Gilford Progeria Syndrome (HGPS) patients. This disease is caused by a heterozygous point mutation that produces an altered Lamin A isoform called progerin (Eriksson et al., 2003Eriksson M. Brown W.T. Gordon L.B. Glynn M.W. Singer J. Scott L. Erdos M.R. Robbins C.M. Moses T.Y. Berglund P. et al.Recurrent de novo point mutations in lamin A cause Hutchinson-Gilford progeria syndrome.Nature. 2003; 423: 293-298Crossref PubMed Scopus (1613) Google Scholar). In contrast to the wild-type protein, progerin is persistently localized to the nuclear periphery, leading to defects in nuclear architecture and changes in LAD-NL interactions (Goldman et al., 2004Goldman R.D. Shumaker D.K. Erdos M.R. Eriksson M. Goldman A.E. Gordon L.B. Gruenbaum Y. Khuon S. Mendez M. Varga R. Collins F.S. Accumulation of mutant lamin A causes progressive changes in nuclear architecture in Hutchinson-Gilford progeria syndrome.Proc. Natl. Acad. Sci. USA. 2004; 101: 8963-8968Crossref PubMed Scopus (820) Google Scholar, McCord et al., 2013McCord R.P. Nazario-Toole A. Zhang H. Chines P.S. Zhan Y. Erdos M.R. Collins F.S. Dekker J. Cao K. Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome.Genome Res. 2013; 23: 260-269Crossref PubMed Scopus (227) Google Scholar). Ikegami and colleagues found about one thousand genes to be differentially expressed in fibroblasts from HGPS patients compared to control cells (Ikegami et al., 2020Ikegami K. Secchia S. Almakki O. Lieb J.D. Moskowitz I.P. Phosphorylated Lamin A/C in the nuclear interior binds active enhancers associated with abnormal transcription in progeria.Dev. Cell. 2020; 52 (this issue): 699-713Abstract Full Text Full Text PDF PubMed Scopus (39) Google Scholar). The upregulated genes in HGPS cells are enriched in genes that have been linked to clinical phenotypes that are also observed in HGPS patients. Strikingly, the dysregulated genes are generally not located in LADs but rather in the inter-LAD regions where phosphorylated Lamin C binds. Furthermore, ChIP-seq in HGPS cells revealed partially shifted binding patterns of phospho-Lamin C and c-Jun, coinciding with changes in accessibility and H3K27ac levels. New binding sites for phospho-Lamin C and c-Jun in HGPS cells were found to often occur in proximity to upregulated genes. The authors therefore propose that the progeria phenotype could be in part due to changes in the binding pattern of phospho-Lamin C, triggering an aberrant transcriptional program. Together, these data provide an exciting new view on the internal pool of phosphorylated Lamin C, suggesting a model in which this pool regulates a set of enhancer-like elements located outside of LADs. It should be noted, however, that the current evidence for such a model is still correlative rather than causal. Whether the internal pool of Lamin C really drives gene regulation near its binding sites might be tested by selective manipulation of the levels of phosphorylated Lamin C (for example, by expression of the phospho-mimetic or phospho-deficient mutants) followed by gene expression analysis and measurements of enhancer activity. Several kinases have been implicated in Lamin A/C phosphorylation, and it will be interesting to unravel their contribution to the targeting of Lamin C to its internal binding sites. The link with AP-1 may be another entry point to further mechanistic dissection. Does AP-1 help to recruit phosphorylated Lamin C to its binding sites or vice versa? An earlier study found that Lamin A/C can interact with c-Fos and sequester it at the NL, while phosphorylation of c-Fos by MAPK kinases leads to release of c-Fos from the NL (González et al., 2008González J.M. Navarro-Puche A. Casar B. Crespo P. Andrés V. Fast regulation of AP-1 activity through interaction of lamin A/C, ERK1/2, and c-Fos at the nuclear envelope.J. Cell Biol. 2008; 183: 653-666Crossref PubMed Scopus (128) Google Scholar). MAPK kinases have also been linked to the phosphorylation of lamins (Peter et al., 1992Peter M. Sanghera J.S. Pelech S.L. Nigg E.A. Mitogen-activated protein kinases phosphorylate nuclear lamins and display sequence specificity overlapping that of mitotic protein kinase p34cdc2.Eur. J. Biochem. 1992; 205: 287-294Crossref PubMed Scopus (90) Google Scholar), raising the interesting possibility that they coordinately control the availability of both c-Fos and Lamin C for binding to the enhancer-like elements (Figure 1). Finally, the link with HGPS warrants further exploration. One conundrum is that it is primarily phosphorylated Lamin C that associates with the putative enhancers. Yet, progerin is a mutant form of Lamin A, not Lamin C; it is not detectably phosphorylated; and it is primarily located at the NL. How might progerin alter the genomic binding pattern of phospho-Lamin C in the interior? Also, it will be particularly relevant to understand the role of the AP-1 complex in regulating the transcriptional program in HGPS. This could open new strategies in the treatment of progeria patients, for example, by drugs that modulate AP-1 activity. Clearly, the report by Ikegami et al., 2020Ikegami K. Secchia S. Almakki O. Lieb J.D. Moskowitz I.P. Phosphorylated Lamin A/C in the nuclear interior binds active enhancers associated with abnormal transcription in progeria.Dev. Cell. 2020; 52 (this issue): 699-713Abstract Full Text Full Text PDF PubMed Scopus (39) Google Scholar enhances our understanding, but there are still many questions to solve. Phosphorylated Lamin A/C in the Nuclear Interior Binds Active Enhancers Associated with Abnormal Transcription in ProgeriaIkegami et al.Developmental CellMarch 23, 2020In BriefNuclear lamins bind heterochromatin domains at the nuclear periphery. Ikegami et al. now show that phosphorylated form of nuclear lamins bind to active enhancers in euchromatin in the nuclear interior. They provide evidence suggesting that disruption of phosphorylated lamin's function at enhancers contributes to the pathogenesis of progeria. Full-Text PDF Open Archive