Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes

In the present study, we carried out a comparative analysis of chromatin characteristics in terms of the scaffold/matrix attachment regions, nucleosome formation potential and the occurrence of repetitive sequences, in the upstream regulatory regions of housekeeping and tissue specific genes. Our data show that putative scaffold/matrix attachment regions are more abundant and nucleosome formation potential is higher in the 5' regions of tissue specific genes as compared to the housekeeping genes.The differences in the chromatin features between the two groups of genes indicate the involvement of chromatin organisation in the control of gene expression. The presence of global regulatory mechanisms mediated through chromatin organisation can decrease the burden of invoking gene specific regulators for maintenance of the active/silenced state of gene expression. This could partially explain the lower number of genes estimated in the human genome.Eukaryotic gene transcription is largely known to be orchestrated by protein factors like activators, co-activators and co-repressors [1]. However, nucleosomal organisation, non-passive structural scaffolds and global structure of chromatin are increasingly being recognised as major players in the regulation of gene expression. The ability of sequences to position nucleosomes and to be anchored to the nuclear matrix to provide a spatial context for regulation of expression are measurable parameters that may influence the interactions with transcription machinery [2,3]. This level of regulation may be distinctly different for genes whose expression is constitutive in comparison to genes that exhibit tissue specific expression. The latter would demand an open chromatin configuration in certain tissues and repressive organisation in others. In this study, we examined whether the potential to utilise global regulatory mechanisms to control gene expression through chromatin organisation varies between housekeeping and tissue specifi