A dynamical model reveals gene co-localizations in nucleus

Co-localization of networks of genes in the nucleus is thought to play an important role in determining gene expression patterns. Based upon experimental data, we built a dynamical model to test whether pure diffusion could account for the observed co-localization of genes within a defined subnuclear region. A simple standard Brownian motion model in two and three dimensions shows that preferential co-localization is possible for co-regulated genes without any direct interaction, and suggests the occurrence may be due to a limitation in the number of available transcription factors. Experimental data of chromatin movements demonstrates that fractional rather than standard Brownian motion is more appropriate to model gene mobilizations, and we tested our dynamical model against recent static experimental data, using a sub-diffusion process by which the genes tend to colocalize more easily. Moreover, in order to compare our model with recently obtained experimental data, we studied the association level between genes and factors, and presented data supporting the validation of this dynamic model. As further applications of our model, we applied it to test against more biological observations. We found that increasing transcription factor number, rather than factory number and nucleus size, might be the reason for decreasing gene co-localization. In the scenario of frequency-or amplitude-modulation of transcription factors, our model predicted that frequency-modulation may increase the co-localization between its targeted genes

A dynamical model reveals gene co-localizations in nucleus

Co-localization of networks of genes in the nucleus is thought to play an important role in determining gene expression patterns. Based upon experimental data, we built a dynamical model to test whether pure diffusion could account for the observed co-localization of genes within a defined subnuclear region. A simple standard Brownian motion model in two and three dimensions shows that preferential co-localization is possible for co-regulated genes without any direct interaction, and suggests the occurrence may be due to a limitation in the number of available transcription factors. Experimental data of chromatin movements demonstrates that fractional rather than standard Brownian motion is more appropriate to model gene mobilizations, and we tested our dynamical model against recent static experimental data, using a sub-diffusion process by which the genes tend to colocalize more easily. Moreover, in order to compare our model with recently obtained experimental data, we studied the association level between genes and factors, and presented data supporting the validation of this dynamic model. As further applications of our model, we applied it to test against more biological observations. We found that increasing transcription factor number, rather than factory number and nucleus size, might be the reason for decreasing gene co-localization. In the scenario of frequency-or amplitude-modulation of transcription factors, our model predicted that frequency-modulation may increase the co-localization between its targeted genes

Parasitic influences on the host genome using the molluscan model organism biomphalaria glabrata

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.The freshwater snail Biomphalaria glabrata is an intermediate host for Schistosoma mansoni parasites, causing one of the most prevalent parasitic infections in mammals, known as schistosomiasis (Bilharzia). Due to its importance in the spread of the disease B. glabrata has been selected for whole genome sequencing and is now a molluscan model organism. In order to aid the sequencing project and to understand the structure and organisation of B. glabrata’s genome at the chromosomal level, a G-banded karyotype has been established. Unlike in any other previous reports, two heteromorphic chromosomes have been identified in the genome of B. glabrata and for the first time snail ideograms have been produced. In addition to characterising the snail chromosomes, a methodology for mapping single copy B. glabrata genes onto these chromosomes has also been established, and 4 genes have successfully been mapped using fluorescence in situ hybridisation. In the relationship between a parasite and a host organism, it is of fundamental importance to understand the basic biology and interfere with the life cycle to reveal how the parasite controls and elicits host gene expression for its own benefit. This study is also directly addressing this aspect of host – parasite interactions by investigating the effects of schistosome infection on the genome and cell nuclei of the host snail B. glabrata. Upon infection with S. mansoni miracidia, genes known to be involved in the host response to the parasite are dramatically relocated within the interphase snail nuclei. These events are in conjunction with the up-regulation of gene expression, indicating a parasite induced nuclear event. Moreover, a differential response between the schistosome-resistant and schistosome-susceptible snails is also reported. This is the first time this has been described in a host – pathogen relationship. The precise organisation of the genome is critical for its correct functioning. The genome is non-randomly organised and this level of organisation is very much influenced by the nuclear architecture. Being a molluscan model organism with the availability of a unique cell line, B. glabrata is a remarkable organism for the studies of nuclear and genome biology. For this reason, in this thesis the snail nuclear architecture was also investigated. For the first time PML bodies, transcription factories, and nuclear myosin 1 beta have been visualised in the snail nuclei. A heat shock system was also developed to study the role of these structures in the snail. Upon heat stimuli gene loci were found to reposition and co-localise with transcription factories, which was in parallel with the up-regulation of gene expression. The mechanism of this genome reorganisation was explored by investigating nuclear motor structures in the snail. By using a motor inhibitor on snail cells, gene repositioning and subsequent expression after heat shock was blocked. This is the first time this has been shown in any organism. Thus, due to the ease of use of the snails with respect to maintenance, handling, and treatments, B. glabrata is making a very useful new model organism to study spatial genomic events

Interplay of chromatin remodeling, transcriptional regulation, and nuclear organization

Transcription is regulated on different levels to ensure that genes are expressed at the correct time and in the amounts required. At the chromatin level, DNA is wound onto histone proteins, forming nucleosomes that influence accessibility of DNA elements. Modifications on those histones and interactions with other chromatin proteins can either encourage or inhibit recruitment of the transcription machinery. Genomic regions of similar character form chromatin domains, organizing the genome based on their transcription states. Within the nucleus, both individual loci and entire chromosomes assume non-random positions, based on their transcription levels and interactions with nuclear landmarks. This thesis examines the effects of the Fun30 chromatin remodeling enzymes on transcription regulation and nuclear organization, both on the local chromatin level as well as on a genome-wide scale. Using the fission yeast Schizosaccharomyces pombe as a model organism, we mapped the interactions between the genome and two inner nuclear membrane proteins, Ima1 and Man1. We observed a preference for lowly expressed genes to associate with the nuclear envelope, similar to what had been observed in mammalian and fruit fly cells. When comparing Ima1 and Man1 binding patterns, we found both common and separate target sites, suggesting a role for inner nuclear membrane proteins in organizing the fission yeast genome. Following up on these results, we went on to examine subtelomeric chromatin domains, which are regulated through the Fun30 remodeler Fft3. These domains contain repressed genes, whose transcription levels increase in cells carrying an fft3Δ deletion. While the subtelomeres associate with the nuclear envelope through Man1 in wild-type cells, this interaction is lost in fft3Δ cells. In these cells, we also observed changes in nucleosome occupancy at the subtelomeric borders. Interestingly, a strain carrying a catalytically inactive version of the Fft3 remodeler showed the same behavior as the deletion strain, with upregulation of subtelomeric genes and loss of Man1 interactions. Together, these results point to an active role of Fft3 in regulating subtelomeric chromatin, transcription, and nuclear periphery interactions. In addition to their role at subtelomeres, Fun30 remodelers also control transcription in other parts of the genome. When we examined a strain lacking Fft2, a paralog of Fft3, we found increased transcription of the fission yeast Tf2 retrotransposons. This increase is accompanied by a shift in transcription start site (TSS) further upstream and is especially pronounced when both fft2 and fft3 are deleted. By mapping nucleosome positioning, we were able to establish that Fft2 and Fft3 collaborate in stabilizing a nucleosome over the upstream TSS, resulting in transcription initiation further downstream and production of an mRNA incapable of transposition. Expression of both remodelers is downregulated in stress conditions, allowing for production of the longer transcript under these circumstances. We propose that the shift in TSS choice allows for bursts of transposition in cells under environmental stress. This can enable cells to adapt to changed conditions through favorable insertion events altering expression of nearby genes