scholarly journals Biology and Physics of Heterochromatin-Like Domains/Complexes

Cells ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 1881
Author(s):  
Prim B. Singh ◽  
Stepan N. Belyakin ◽  
Petr P. Laktionov
Keyword(s):  
Phase Separation ◽  
Fission Yeast ◽  
Thermodynamic Description ◽  
Dynamic Structure ◽  
Vertebrate Development ◽  
Type Region ◽  
Additional Tool ◽  
3D Genome ◽  
Chromatin Template ◽  
Cis And Trans

The hallmarks of constitutive heterochromatin, HP1 and H3K9me2/3, assemble heterochromatin-like domains/complexes outside canonical constitutively heterochromatic territories where they regulate chromatin template-dependent processes. Domains are more than 100 kb in size; complexes less than 100 kb. They are present in the genomes of organisms ranging from fission yeast to human, with an expansion in size and number in mammals. Some of the likely functions of domains/complexes include silencing of the donor mating type region in fission yeast, preservation of DNA methylation at imprinted germline differentially methylated regions (gDMRs) and regulation of the phylotypic progression during vertebrate development. Far cis- and trans-contacts between micro-phase separated domains/complexes in mammalian nuclei contribute to the emergence of epigenetic compartmental domains (ECDs) detected in Hi-C maps. A thermodynamic description of micro-phase separation of heterochromatin-like domains/complexes may require a gestalt shift away from the monomer as the “unit of incompatibility” that determines the sign and magnitude of the Flory–Huggins parameter, χ. Instead, a more dynamic structure, the oligo-nucleosomal “clutch”, consisting of between 2 and 10 nucleosomes is both the long sought-after secondary structure of chromatin and its unit of incompatibility. Based on this assumption we present a simple theoretical framework that enables an estimation of χ for domains/complexes flanked by euchromatin and thereby an indication of their tendency to phase separate. The degree of phase separation is specified by χN, where N is the number of “clutches” in a domain/complex. Our approach could provide an additional tool for understanding the biophysics of the 3D genome.

scholarly journals Biology and physics of heterochromatin-like domains/complexes

2020 ◽  
Author(s):  
Prim B. Singh ◽  
Stepan N. Belyakin ◽  
Petr P. Laktionov
Keyword(s):  
Phase Separation ◽  
Fission Yeast ◽  
Constitutive Heterochromatin ◽  
Thermodynamic Description ◽  
Dynamic Structure ◽  
Vertebrate Development ◽  
Type Region ◽  
Additional Tool ◽  
3D Genome ◽  
Yeast Regulation

AbstractThe hallmarks of constitutive heterochromatin, HP1 and H3K9me2/3, assemble heterochromatin-like domains/complexes outside canonical constitutively heterochromatic territories where they regulate chromatin-templated processes. Domains are more than 100kb in size; complexes less than 100kb. They are present in the genomes of organisms ranging from fission yeast to man, with an expansion in size and number in mammals. Some of the likely functions of the domains/complexes include silencing of the donor mating type region in fission yeast, regulation of mammalian imprinted genes and the phylotypic progression during vertebrate development. Far cis- and trans-contacts between micro-phase separated domains/complexes in mammalian nuclei contribute to the emergence of epigenetic compartmental domains (ECDs) detected in Hi-C maps. We speculate that a thermodynamic description of micro-phase separation of heterochromatin-like domains/complexes will require a gestalt shift away from the monomer as the “unit of incompatibility”, where it is the choice of monomer that determines the sign and magnitude of the Flory-Huggins parameter, χ. Instead, a more dynamic structure, the oligo-nucleosomal “clutch”, consisting of between 2 to 10 nucleosomes is both the long sought-after secondary structure of chromatin and its unit of incompatibility. Based on this assumption we present a simple theoretical framework that enables an estimation of χ for domains/complexes flanked by euchromatin and thereby an indication of their tendency to phase separate. The degree of phase separation is specified by χN, where N is the number of “clutches” in a domain/complex. Our approach may provide an additional tool for understanding the biophysics of the 3D genome.

scholarly journals Liquid-liquid phase separation of the chromosomal passenger complex drives parallel bundling of midzone microtubules

2022 ◽  
Author(s):  
Ewa Niedzialkowska ◽  
Tan M Truong ◽  
Luke A Eldredge ◽  
Stefanie Redemann ◽  
Denis Chretien ◽  
...  
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Chromosome Segregation ◽  
Dynamic Structure ◽  
Liquid Phase Separation ◽  
Chromosomal Passenger Complex ◽  
Chromosomal Passenger ◽  
Spindle Midzone ◽  
Liquid Liquid Phase Separation

