Szczepińska Teresa, Pawłowski Krzysztof
Nencki Institute of Experimental Biology, PAS, Pasteura 3, Warsaw 02-093, Poland.
BMC Res Notes. 2013 Jun 13;6:229. doi: 10.1186/1756-0500-6-229.
The relationships between gene expression and nuclear structure, chromosome territories in particular, are currently being elucidated experimentally. Each chromosome occupies an individual, spatially-limited space with a preferential position relative to the nuclear centre that may be specific to the cell and tissue type. We sought to discover whether patterns in gene expression databases might exist that would mirror prevailing or recurring nuclear structure patterns, chromosome territory interactions in particular.
We used human gene expression datasets, both from a tissue expression atlas and from a large set including diverse types of perturbations. We identified groups of positional gene clusters over-represented in gene expression clusters. We show that some pairs of chromosomes and pairs of 10 Mbp long chromosome regions are significantly enriched in the expression clusters. The functions of genes involved in inter-chromosome co-expression relationships are non-random and predominantly related to cell-cell communication and reaction to external stimuli.
We suggest that inter-chromosomal gene co-expression can be interpreted in the context of nuclear structure, and that even expression datasets that include very diverse conditions and cell types show consistent relationships.
目前正在通过实验阐明基因表达与核结构（尤其是染色体领地）之间的关系。每条染色体都占据一个独立的、空间有限的空间，相对于核中心具有一个优先位置，该位置可能因细胞和组织类型而异。我们试图发现基因表达数据库中是否存在能够反映主要或反复出现的核结构模式（尤其是染色体领地相互作用）的模式。
我们使用了来自组织表达图谱和包含多种类型扰动的大型数据集的人类基因表达数据集。我们在基因表达簇中鉴定出了位置基因簇的过度富集组。我们表明，一些染色体对和10兆碱基长的染色体区域对在表达簇中显著富集。参与染色体间共表达关系的基因功能并非随机，且主要与细胞间通讯和对外部刺激的反应有关。
我们认为染色体间基因共表达可以在核结构的背景下进行解释，并且即使是包含非常多样的条件和细胞类型的表达数据集也显示出一致的关系。
