Functional characterization of NSE4A subunit of SMC5/6 complex in Arabidopsis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA450796 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7028510.fastq.gz | Fastqsanger.gz | |||
| SRR7028511.fastq.gz | Fastqsanger.gz | |||
| SRR7028512.fastq.gz | Fastqsanger.gz | |||
| SRR7028513.fastq.gz | Fastqsanger.gz | |||
| SRR7028514.fastq.gz | Fastqsanger.gz |
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Project description:The control of genome integrity throughout cellular generations is critical for plant development and the correct transmission of genetic information to the progeny. A key factor involved in this process is STRUCTURAL MAINTAINANCE OF CHROMOSOME 5/6 (SMC5/6) complex, related to cohesin and condensin complexes. Here, we analyzed mRNA abundance changes in the partial loss of function mutant of NON-SMC ELEMENT 4A (nse4a-2 mutant allele), a subunit of SMC5/6 complex, in Arabidopsis.
2018-06-06 | GSE113310 | GEO
Project description:Silencing of nuclear DNA is an essential feature of the innate immune response to invading pathogens. Early in lentiviral infection, unintegrated viral cDNA accumulates in the nucleus, yet remains poorly expressed. In HIV-1-like lentiviruses, the Vpr accessory protein enhances unintegrated viral DNA expression, suggesting Vpr antagonises cellular restriction. We previously showed how Vpr remodels the host proteome, identifying multiple cellular targets. We now screen these using a targeted CRISPR-Cas9 library, identifying SMC5-SMC6 complex localization factor 2 (SLF2) as the Vpr target responsible for silencing unintegrated HIV-1. SLF2 recruits the SMC5/6 complex to unintegrated lentiviruses, and depletion of SLF2, or the SMC5/6 complex, increases viral expression. Using ATAC-seq, we show that Vpr-mediated SLF2 depletion increases chromatin accessibility of unintegrated virus, suggesting the SMC5/6 complex compacts viral chromatin to silence gene expression. This work implicates the SMC5/6 complex in nuclear immunosurveillance of extrachromosomal DNA and defines an evolutionarily conserved antagonism by Vpr.
2021-03-01 | GSE156630 | GEO
Project description:Structural Maintenance of Chromosomes (SMC) complexes - cohesin, condensin and SMC5/6 - are important for many aspects of the chromosomal organization. These complexes are composed of Smc and non-Smc element (Nse) subunits. The Nse1 subunit of SMC5/6 contains a variant RING domain, characteristic of ubiquitin ligases. Human NSE1 has been shown to possess ubiquitin ligase activity in vitro; however, other studies were unable to show such activity. Here, we confirm Nse1 ubiquitin-ligase activity in vitro using purified Schizosaccharomyces pombe proteins. We demonstrate that the Nse1 ligase activity is stimulated by Nse3 and Nse4, it specifically utilizes Ubc13/Mms2 E2 enzyme and Nse1 interacts directly with ubiquitin. We identify Nse1 mutation (R188E) that specifically disrupts its E3 activity, and show that the Nse1-dependent ubiquitination is particularly important under replication stress. Moreover, we identify Nse4 (lysine K181) as the first known SMC5/6-associated Nse1 substrate. Interestingly, abolition of Nse4 modification at K181 leads to suppression of DNA-damage sensitivity of other SMC5/6 mutants. Altogether, this study brings new evidence for Nse1 ubiquitin ligase activity, significantly advancing our under-standing of this enigmatic SMC5/6 function.
2022-01-24 | PXD029573 | Pride
Project description:The essential functions of the conserved Smc5/6 complex remain elusive. To uncover its roles in genome maintenance, we established Saccharomyces cerevisiae cell cycle-regulated alleles that enable restriction of Smc5/6 components to S or G2/M. Unexpectedly, the essential functions of Smc5/6 segregated fully and selectively to G2/M. Genetic screens that became possible with generated alleles identified processes that crucially rely on Smc5/6 specifically in G2/M: metabolism of DNA recombination structures triggered by endogenous replication stress, and replication through natural pausing sites located in late-replicating regions. In the first process, Smc5/6 modulates remodeling of recombination intermediates, cooperating with dissolution activities. In the second, Smc5/6 prevents chromosome fragility and toxic recombination instigated by prolonged pausing and the fork protection complex, Tof1-Csm3. Our results thus dissect Smc5/6 essential roles, and reveal that combined defects in DNA damage tolerance and pausing site-replication cause recombination-mediated DNA lesions, which we propose to drive developmental and cancer-prone disorders.
