Investigating Mitotic Inheritance of Histone Modifications Using Tethering Strategies

Larkin, Ajay; Ames, Amanda; Seman, Melissa; Ragunathan, Kaushik

doi:10.1007/978-1-0716-2481-4_18

“…In this case, the histone methyltransferase complex (“reader/writer”) Clr4/Suv39h recognizes H3K9me3 and spreads the mark throughout the domain via RNAi mechanism [ 39 , 40 ]. Recently there have been experiments that probe the heterochromatin assembly and the signaling pathways that govern it [ 41 – 43 ].…”

Section: Introductionmentioning

confidence: 99%

Role of diffusion and reaction of the constituents in spreading of histone modification marks

Manivannan,

Inamdar,

Padinhateeri

2024

PLoS Comput Biol

0

View full text Add to dashboard Cite

Cells switch genes ON or OFF by altering the state of chromatin via histone modifications at specific regulatory locations along the chromatin polymer. These gene regulation processes are carried out by a network of reactions in which the histone marks spread to neighboring regions with the help of enzymes. In the literature, this spreading has been studied as a purely kinetic, non-diffusive process considering the interactions between neighboring nucleosomes. In this work, we go beyond this framework and study the spreading of modifications using a reaction-diffusion (RD) model accounting for the diffusion of the constituents. We quantitatively segregate the modification profiles generated from kinetic and RD models. The diffusion and degradation of enzymes set a natural length scale for limiting the domain size of modification spreading, and the resulting enzyme limitation is inherent in our model. We also demonstrate the emergence of confined modification domains without the explicit requirement of a nucleation site. We explore polymer compaction effects on spreading and show that single-cell domains may differ from averaged profiles. We find that the modification profiles from our model are comparable with existing H3K9me3 data of S. pombe.

show abstract

“…In this case, the histone methyltransferase complex ("reader/writer") Clr4/Suv39h recognizes H3K9me3 and spreads the mark throughout the domain via RNAi mechanism [39,40]. Recently there have been experiments that probe the heterochromatin assembly and the signaling pathways that govern it [41][42][43].…”

Section: Introductionmentioning

confidence: 99%

Role of diffusion and reaction of the constituents in spreading of histone modification marks

Manivannan,

Inamdar,

Padinhateeri

2023

Preprint

0

View full text Add to dashboard Cite

Cells switch genes ON or OFF by altering the state of chromatin via histone modifications at specific regulatory locations along the chromatin polymer. These gene regulation processes are carried out by a network of reactions in which the histone marks spread to neighboring regions with the help of enzymes. In the literature, this spreading has been studied as a purely kinetic, non-diffusive process considering the interactions between neighboring nucleosomes. In this work, we go beyond this framework and study the spreading of modifications using a reaction-diffusion (RD) model accounting for the diffusion of the constituents. We quantitatively segregate the modification profiles generated from kinetic and RD models. The diffusion and degradation of enzymes set a natural length scale for limiting the domain size of modification spreading, and the resulting enzyme limitation is inherent in our model. We also demonstrate the emergence of confined modification domains without the explicit requirement of a nucleation site. We explore polymer compaction effects on spreading and show that single-cell domains may differ from averaged profiles. We find that the modification profiles from our model are comparable with existing H3K9me3 data ofS. pombe.

show abstract

Understanding the molecular mechanisms of human diseases: the benefits of fission yeasts

Acs-Szabo,

Papp,

Miklos

2024

Microbial Cell

0

View full text Add to dashboard Cite

The role of model organisms such as yeasts in life science research is crucial. Although the baker’s yeast (Saccharomyces cerevisiae) is the most popular model among yeasts, the contribution of the fission yeasts (Schizosaccharomyces) to life science is also indisputable. Since both types of yeasts share several thousands of common orthologous genes with humans, they provide a simple research platform to investigate many fundamental molecular mechanisms and functions, thereby contributing to the understanding of the background of human diseases. In this review, we would like to highlight the many advantages of fission yeasts over budding yeasts. The usefulness of fission yeasts in virus research is shown as an example, presenting the most important research results related to the Human Immunodeficiency Virus Type 1 (HIV-1) Vpr protein. Besides, the potential role of fission yeasts in the study of prion biology is also discussed. Furthermore, we are keen to promote the uprising model yeast Schizosaccharomyces japonicus, which is a dimorphic species in the fission yeast genus. We propose the hyphal growth of S. japonicus as an unusual opportunity as a model to study the invadopodia of human cancer cells since the two seemingly different cell types can be compared along fundamental features. Here we also collect the latest laboratory protocols and bioinformatics tools for the fission yeasts to highlight the many possibilities available to the research community. In addition, we present several limiting factors that everyone should be aware of when working with yeast models.

show abstract

Investigating Mitotic Inheritance of Histone Modifications Using Tethering Strategies

Cited by 3 publications

References 37 publications

Role of diffusion and reaction of the constituents in spreading of histone modification marks

Role of diffusion and reaction of the constituents in spreading of histone modification marks

Role of diffusion and reaction of the constituents in spreading of histone modification marks

Understanding the molecular mechanisms of human diseases: the benefits of fission yeasts

Contact Info

Product

Resources

About