scholarly journals An Inducible System for Silencing Establishment Reveals a Stepwise Mechanism in Which Anchoring at the Nuclear Periphery Precedes Heterochromatin Formation

Cells ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2810
Author(s):  
Isabelle Loïodice ◽  
Mickael Garnier ◽  
Ivaylo Nikolov ◽  
Angela Taddei
Keyword(s):  
Nuclear Periphery ◽  
Dna Binding Protein ◽  
Eukaryotic Cells ◽  
Silent Chromatin ◽  
Cell Cycles ◽  
Heterochromatin Formation ◽  
Subnuclear Localization ◽  
Sir Complex ◽  
Set Up ◽  
Laco Array

In eukaryotic cells, silent chromatin is mainly found at the nuclear periphery forming subnuclear compartments that favor silencing establishment. Here, we set up an inducible system to monitor silencing establishment at an ectopic locus in relation with its subnuclear localization in budding yeast. We previously showed that introducing LacI bound lacO arrays in proximity to gene flanked by HML silencers favors the recruitment of the yeast silencing complex SIR at this locus, leading to its silencing and anchoring at the nuclear periphery. Using an inducible version of this system, we show that silencing establishment is a stepwise process occurring over several cell cycles, with the progressive recruitment of the SIR complex. In contrast, we observed a rapid, SIR-independent perinuclear anchoring, induced by the high amount of LacI binding at the lacO array leading to nucleosome eviction at this array and to the phosphorylation of H2A in the neighboring nucleosomes by Mec1 kinase. While the initial phosphorylation of H2A (H2A-P) and perinuclear anchoring are independent of the SIR complex, its latter recruitment stabilizes H2A-P and reinforces the perinuclear anchoring. Finally, we showed that Sir3 spreading stabilizes nucleosomes and limits the access of specific DNA-binding protein to DNA.

High Mobility Group Box-1 (HMGB1): A Potential Target in Therapeutics

2019 ◽  
Vol 20 (14) ◽  
pp. 1474-1485 ◽  
Author(s):  
Eyaldeva C. Vijayakumar ◽  
Lokesh Kumar Bhatt ◽  
Kedar S. Prabhavalkar
Keyword(s):  
Myocardial Infarction ◽  
Vagus Nerve Stimulation ◽  
Nuclear Protein ◽  
Therapeutic Potential ◽  
High Mobility ◽  
Dna Binding Protein ◽  
High Mobility Group ◽  
Eukaryotic Cells ◽  
Hmgb1 Protein

High mobility group box-1 (HMGB1) mainly belongs to the non-histone DNA-binding protein. It has been studied as a nuclear protein that is present in eukaryotic cells. From the HMG family, HMGB1 protein has been focused particularly for its pivotal role in several pathologies. HMGB-1 is considered as an essential facilitator in diseases such as sepsis, collagen disease, atherosclerosis, cancers, arthritis, acute lung injury, epilepsy, myocardial infarction, and local and systemic inflammation. Modulation of HMGB1 levels in the human body provides a way in the management of these diseases. Various strategies, such as HMGB1-receptor antagonists, inhibitors of its signalling pathway, antibodies, RNA inhibitors, vagus nerve stimulation etc. have been used to inhibit expression, release or activity of HMGB1. This review encompasses the role of HMGB1 in various pathologies and discusses its therapeutic potential in these pathologies.

scholarly journals Multiple Interactions in Sir Protein Recruitment by Rap1p at Silencers and Telomeres in Yeast

2001 ◽  
Vol 21 (23) ◽  
pp. 8082-8094 ◽  
Author(s):  
Paolo Moretti ◽  
David Shore
Keyword(s):  
Complex Formation ◽  
Mating Type ◽  
Small Region ◽  
Carboxyl Terminus ◽  
Silent Chromatin ◽  
Histone Binding ◽  
Amino Terminal ◽  
Sir Complex ◽  
Two Hybrid

