Tatyana Pichugina,PhD

The locations of proteins and epigenetic marks on the chromosomal DNA sequence are believed to demarcate the eukaryotic genome into distinct structural and functional domains that contribute to gene regulation and genome organization. However, how these proteins and epigenetic marks are organized in three dimensions remains unknown. Recent advances in proximity-ligation methodologies and high resolution microscopy have begun to expand our understanding of these spatial relationships. Here we… Show more

The locations of proteins and epigenetic marks on the chromosomal DNA sequence are believed to demarcate the eukaryotic genome into distinct structural and functional domains that contribute to gene regulation and genome organization. However, how these proteins and epigenetic marks are organized in three dimensions remains unknown. Recent advances in proximity-ligation methodologies and high resolution microscopy have begun to expand our understanding of these spatial relationships. Here we use polymer models to examine the spatial organization of epigenetic marks, euchromatin and heterochromatin, and origins of replication within the Schizosaccharomyces pombe genome. These models incorporate data from microscopy and proximity-ligation experiments that inform on the positions of certain elements and contacts within and between chromosomes. Our results show a striking degree of compartmentalization of epigenetic and genomic features and lead to the proposal of a diffusion based mechanism, centred on the spindle pole body, for the coordination of DNA replication in S. pombe. Show less

Successful progression through the cell cycle requires spatial and temporal regulation of gene transcript levels and the number, positions and condensation levels of chromosomes. Here we present a high resolution survey of genome interactions in Schizosaccharomyces pombe using synchronized cells to investigate cell cycle dependent changes in genome organization and transcription. Cell cycle dependent interactions were captured between and within S. pombe chromosomes. Known features of genome… Show more

Successful progression through the cell cycle requires spatial and temporal regulation of gene transcript levels and the number, positions and condensation levels of chromosomes. Here we present a high resolution survey of genome interactions in Schizosaccharomyces pombe using synchronized cells to investigate cell cycle dependent changes in genome organization and transcription. Cell cycle dependent interactions were captured between and within S. pombe chromosomes. Known features of genome organization (e.g. the clustering of telomeres and retrotransposon long terminal repeats (LTRs)) were observed throughout the cell cycle. There were clear correlations between transcript levels and chromosomal interactions between genes, consistent with a role for interactions in transcriptional regulation at specific stages of the cell cycle. In silico reconstructions of the chromosome organization within the S. pombe nuclei were made by polymer modeling. These models suggest that groups of genes with high and low, or differentially regulated transcript levels have preferred positions within the S. pombe nucleus. We conclude that the S. pombe nucleus is spatially divided into functional sub-nuclear domains that correlate with gene activity. The observation that chromosomal interactions are maintained even when chromosomes are fully condensed in M phase implicates genome organization in epigenetic inheritance and bookmarking. Show less

Since Jacob and Monod’s characterization of the role of DNA elements in gene control, it has been recognized that the linear organization of genome structure is important for the regulation of gene transcription and hence the manifestation of phenotypes. Similarly, it has long been hypothesized that the spatial organization (in three dimensions evolving through time), as part of the epigenome, makes a significant contribution to the genotype-phenotype transition. Proximity ligation assays… Show more

Since Jacob and Monod’s characterization of the role of DNA elements in gene control, it has been recognized that the linear organization of genome structure is important for the regulation of gene transcription and hence the manifestation of phenotypes. Similarly, it has long been hypothesized that the spatial organization (in three dimensions evolving through time), as part of the epigenome, makes a significant contribution to the genotype-phenotype transition. Proximity ligation assays commonly known as chromosome conformation capture (3C) and 3C based methodologies (e.g., GCC, HiC, and ChIA-Pet) are increasingly being incorporated into empirical studies to investigate the role that three-dimensional genome structure plays in the regulation of phenotype. The apparent simplicity of these methodologies—crosslink chromatin, digest, dilute, ligate, detect interactions—belies the complexity of the data and the considerations that should be taken into account to ensure the generation and accurate interpretation of reliable data. Here we discuss the probabilistic nature of these methodologies and how this contributes to their endogenous limitations. Show less

X-band echo-detected electron paramagnetic resonance (ED EPR) spectra of triplet state of fullerene C(70) generated by continuous light illumination were found to correspond below 30K to a non-equilibrium electron spin polarization. Above 30K spectra are characteristic of Boltzmann equilibrium. Spectra were simulated fairly well with zero-field splitting parameters D=153 MHz and E and distributed within the range of 6-42 MHz. The origin of E distribution is attributed to the Jahn-Teller effect,… Show more

X-band echo-detected electron paramagnetic resonance (ED EPR) spectra of triplet state of fullerene C(70) generated by continuous light illumination were found to correspond below 30K to a non-equilibrium electron spin polarization. Above 30K spectra are characteristic of Boltzmann equilibrium. Spectra were simulated fairly well with zero-field splitting parameters D=153 MHz and E and distributed within the range of 6-42 MHz. The origin of E distribution is attributed to the Jahn-Teller effect, which in glassy matrix is expected to depend on the local surrounding of a fullerene molecule (a so-called E-strain). In the center of ED EPR spectra a narrow hole was observed. With increase of the microwave pulse turning angle this hole transforms into a single narrow absorptive line. Numerical simulations by density matrix formalism confirm that central hole originates from a simultaneous excitation of both allowed electron spin transitions of the triplet (T(0)↔T(+) and T(0)↔T(-)), because of their degeneracy at this spectral position. Also explanations are given why this hole has not been observed in the previously reported experiments on continuous wave EPR and on ED EPR under laser pulse excitation. Show less