Spatial Organization of DNA in the Nucleus May Determine Positions of Recombination Hot Spots

Transposable elements as scaffold/matrix attachment regions: shaping organization and functions in genomes

The hierarchical structure of eukaryotic genomes has regulatory layers, one of them being epigenetic "indexing" of the genome that leads to cell-type-specific patterns of gene expression. By establishing loops and defining chromatin domains, cells can achieve coordinated control over multi-locus segments of the genome. This is thought to be achieved using scaffold/matrix attachment regions (S/MARs) that establish structural and functional loops and topologically associating domains (TADs) that define a self-interacting region of the genome. Large-scale genome-wide mapping of S/MARs has begun to uncover these aspects of genome organization. A recent genome-wide study showed the association of transposable elements (TEs) with a significant fraction of S/MARs, suggesting that the multitude of TE-derived repeats constitute a class of anchorage sites of chromatin loops to nuclear architecture. In this study, we provide an insight that TE-driven dispersal of S/MARs has the potential to restructure the chromosomes by creating novel loops and domains. The combination of TEs and S/MARs, as elements that can hop through the genome along with regulatory capabilities, may provide an active mechanism of genome evolution leading to the emergence of novel features in biological systems. The significance is that a genome-wide study mapping developmental S/MARs reveals an intriguing link between these elements and TEs. This article highlights the potential of the TE-S/MAR combination to drive evolution by restructuring and shaping the genome.

Mining Complex Spatial Patterns: Issues and Techniques

Spatial data mining is the quantitative study of phenomena that are located in space. This paper investigates methods of mining patterns of a complex spatial data set (which generally describes any kind of data where the location in space of object holds importance). We based this research on the analysis of some spatial characteristics of certain objects. We began with describing the spatial pattern of events or objects with respect to their attributes; we looked at how to describe the spatial nature/characteristics of entities in an environment with respect to their spatial and non-spatial attributes. We also looked at modelling (predictive modelling/knowledge management of complex spatial systems), querying and implementing a complex spatial database (using data structure and algorithms). Critically speaking, the presence of spatial auto-correlation and the fact that continuous data types are always present in spatial data makes it important to create methods, tools and algorithms to mine spatial patterns in a complex spatial data set. This work is particularly useful to researchers in the field of data mining as it contributes a whole lot of knowledge to different application areas of data mining especially spatial data mining. It can also be useful in teaching and likewise for other study purposes.