ABSTRACT Initiation of transcriptional silencing at mating type loci and telomeres in Saccharomyces cerevisiaerequires the recruitment of a Sir2/3/4 (silent information regulator) protein complex to the chromosome, which occurs at least in part through its association with the silencer- and telomere-binding protein Rap1p. Sir3p and Sir4p are structural components of silent chromatin that can self-associate, interact with each other, and bind to the amino-terminal tails of histones H3 and H4. We have identified a small region of Sir3p between amino acids 455 and 481 that is necessary and sufficient for association with the carboxyl terminus of Rap1p but not required for Sir complex formation or histone binding.SIR3 mutations that delete this region cause a silencing defect at HMR and telomeres. However, this impairment of repression is considerably less than that displayed by Rap1p carboxy-terminal truncations that are defective in Sir3p binding. This difference may be explained by the ability of the Rap1p carboxyl terminus to interact independently with Sir4p, which we demonstrate by in vitro binding and two-hybrid assays. Significantly, the Rap1p-Sir4p two-hybrid interaction does not require Sir3p and is abolished by mutation of the carboxyl terminus of Rap1p. We propose that both Sir3p and Sir4p can directly and independently bind to Rap1p at mating type silencers and telomeres and suggest that Rap1p-mediated recruitment of Sir proteins operates through multiple cooperative interactions, at least some of which are redundant. The physical separation of the Rap1p interaction region of Sir3p from parts of the protein required for Sir complex formation and histone binding raises the possibility that Rap1p can participate directly in the maintenance of silent chromatin through the stabilization of Sir complex-nucleosome interactions.

scholarly journals Silencing of Euchromatic Transposable Elements as a Consequence of Nuclear Lamina Dysfunction

Cells ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 625
Author(s):  
Valeria Cavaliere ◽  
Giovanna Lattanzi ◽  
Davide Andrenacci
Keyword(s):  
Transposable Elements ◽  
Genome Instability ◽  
Nuclear Periphery ◽  
Nuclear Lamina ◽  
Rna Degradation ◽  
Loss Of Function ◽  
Heterochromatin Formation ◽  
Repressive Effect ◽  
Regulatory Effects ◽  
Genomic Regions

Transposable elements (TEs) are mobile genomic sequences that are normally repressed to avoid proliferation and genome instability. Gene silencing mechanisms repress TEs by RNA degradation or heterochromatin formation. Heterochromatin maintenance is therefore important to keep TEs silent. Loss of heterochromatic domains has been linked to lamin mutations, which have also been associated with derepression of TEs. In fact, lamins are structural components of the nuclear lamina (NL), which is considered a pivotal structure in the maintenance of heterochromatin domains at the nuclear periphery in a silent state. Here, we show that a lethal phenotype associated with Lamin loss-of-function mutations is influenced by Drosophila gypsy retrotransposons located in euchromatic regions, suggesting that NL dysfunction has also effects on active TEs located in euchromatic loci. In fact, expression analysis of different long terminal repeat (LTR) retrotransposons and of one non-LTR retrotransposon located near active genes shows that Lamin inactivation determines the silencing of euchromatic TEs. Furthermore, we show that the silencing effect on euchromatic TEs spreads to the neighboring genomic regions, with a repressive effect on nearby genes. We propose that NL dysfunction may have opposed regulatory effects on TEs that depend on their localization in active or repressed regions of the genome.

scholarly journals Clock proteins regulate spatiotemporal organization of clock genes to control circadian rhythms

2021 ◽  
Vol 118 (28) ◽  
pp. e2019756118
Author(s):  
Yangbo Xiao ◽  
Ye Yuan ◽  
Mariana Jimenez ◽  
Neeraj Soni ◽  
Swathi Yadlapalli
Keyword(s):  
Gene Expression ◽  
Circadian Rhythms ◽  
Nuclear Envelope ◽  
Molecular Mechanisms ◽  
Clock Genes ◽  
Nuclear Periphery ◽  
Spatiotemporal Organization ◽  
Subnuclear Localization ◽  
Clock Proteins ◽  
Spatial Reorganization

