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BMC Genomics  2008 

Strand bias structure in mouse DNA gives a glimpse of how chromatin structure affects gene expression

DOI: 10.1186/1471-2164-9-16

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Abstract:

The mouse genome is shown to have a segmented structure defined by strand bias. Transcription is known to cause a strand bias and numerous analyses are presented to show that the strand bias in question is not caused by transcription. However, these strand bias segments influence the position of genes and their unspliced length. The position of genes within the strand bias structure affects the probability that a gene is switched on and its expression level. Transcription has a highly directional flow within this structure and the peak volume of transcription is around 20 kb from the A-rich/T-rich segment boundary on the T-rich side, directed away from the boundary. The A-rich/T-rich boundaries are SATB1 binding regions, whereas the T-rich/A-rich boundary regions are not.The direct cause of the strand bias structure may be DNA replication. The strand bias segments represent a further biological feature, the chromatin structure, which in turn influences the ease of transcription.Because of the Watson-Crick structure of DNA – A paired with T and C with G – the number of As must equal the number of Ts when the bases on both strands are counted. Although this equality does not have to be true for a single strand, Chargaff's second law refers to the equality of A/T and C/G bases on a single strand [1] and broadly speaking eukaryote genomes are free of intrastrand bias [2].Early work on strand bias analysed prokaryote and viral genomes where strand biases have been observed and associated with origins of replication: the leading strand is found to be G-rich and T-rich, with the G-C bias often being found to be more consistent than the A-T bias [3-6].Strand bias has been discovered at transcription start sites in plants and fungi [7], animals [8,9], and splice sites [10]. Strand bias has been found for long regions of DNA around actual and putative origins of replication [11]. An analysis of nearby divergent genes concluded that both replication and transcription effects w

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