The spindle midzone is a dynamic structure that forms during anaphase, mediates chromosome segregation, and provides a signaling platform to position the cleavage furrow. The spindle midzone comprises two antiparallel bundles of microtubules (MTs) but the process of their formation is poorly understood. Here, we show that the Chromosomal Passenger Complex (CPC) undergoes liquid-liquid phase separation (LLPS) to generate parallel MT bundles in vitro when incubated with free tubulin and GTP. MT bundles emerge from CPC droplets with protruding minus-ends that then grow into long, tapered MT structures. During this growth, the CPC in condensates apparently reorganize to coat and bundle the resulting MT structures. CPC mutants attenuated for LLPS or MT binding prevented the generation of parallel MT bundles in vitro and reduced the number of MTs present at spindle midzones in HeLa cells. Our data uncovers a kinase-independent function of the CPC and provides models for how cells generate parallel-bundled MT structures that are important for the assembly of the mitotic spindle.

Mutations in the fission yeast silencing factors clr4+ and rik1+ disrupt the localisation of the chromo domain protein Swi6p and impair centromere function

1996 ◽  
Vol 109 (11) ◽  
pp. 2637-2648 ◽  
Author(s):  
K. Ekwall ◽  
E.R. Nimmo ◽  
J.P. Javerzat ◽  
B. Borgstrom ◽  
R. Egel ◽  
...  
Keyword(s):  
Fission Yeast ◽  
Mating Type ◽  
Transcriptional Repression ◽  
In Situ Hybridisation ◽  
Chromosome Loss ◽  
Fluorescence In Situ Hybridisation ◽  
Type Region ◽  
Centromere Function ◽  
Mutant Cells

Transcriptional silencing is known to occur at centromeres, telomeres and the mating type region in the nucleus of fission yeast, Schizosaccharomyces pombe. Mating-type silencing factors have previously been shown also to affect transcriptional repression within centromeres and to some extent at telomeres. Mutations in the clr4+, rik1+ and swi6+ genes dramatically reduce silencing at certain centromeric regions and cause elevated chromosome loss rates. Recently, Swi6p was found to co-localise with the three silent chromosomal regions. Here the involvement of clr4+, rik1+ and swi6+ in centromere function is investigated in further detail. Fluorescence in situ hybridisation (FISH) was used to show that, as in swi6 mutant cells, centromeres lag on late anaphase spindles in clr4 and rik1 mutant cells. This phenotype is consistent with a role for these three gene products in fission yeast centromere function. The Swi6 protein was found to be delocalised from all three silent chromosomal regions, and dispersed within the nucleus, in both clr4 and rik1 mutant cells. The phenotypic similarity observed in all three mutants is consistent with the products of both the clr4+ and rik1+ genes being required to recruit Swi6p to the centromere and other silent regions. Mutations in clr4, rik1 and swi6 also result in elevated sensitivity to reagents which destabilise microtubules and show a synergistic interaction with a mutation in the beta-tubulin gene (nda3). These observations suggest that clr4+ and rik1+ must play a role in the assembly of Swi6p into a transcriptionally silent, inaccessible chromatin structure at fission yeast centromeres which is required to facilitate interactions with spindle microtubules and to ensure normal chromosome segregation.

scholarly journals The Fission Yeast Ubiquitin-Conjugating Enzymes UbcP3, Ubc15, and Rhp6 Affect Transcriptional Silencing of the Mating-Type Region

2002 ◽  
Vol 1 (4) ◽  
pp. 613-625 ◽  
Author(s):  
Inga Sig Nielsen ◽  
Olaf Nielsen ◽  
Johanne M. Murray ◽  
Geneviève Thon
Keyword(s):  
Fission Yeast ◽  
Rna Polymerase Ii ◽  
Mating Type ◽  
26S Proteasome ◽  
Obvious Effect ◽  
Type Region ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzymes ◽  
Ubiquitin Conjugating Enzymes ◽  
Active Site Mutants