Circadian clocks regulate ∼24-h oscillations in gene expression, behavior, and physiology. While the genetic and molecular mechanisms of circadian rhythms are well characterized, what remains poorly understood are the intracellular dynamics of circadian clock components and how they affect circadian rhythms. Here, we elucidate how spatiotemporal organization and dynamics of core clock proteins and genes affect circadian rhythms in Drosophila clock neurons. Using high-resolution imaging and DNA-fluorescence in situ hybridization techniques, we demonstrate that Drosophila clock proteins (PERIOD and CLOCK) are organized into a few discrete foci at the nuclear envelope during the circadian repression phase and play an important role in the subnuclear localization of core clock genes to control circadian rhythms. Specifically, we show that core clock genes, period and timeless, are positioned close to the nuclear periphery by the PERIOD protein specifically during the repression phase, suggesting that subnuclear localization of core clock genes might play a key role in their rhythmic gene expression. Finally, we show that loss of Lamin B receptor, a nuclear envelope protein, leads to disruption of PER foci and per gene peripheral localization and results in circadian rhythm defects. These results demonstrate that clock proteins play a hitherto unexpected role in the subnuclear reorganization of core clock genes to control circadian rhythms, revealing how clocks function at the subcellular level. Our results further suggest that clock protein foci might regulate dynamic clustering and spatial reorganization of clock-regulated genes over the repression phase to control circadian rhythms in behavior and physiology.

Nuclear lamina and regulation of nuclear envelofe structure

1987 ◽  
Vol 45 ◽  
pp. 806-807
Author(s):  
Larry Gerace ◽  
Ueli Aebi ◽  
Brian Burke ◽  
Frank Suprynowicz
Keyword(s):  
Electron Microscopy ◽  
Nuclear Envelope ◽  
Xenopus Oocytes ◽  
Nuclear Periphery ◽  
Nuclear Architecture ◽  
Supramolecular Assembly ◽  
Nuclear Lamina ◽  
Eukaryotic Cells ◽  
Functional Studies ◽  
Tetragonal Lattice

The nuclear lamina is a protein meshwork that lines the nucleoplasmic surface of the nuclear envelope. In numerous higher eukaryotic cells, the lamina is known to contain a polymer of 1-3 major polypeptides (“lamins“) that form an insoluble supramolecular assembly during interphase. The lamina is thought to provide both a skeletal framework for the nuclear envelope (that regulates its disassembly and reformation during mitosis) and an anchoring site at the nuclear periphery for interphase chromosomes. Recent structural and functional studies on the nuclear lamina have yielded important new insight on its roles in nuclear architecture.Using electron microscopy, we found that the nuclear lamina of Xenopus oocytes is a meshwork of intermediate-sized (8-12 nm) filaments arranged in a near-tetragonal lattice having a spacing of 52 nm.

Gene insulation. Part I: natural strategies in yeast and Drosophila

2010 ◽  
Vol 88 (6) ◽  
pp. 875-884 ◽  
Author(s):  
Michèle Amouyal
Keyword(s):  
Gene Expression ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Initiation ◽  
Rna Polymerase Iii ◽  
Eukaryotic Cells ◽  
Trna Genes ◽  
Initiation Complex ◽  
Heterochromatin Formation ◽  
Transcription Initiation Complex

This review in two parts deals with the increasing number of processes known to be used by eukaryotic cells to protect gene expression from undesired genomic enhancer or chromatin effects, by means of the so-called insulators or barriers. The most advanced studies in this expanding field concern yeasts and Drosophila (this article) and the vertebrates (next article in this issue). Clearly, the cell makes use of every gene context to find the appropriate, economic, solution. Thus, besides the elements formerly identified and specifically dedicated to insulation, a number of unexpected elements are diverted from their usual function to structure the genome and enhancer action or to prevent heterochromatin spreading. They are, for instance, genes actively transcribed by RNA polymerase II or III, partial elements of these transcriptional machineries (stalled RNA polymerase II, normally required by genes that must respond quickly to stimuli, or TFIIIC bound at its B-box, normally required by RNA polymerase III for assembly of the transcription initiation complex at tRNA genes), or genomic sequences occupied by variants of standard histones, which, being rapidly and permanently replaced, impede heterochromatin formation.