2015-11-19 | GSE72241 | GEO
Project description:The essential functions of the conserved Smc5/6 complex remain elusive. To uncover its roles in genome maintenance, we established Saccharomyces cerevisiae cell cycle-regulated alleles that enable restriction of Smc5/6 components to S or G2/M. Unexpectedly, the essential functions of Smc5/6 segregated fully and selectively to G2/M. Genetic screens that became possible with generated alleles identified processes that crucially rely on Smc5/6 specifically in G2/M: metabolism of DNA recombination structures triggered by endogenous replication stress, and replication through natural pausing sites located in late-replicating regions. In the first process, Smc5/6 modulates remodeling of recombination intermediates, cooperating with dissolution activities. In the second, Smc5/6 prevents chromosome fragility and toxic recombination instigated by prolonged pausing and the fork protection complex, Tof1-Csm3. Our results thus dissect Smc5/6 essential roles, and reveal that combined defects in DNA damage tolerance and pausing site-replication cause recombination-mediated DNA lesions, which we propose to drive developmental and cancer-prone disorders. BrdU incorporation profiles by ssDNA-BrdU IP on chip have been generated as described (Katou et al., 2003). Protein binding profiles by ChIP-chip analysis were generated as described (Bermejo et al., 2009). Labeled probes were hybridized to Affymetrix S.cerevisiae Tiling 1.0 (P/N 900645) arrays and processed with TAS software.
2015-11-19 | E-GEOD-72241 | biostudies-arrayexpress
Project description:Beyond its essential roles in ensuring faithful chromosome segregation and genomic stability, the human Smc5/6 complex acts as an antiviral factor. It binds to and impedes the transcription of extrachromosomal DNA templates; an ability which is lost upon chromosomal DNA integration. How the complex distinguishes among different DNA templates is unknown. Here we show that, in human cells, Smc5/6 preferentially binds to circular rather than linear extrachromosomal DNA. We further show that this binding is unlikely due to differences in the chromatin composition. Instead, the transcriptional process, per se, and more specifically the accumulation of DNA secondary structures known to be substrates for topoisomerases, is responsible for Smc5/6 recruitment. Those findings, in conjunction with our genome-wide Smc5/6 binding analysis showing that Smc5/6 localises at few but highly transcribe chromosome loci, reveal a previously unforeseen role of Smc5/6 in DNA topology management during transcription.