ABSTRACT Genes transcribed by RNA polymerase II are silenced when introduced near the mat2 or mat3 mating-type loci of the fission yeast Schizosaccharomyces pombe. Silencing is mediated by a number of gene products and cis-acting elements. We report here the finding of novel trans-acting factors identified in a screen for high-copy-number disruptors of silencing. Expression of cDNAs encoding the putative E2 ubiquitin-conjugating enzymes UbcP3, Ubc15 (ubiquitin-conjugating enzyme), or Rhp6 (Rad homolog pombe) from the strong nmt1 promoter derepressed the silent mating-type loci mat2 and mat3 and reporter genes inserted nearby. Deletion of rhp6 slightly derepressed an ade6 reporter gene placed in the mating-type region, whereas disruption of ubcP3 or ubc15 had no obvious effect on silencing. Rhp18 is the S. pombe homolog of Saccharomyces cerevisiae Rad18p, a DNA-binding protein that physically interacts with Rad6p. Rhp18 was not required for the derepression observed when UbcP3, Ubc15, or Rhp6 was overproduced. Overexpressing Rhp6 active-site mutants showed that the ubiquitin-conjugating activity of Rhp6 is essential for disruption of silencing. However, high dosage of UbcP3, Ubc15, or Rhp6 was not suppressed by a mutation in the 26S proteasome, suggesting that loss of silencing is not due to an increased degradation of silencing factors but rather to the posttranslational modification of proteins by ubiquitination. We discuss the implications of these results for the possible modes of action of UbcP3, Ubc15, and Rhp6.

The dynamic structure of cis and trans conformers of substituted phosphinous acids

2008 ◽  
Vol 2 (5) ◽  
pp. 684-689 ◽  
Author(s):  
Yu. V. Babin ◽  
A. V. Prisyazhnyuk ◽  
Yu. A. Ustynyuk
Keyword(s):  
Dynamic Structure ◽  
Cis And Trans

Transient inhibition of histone deacetylase activity overcomes silencing in the mating-type region in fission yeast

1999 ◽  
Vol 35 (2) ◽  
pp. 82-87 ◽  
Author(s):  
T. G. S. Olsson ◽  
Rebecca A. Silverstein ◽  
Karl Ekwall ◽  
Per Sunnerhagen
Keyword(s):  
Fission Yeast ◽  
Histone Deacetylase ◽  
Mating Type ◽  
Type Region

The clr1 locus regulates the expression of the cryptic mating-type loci of fission yeast.

Genetics ◽  
1992 ◽  
Vol 131 (2) ◽  
pp. 287-296 ◽  
Author(s):  
G Thon ◽  
A J Klar
Keyword(s):  
Fission Yeast ◽  
Mating Type ◽  
Cold Spot ◽  
Type Region ◽  
Type Locus ◽  
Silent Genes ◽  
The Right ◽  
Chromosome Ii ◽  
Donor Locus ◽  
Type Information

Abstract The mat2-P and mat3-M loci of fission yeast contain respectively the plus (P) and minus (M) mating-type information in a transcriptionally silent state. That information is transposed from the mat2 or mat3 donor locus via recombination into the expressed mating-type locus (mat1) resulting in switching of the cellular mating type. We have identified a gene, named clr1 (for cryptic loci regulator), whose mutations allow expression of the mat2 and mat3 loci. clr1 mutants undergo aberrant haploid meiosis, indicative of transcription of the silent genes. Production of mRNA from mat3 is detectable in clr1 mutants. Furthermore, the ura4 gene inserted near mat3, weakly expressed in wild-type cells, is derepressed in clr1 mutants. The clr1 mutations also permit meiotic recombination in the 15-kb mat2-mat3 interval, where recombination is normally inhibited. The clr1 locus is in the right arm of chromosome II. We suggest that clr1 regulates silencing of the mat2 and mat3 loci, and participates in establishing the "cold spot" for recombination by organizing the chromatin structure of the mating-type region.

scholarly journals A Recombinationally Repressed Region Between mat2 and mat3 Loci Shares Homology to Centromeric Repeats and Regulates Directionality of Mating-Type Switching in Fission Yeast

Genetics ◽  
1997 ◽  
Vol 146 (4) ◽  
pp. 1221-1238 ◽  
Author(s):  
Shiv I S Grewal ◽  
Amar J S Klar
Keyword(s):  
Fission Yeast ◽  
Mating Type ◽  
Sequencing Analysis ◽  
Cell Type ◽  
Cloning And Sequencing ◽  
Type Region ◽  
Repeat Sequences ◽  
Mating Type Switching ◽  
Cell Type Specific