scholarly journals Separate information required for nuclear and subnuclear localization: additional complexity in localizing an enzyme shared by mitochondria and nuclei.

1992 ◽  
Vol 12 (12) ◽  
pp. 5652-5658 ◽  
Author(s):  
A M Rose ◽  
P B Joyce ◽  
A K Hopper ◽  
N C Martin
Keyword(s):  
Amino Acids ◽  
Nuclear Periphery ◽  
Immunofluorescent Staining ◽  
Coding Region ◽  
Nuclear Targeting ◽  
Subnuclear Localization ◽  
Amino Terminal ◽  
Linear Sequence ◽  
Trna Methyltransferase ◽  
Terminal Amino

The TRM1 gene of Saccharomyces cerevisiae codes for a tRNA modification enzyme, N2,N2-dimethylguanosine-specific tRNA methyltransferase (m2(2)Gtase), shared by mitochondria and nuclei. Immunofluorescent staining at the nuclear periphery demonstrates that m2(2)Gtase localizes at or near the nuclear membrane. In determining sequences necessary for targeting the enzyme to nuclei and mitochondria, we found that information required to deliver the enzyme to the nucleus is not sufficient for its correct subnuclear localization. We also determined that mislocalizing the enzyme from the nucleus to the cytoplasm does not destroy its biological function. This change in location was caused by altering a sequence similar to other known nuclear targeting signals (KKSKKKRC), suggesting that shared enzymes are likely to use the same import pathway as proteins that localize only to the nucleus. As with other well-characterized mitochondrial proteins, the mitochondrial import of the shared methyltransferase depends on amino-terminal amino acids, and removal of the first 48 amino acids prevents its import into mitochondria. While this truncated protein is still imported into nuclei, the immunofluorescent staining is uniform throughout rather than at the nuclear periphery, a staining pattern identical to that described for a fusion protein consisting of the first 213 amino acids of m2(2)Gtase in frame with beta-galactosidase. As both of these proteins together contain the entire m2(2)Gtase coding region, the information necessary for association with the nuclear periphery must be more complex than the short linear sequence necessary for nuclear localization.

scholarly journals Sir3-Nucleosome Interactions in Spreading of Silent Chromatin in Saccharomyces cerevisiae

2008 ◽  
Vol 28 (22) ◽  
pp. 6903-6918 ◽  
Author(s):  
Johannes R. Buchberger ◽  
Megumi Onishi ◽  
Geng Li ◽  
Jan Seebacher ◽  
Adam D. Rudner ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Binding Activity ◽  
Chromatin Fiber ◽  
Silent Chromatin ◽  
Histone H4 ◽  
Histone Binding ◽  
Aaa Atpase ◽  
Binding Domains ◽  
Sir Complex

ABSTRACT Silent chromatin in Saccharomyces cerevisiae is established in a stepwise process involving the SIR complex, comprised of the histone deacetylase Sir2 and the structural components Sir3 and Sir4. The Sir3 protein, which is the primary histone-binding component of the SIR complex, forms oligomers in vitro and has been proposed to mediate the spreading of the SIR complex along the chromatin fiber. In order to analyze the role of Sir3 in the spreading of the SIR complex, we performed a targeted genetic screen for alleles of SIR3 that dominantly disrupt silencing. Most mutations mapped to a single surface in the conserved N-terminal BAH domain, while one, L738P, localized to the AAA ATPase-like domain within the C-terminal half of Sir3. The BAH point mutants, but not the L738P mutant, disrupted the interaction between Sir3 and nucleosomes. In contrast, Sir3-L738P bound the N-terminal tail of histone H4 more strongly than wild-type Sir3, indicating that misregulation of the Sir3 C-terminal histone-binding activity also disrupted spreading. Our results underscore the importance of proper interactions between Sir3 and the nucleosome in silent chromatin assembly. We propose a model for the spreading of the SIR complex along the chromatin fiber through the two distinct histone-binding domains in Sir3.

