A Dynamical Model Reveals Gene Co-Localizations in Nucleus

@article{Kang2011ADM,
  title={A Dynamical Model Reveals Gene Co-Localizations in Nucleus},
  author={Jing Kang and Bing Xu and Ye Yao and Wei Lin and Conor Hennessy and Peter Fraser and Jianfeng Feng},
  journal={PLoS Computational Biology},
  year={2011},
  volume={7}
}
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… 

Tables from this paper

Transcription factories: genome organization and gene regulation.
I will argue that transcription 'factories' are central organizers of the human genome during interphase, and that proximity to an appropriate factory determines the activity of a gene. The nucleolus
Nuclear compartments, genome folding, and enhancer-promoter communication.
From 1D sequence to 3D chromatin dynamics and cellular functions: a phase separation perspective
TLDR
CGI forest and prairie genomic domains are identified based on CGI density, which better segregates genomic elements along the genome than GC content, and it is proposed that the phase separation of the 1D mosaic sequence in space shapes the chromatin structure in different cell types and renders them distinct genomic properties.
Chromatin interactions correlate with local transcriptional activity in Saccharomyces cerevisiae
TLDR
This study relates the genome organization of Saccharomyces cerevisiae (budding yeast) to its transcription activity by analyzing published circularized chromosome conformation capture data in conjunction with eight separate datasets describing genome-wide transcription rate or RNA polymerase II (Pol II) occupancy.
Gene promoters show chromosome-specificity and reveal chromosome territories in humans
TLDR
It is shown that gene promoters appear to be specific to each chromosome, and the proximity between chromosomes seems to be in accordance to the structural similarity of their gene promoters.
Interplay of chromatin remodeling, transcriptional regulation, and nuclear organization
TLDR
It is proposed that the shift in TSS choice allows for bursts of transposition in cells under environmental stress, which can enable cells to adapt to changed conditions through favorable insertion events altering expression of nearby genes.
Molecular Pathways: Transcription Factories and Chromosomal Translocations
TLDR
The relationships between genome organization, transcription, and chromosomal translocation formation will have important implications in understanding the causes of therapy-related cancers.
Capturing genomic relationships that matter
TLDR
The recent and prospective development and implementation of new methodologies and analytical tools that are allowing an in-depth, yet focussed characterisation of genomic contacts that are associated with functional activities in the nucleus are discussed.
...
...

References

SHOWING 1-10 OF 41 REFERENCES
Spatial and Topological Organization of DNA Chains Induced by Gene Co-localization
TLDR
A thermodynamic framework based on a worm-like chain model of chromosomes where sparse designated sites along the DNA are able to interact whenever they are spatially close by is considered, suggesting transcription factors to be appropriate candidates for mediating the physical interactions between genes.
Frequency-modulated nuclear localization bursts coordinate gene regulation
TLDR
It is shown that Crz1 exhibits short bursts of nuclear localization that occur stochastically in individual cells and propagate to the expression of downstream genes, and frequency-modulation regulation of localization bursts ensures proportional expression of multiple target genes across a wide dynamic range of expression levels, independent of promoter characteristics.
Periodic epi-organization of the yeast genome revealed by the distribution of promoter sites.
Thermodynamic pathways to genome spatial organization in the cell nucleus.
The emergence of lineage-specific chromosomal topologies from coordinate gene regulation
TLDR
This work model the dynamic relationship between gene expression and chromosomal associations during the differentiation of a multipotential hematopoietic progenitor and reveals dramatic changes in total genomic order.
Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells
TLDR
The first genome-wide analysis of transcriptional interactions using the mouse globin genes in erythroid tissues reveals extensive and preferential intra- and interchromosomal transcription interactomes, establishing a new gene expression paradigm.
Actin-dependent intranuclear repositioning of an active gene locus in vivo
TLDR
Simultaneous four-dimensional tracking of CBs and U2 genes reveals that target loci are recruited toward relatively stably positioned CBs by long-range chromosomal motion, which supports a model in which nuclear actin is required for these rapid, long- range chromosomal movements.
Active genes dynamically colocalize to shared sites of ongoing transcription
TLDR
It is shown that, during transcription in vivo, distal genes colocalize to the same transcription factory at high frequencies.
The influence of volume exclusion by chromatin on the time required to find specific DNA binding sites by diffusion
TLDR
Random permutation of the voxel values of chromatin density abolishes the minimum, thus demonstrating that the speedup seen with increasing volume exclusivity at low to moderateVolume exclusivity is dependent upon the spatial structure of Chromatin within the nucleus.
The role of transcription factories in large-scale structure and dynamics of interphase chromatin.
...
...