2024-06-10 | GSE231328 | GEO
Project description:During meiosis, Structural Maintenance of Chromosome (SMC) complexes underpin two fundamental features of meiosis: homologous recombination and chromosome segregation. While meiotic functions of the cohesin and condensin complexes have been delineated, the role of the third SMC complex, Smc5/6, remains enigmatic. Diminished Smc5/6 function causes severe defects in nuclear division, but the underlying causes of these defects remain unclear. Here we identify specific, essential meiotic functions for the Smc5/6 complex in homologous recombination and regulation of cohesin. We show that Smc5/6 is enriched at centromeres and cohesin-association sites where it regulates sister-chromatid cohesion and the timely removal of cohesin from chromosomal arms, respectively. Smc5/6 also localizes to recombination hotspots, where it promotes normal formation and resolution of joint-molecule intermediates. Furthermore, we find that Smc5/6 specifically promotes resolution of joint molecules via the XPF-family endonuclease, Mus81-Mms4Eme1. We propose that Smc5/6 acts as a chaperone for M-bM-^@M-^XmitoticM-bM-^@M-^Y-like recombination processes during meiosis. ChIP-chip was used to compare Smc5 localization in wild-type and spo11 strains
2013-12-27 | E-GEOD-44852 | biostudies-arrayexpress
Project description:The SMC protein complexes safeguard genomic integrity through their functions in chromosome segregation and repair. The chromosomal localization of the budding yeast Smc5/6 complex here determined reveals that the complex works specifically on the duplicated genome in differently regulated pathways. One controls the association to centromeres and chromosome arms in unchallenged cells, the second regulates the association to DNA breaks, and the third directs the complex to the chromosome arm that harbors the ribosomal DNA arrays. The chromosomal interaction pattern predicts a function that becomes more important with increasing chromosome length, and that the complex's role in unchallenged cells is independent of DNA damage. Additionally, localization of Smc6 to collapsed replication forks indicates an involvement in their rescue. Altogether this shows that the complex maintains genomic integrity in multiple ways, and evidence is presented that the Smc5/6 complex is needed during replication to prevent the accumulation of branched chromosome structures. Keywords: ChIP-chip analysis
2006-06-23 | GSE4808 | GEO
Project description:A family of Structural Maintenance of Chromosome (SMC) complexes is essential for key cellular processes ensuring proper cohesion, condensation and replication. They share common SMC-kleisin architecture allowing them to embrace DNA. The prokaryotic and eukaryotic SMC5/6 complexes contain additional kleisin-interacting KITE subunits which regulate SMC-kleisin dynamics. In SMC5/6, the Nse1 and Nse3 KITE proteins and Nse4 kleisin subunits form stable subcomplex which binds DNA and regulates essential processes. In addition, non-essential Nse5 and Nse6 subunits associate with the core SMC5/6 complex and recruit it to DNA repair sites. The architecture of the SMC5/6 complex is crucial for its proper functioning and mutations within the human SMC5/6 subunits result in severe syndromes. Therefore, we aimed to analyse interactions within the human SMC5/6 complex and determine its architecture at detail levels. First, we analysed the human hNSE1-hNSE3 dimer and the hNSE1-hNSE3-hNSE4 trimer by crosslinking and MS/MS analysis. Our data suggested domain arrangements of hNSE1-hNSE3 and orientation of hNSE4 within the trimer. The crosslinking and electron microscopy analysis of the SMC5/6 core complex showed its rod-like shaped architecture with juxtaposed hSMC5-hSMC6 arms. In addition, we observed fully or partially opened hSMC5-hSMC6 shapes with the hNSE1-hNSE3-hNSE4 trimer localized at the SMC head domains. To complete mapping of the human SMC5/6 complex architecture, we analysed positions of hNSE5-hNSE6 at the hSMC5-hSMC6 arms. Interestingly, hNSE6 bound both hSMC5-hSMC6 arms, suggesting that hNSE6 may lock the arms and regulate their dynamics. All together, we gained new insights into the architecture and dynamics of the human SMC5/6 complex.
2023-08-18 | PXD017379 | Pride
Project description:The human SMC5-SMC6 complex (SMC5/6) is a conserved guardian of genome stability and an emerging component of the antiviral response in animals and plants. In yeast, Smc5/6 is recruited to and loaded on chromatin by the poorly conserved Nse5-Nse6 heterodimer (Nse5/6), which remains largely undefined in humans. Here we report that SIMC1 is an Nse5 orthologue and novel subunit of the human SMC5/6 complex. SIMC1 binds to SLF2, the proposed Nse6 orthologue, forming a stable complex structurally similar to yeast Nse5/6. SIMC1 localizes SMC5/6 to polyomavirus replication centers in a SUMO interaction-dependent manner. Further structure prediction analyses indicate that SLF1, a putative Nse5 counterpart that recruits SMC5/6 to DNA lesions, interacts with SLF2 in a very similar manner as SIMC1. Consistently, SIMC1 and SLF1 form mutually exclusive complexes with SLF2. Thus, both SIMC1 and SLF1 act as orthologues of yeast Nse5 to independently direct the functions of SMC5/6.
2022-11-29 | PXD033923 | Pride