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

2021 ◽  
Author(s):  
Lucia Martin Caballero ◽  
Matias Capella ◽  
Ramon Ramos Barrales ◽  
Nikolay Dobrev ◽  
Thomas S van Emden ◽  
...  
Keyword(s):  
Nuclear Periphery ◽  
Rna Degradation ◽  
Nuclear Bodies ◽  
Silent Chromatin ◽  
Rna Surveillance ◽  
Environmentally Responsive ◽  
Nuclear Exosome ◽  
Non Coding Rnas ◽  
A Site ◽  
Inner Nuclear Membrane Protein

Transcriptionally silent chromatin often localizes to the nuclear periphery. However, whether the nuclear envelope (NE) is a site for post-transcriptional gene repression is unknown. Here we demonstrate that S. pombe Lem2, an NE protein, regulates nuclear exosome-mediated RNA degradation. Lem2 deletion causes accumulation of non-coding RNAs and meiotic transcripts. Indeed, an engineered exosome substrate RNA shows Lem2-dependent localization to the nuclear periphery. Lem2 does not directly bind RNA, but instead physically interacts with the exosome-targeting MTREC complex and promotes RNA recruitment. The Lem2-assisted pathway acts independently of nuclear bodies where exosome factors assemble, revealing that multiple spatially distinct degradation pathways exist. The Lem2 pathway is environmentally responsive: nutrient availability modulates Lem2 regulation of meiotic transcripts. Our data indicate that Lem2 recruits exosome co-factors to the nuclear periphery to coordinate RNA surveillance and regulates transcripts during the mitosis-to-meiosis switch.

scholarly journals The budding yeast heterochromatic SIR complex resets upon exit from stationary phase

2019 ◽  
Author(s):  
Hrvoje Galic ◽  
Pauline Vasseur ◽  
Marta Radman-Livaja
Keyword(s):  
Cell Cycle ◽  
Stationary Phase ◽  
De Novo ◽  
Budding Yeast ◽  
Growth Conditions ◽  
Clear Understanding ◽  
Turnover Rates ◽  
Heterochromatin Formation ◽  
Genome Wide ◽  
Sir Complex

AbstractThe budding yeast SIR complex (Silent Information Regulator) is the principal actor in heterochromatin formation, which causes epigenetically regulated gene silencing phenotypes. The maternal chromatin bound SIR complex is disassembled during replication. Consequently, if heterochromatin is to be restored on both daughter strands, the SIR complex has to be reformed on both strands to pre-replication levels. The dynamics of SIR complex maintenance and re-formation during the cell-cycle and in different growth conditions are however not clear. Understanding exchange rates of SIR subunits during the cell cycle and their distribution pattern to daughter chromatids after replication has important implications for how heterochromatic states may be inherited and therefore how epigenetic states are maintained from one cellular generation to the next. We used the tag switch RITE system to measure genome wide turnover rates of the SIR subunit Sir3 before and after exit from stationary phase and show that maternal Sir3 subunits are completely replaced with newly synthesized Sir3 at subtelomeric regions during the first cell cycle after release from stationary phase. The SIR complex is therefore not “inherited” and the silenced state has to be established de novo upon exit from stationary phase. Additionally, our analysis of genome-wide transcription dynamics shows that precise Sir3 dosage is needed for the optimal up-regulation of “growth” genes during the first cell-cycle after release from stationary phase.

Sign in / Sign up

Export Citation Format

Share Document