Sequence periodicity discovered in human genome


In an article just published in Genome Biology, Charles Hebert and Hugues Roest Crollius of the Ecole Normale Supérieure in Paris have shown the existence of a novel periodicity of nucleotide frequencies in the human genome that may have implications for the positioning of nucleosomes and gene regulation.

In their study, Hebert and Roest Crollius have aligned human genes relative to their transcription start sites and observe a pattern of YY dinucleotides (where Y is either C or T) spaced 10 base pairs apart in phase with the transcription start site. Importantly, analysis of nucleosome-positioning data shows that the nucleosomes are associated with the dinucleotides. The pattern is enriched in genes with binding sites for the EP300 nucleosome-modelling protein. The authors speculate that the repeating pattern may help to position the nucleosomes in such a way that they are easily modified by EP300, thus facilitating their displacement by RNA polymerase, although this model is currently speculative and will require confirmation in future work.

Nevertheless, this work presents an exciting new pattern in the human genome, and has implications for how positioned nucleosomes affect the transcription of genes.

Nucleosome rotational setting is associated with transcriptional regulation in promoters of tissue-specific human genes

Charles Hebert and Hugues Roest Crollius, Genome Biology 2010, 11:R51 

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dr. gunn

Attributed to Lars Juhl Jensen:

As I understand the paper, the new discovery is supposed to be that you see this signal when you align promoters at the TSS +1 site. But as far as I can tell, Ioshikhes et al. found something similar in 1999.

Digging a bit further: Mavrich et al. showed in 2008 that nucleosomes are positioned in a very regular manner relative to transcription start sites (doi:10.1101/gr.078261.108). Combining that with the 10bp periodicity found by Satchwell et al. in 1986 would seem to trivially lead to the observed 10bp periodicity relative to transcription start.

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