Sumoylation at chromatin governs coordinated repression of a transcriptional program essential for cell growth and proliferation

Abstract

Despite numerous studies on specific sumoylated transcriptional regulators, the global role of SUMO on chromatin in relation to transcription regulation remains largely unknown. Here, we determined the genome-wide localization of SUMO1 and SUMO2/3, as well as of UBC9 (encoded by UBE2I ) and PIASY (encoded by PIAS4), two markers for active sumoylation, along with Pol II and histone marks in proliferating versus senescent human fibroblasts together with gene expression profiling. We found that, whereas SUMO alone is widely distributed over the genome with strong association at active promoters, active sumoylation occurs most prominently at promoters of histone and protein biogenesis genes, as well as Pol I rRNAs and Pol III tRNAs. Remarkably, these four classes of genes are up-regulated by inhibition of sumoylation, indicating that SUMO normally acts to restrain their expression. In line with this finding, sumoylationdeficient cells show an increase in both cell size and global protein levels. Strikingly, we found that in senescent cells, the SUMO machinery is selectively retained at histone and tRNA gene clusters, whereas it is massively released from all other unique chromatin regions. These data, which reveal the highly dynamic nature of the SUMO landscape, suggest that maintenance of a repressive environment at histone and tRNA loci is a hallmark of the senescent state. The approach taken in our study thus permitted the identification of a common biological output and uncovered hitherto unknown functions for active sumoylation at chromatin as a key mechanism that, in dynamically marking chromatin by a simple modifier, orchestrates concerted transcriptional regulation of a network of genes essential for cell growth and proliferation.[Supplemental material is available for this article.]The post-translational modification by SUMO is an essential regulatory mechanism of protein function involved in most challenges faced by eukaryotic cells (Hay 2005;Geiss-Friedlander and Melchior 2007;Hochstrasser 2009). Higher eukaryotes have three SUMO paralogs, SUMO1, SUMO2, and SUMO3, with SUMO2 and SUMO3 collectively termed SUMO2/3 because of structural and functional differences from SUMO1. Similarly to ubiquitin, SUMO is covalently conjugated to its targets via a three-step process, including unique E1 (SAE1/UBA2), E2 (UBC9 encoded by UBE2I ), and a series of E3 enzymes including the five PIAS members, CBX4, and RANBP2. The SUMO proteases (SENPs) then remove SUMO from its substrates (Yeh 2009).Investigation of numerous sumoylated transcription factors and chromatin-associated proteins reveals that, in most cases, sumoylation is associated with transcriptional repression (Ouyang and Gill 2009). Moreover, important roles for sumoylation were underscored in heterochromatin configuration (Shin et al. 2005;Maison et al. 2011), and sumoylation of core histones was shown to negatively regulate transcription in yeast and human cells (Shiio and Eisenman 2003;Nathan et al. 2006). However a growing body of evidence also links sumoyla...

Sumoylation of Rap1 mediates the recruitment of TFIID to promote transcription of ribosomal protein genes

“…The distribution of Sumo strongly resembles the genomic distribution of Sumo in mammalian cells (Neyret-Kahn et al 2013). There have been conflicting reports as to how Sumo affects transcription at these genes in mammals; one study reported that Sumo promotes their transcription (Liu et al 2012), whereas another study found that Sumo is inhibitory (Neyret-Kahn et al 2013). The reason for these differences is unclear, but could be technical (Neyret-Kahn et al 2013).…”

“…There have been conflicting reports as to how Sumo affects transcription at these genes in mammals; one study reported that Sumo promotes their transcription (Liu et al 2012), whereas another study found that Sumo is inhibitory (Neyret-Kahn et al 2013). The reason for these differences is unclear, but could be technical (Neyret-Kahn et al 2013). These two studies did not identify the Sumo target at these genes, making it difficult to interpret their different findings.…”

SUMOylation-Mediated Regulation of Cell Cycle Progression and Cancer

“…Similarly, knockdowns of Ubc9 or the SUMO E1 subunit SAE2 in human cells severely reduced the cell proliferation rate but did not arrest cells in a specific cell cycle stage [22,23]. This could be explained by SUMO having essential functions during all cell cycle phases in mammalian cells, not just during the G2/M transition.…”

Analysis of Small Ubiquitin-Like Modifier (SUMO) Targets Reflects the Essential Nature of Protein SUMOylation and Provides Insight to Elucidate the Role of SUMO in Plant Development

“…Chromatin immunoprecipitation studies in yeast revealed the association of SUMO and the SUMO E2 with constitutively active and inducible promoters (Rosonina et al, 2010). Additionally, a recent elegant and comprehensive study was performed in proliferating and senescent human fibroblasts using chromatin immunoprecipitation to identify genome-wide association sites of several SUMO isoforms, SUMO machinery enzymes, different histone and chromatin marks, and RNA polymerase II (Pol II) and combined this with genome-wide expression profiling (Neyret-Kahn et al, 2013). This study revealed the association of either SUMO1 or SUMO2 with the transcriptional start sites (TSSs) of approximately 7,700 genes, and of these genes, 67% were significantly expressed.…”