Cells of the fission yeast Schizosaccharomyces pombe switch mating type by replacing genetic information at the transcriptionally active mat1 locus with sequences copied from one of two closely linked silent loci, mat2-P or mat3-M. By a process referred to as directionality of switching, cells predominantly switch to the opposite mat1 allele; the mat1-P allele preferentially recombines with mat3, while mat1-M selects the mat2. In contrast to efficient recombination at mat1, recombination within the adjoining mat2-mat3 interval is undetectable. We defined the role of sequences between mat2 and mat3, designated the K-region, in directionality as well as recombinational suppression. Cloning and sequencing analysis revealed that a part of the K-region is homologous to repeat sequences present at centromeres, which also display transcriptional and recombinational suppression. Replacement of 7.5 kb of the K-region with the ura4  + gene affected directionality in a variegated manner. Analysis of the swi6-mod locus, which was previously shown to affect directionality, in KΔ::ura4  + strains suggested the existence of at least two overlapping directionality mechanisms. Our work furthers the model that directionality is regulated by cell-type-specific organization of the heterochromatin-like structure in the mating-type region and provides evidence that the K-region contributes to silencing of the mat2-mat3 interval.

scholarly journals Epigenetic Inheritance of Transcriptional Silencing and Switching Competence in Fission Yeast

Genetics ◽  
1997 ◽  
Vol 145 (3) ◽  
pp. 685-696 ◽  
Author(s):  
Geneviève Thon ◽  
Tove Friis
Keyword(s):  
Fission Yeast ◽  
Mating Type ◽  
Cumulative Effect ◽  
Transcriptional Silencing ◽  
Epigenetic Inheritance ◽  
Yeast Cells ◽  
Type Region ◽  
Epigenetic Events ◽  
Epigenetic Phenomenon ◽  
Gene Conversions

Epigenetic events allow the inheritance of phenotypic changes that are not caused by an alteration in DNA sequence. Here we characterize an epigenetic phenomenon occuring in the mating-type region of fission yeast. Cells of fission yeast switch between the P and M mating-type by interconverting their expressed mating-type cassette between two allelic forms, mat1-P and mat1-M. The switch results from gene conversions of mat1 by two silent cassettes, mat2-P and mat3-M, which are linked to each other and to mat1. Grewal and Klar observed that the ability to both switch mat1 and repress transcription near mat2-P and mat3-M was maintained epigenetically in a strain with an 8-kb deletion between mat2 and mat3. Using a strain very similar to theirs, we determined that interconversions between the switching- and silencing-proficient state and the switching and silencing-deficient state occurred less frequently than once per 1000 cell divisions. Although transcriptional silencing was alleviated by the 8-kb deletion, it was not abolished. We performed a mutant search and obtained a class of trans-acting mutations that displayed a strong cumulative effect with the 8-kb deletion. These mutations allow to assess the extent to which silencing is affected by the deletion and provide new insights on the redundancy of the silencing mechanism.

scholarly journals Characterization of Liquid-liquid phase Separation in 3D Genome Organization

2020 ◽  
Author(s):  
Tingting Li ◽  
Jiaqing Xing ◽  
Tao Li ◽  
Teng Li ◽  
Weihua Li
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Genome Organization ◽  
Enrichment Analysis ◽  
Liquid Phase Separation ◽  
Rna Recognition Motif ◽  
3D Genome ◽  
Shiny App ◽  
Modular Domains ◽  
Liquid Liquid Phase Separation

Abstract Many proteins have been demonstrated to participate in 3D genome organization through liquid-liquid phase separation (LLPS) such as RNPII, HP1a. However, systematic investigation of relationships between LLPS and 3D genome organization remains lacking. Here, we predicted the intrinsic disordered regions (IDRs) and modular domains of all human proteins and performed GSEA analysis according to their proportions of IDRs. Our results showed that main biological processes involved in 3D genome organization are highly enriched with IDRs, including chromatin organization, RNA splicing and histone modification, demonstrating the key role of LLPS in regulating nuclear structure. Of the 3885 IDR-rich proteins, 1427 proteins are involved in 3D genome organization. IDR regions of these proteins have strong preference of Ser, Leu, Pro, Ala, Gly, Glu and Lys, and lack of hydrophobic amino acids such as Trp, Tyr, Phe and Met, suggesting dipolar interactions rather than aromatic-involved interactions involved. Further motif enrichment analysis suggests that RNA recognition motif and zinc finger motif are the two most abundant repeatedly-occurred modular domains within IDR-containing proteins. Finally, we developed a Shiny APP named phasepro that interactively analyze and visualize a protein’s potential of LLPS, including IDRs, motifs, amino acid preferences and electric charges.

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