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. 2009 Nov;37(20):6716-22.
doi: 10.1093/nar/gkp740. Epub 2009 Sep 10.

Genome-wide analysis of a G-quadruplex-specific single-chain antibody that regulates gene expression

Himesh Fernando  1 , Sven Sewitz, Jeremy Darot, Simon Tavaré, Julian Leon Huppert, Shankar Balasubramanian
Affiliations

Genome-wide analysis of a G-quadruplex-specific single-chain antibody that regulates gene expression

Himesh Fernando et al. Nucleic Acids Res. 2009 Nov.

Abstract

G-quadruplex nucleic acids have been proposed to play a role in a number of fundamental biological processes that include transcription and translation. We have developed a single-chain antibody that is selective for G-quadruplex DNA over double-stranded DNA, and here show that when it is expressed in human cells, it significantly affects the expression of a wide variety of genes, in a manner that correlates with the presence of predicted G-quadruplexes. We observe cases where gene expression is increased or decreased, and that there are apparent interactions with G-quadruplex motifs at the beginning and end of the genes, and on either strand. The outcomes of this genome-wide study demonstrate that G-quadruplex recognition by the antibody has physiological consequences, and provides insights into some of the complexity associated with G-quadruplex-based regulation.

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Figures

Figure 1.
Figure 1.
PQS density at the promoter region. (A) Up-regulated genes (bold) compared with all genes. (B) Down-regulated genes (bold) compared with all genes. Red lines indicate data for the coding strand, blue lines for the template strand, black for the sum. The numbers are relative to the TSS.
Figure 2.
Figure 2.
Relative enrichment of PQS in the regions studied. (A and B) Up-regulated genes. Enrichment of PQS in the coding strand (red), the template strand (blue) and both (black) of up-regulated genes, compared with all known genes. (C and D) Down-regulated genes, colours as in (A). All enrichments are compared with PQS densities in specified regions and strands for all genes. Numbers are relative to the TSS or TSS.
See this image and copyright information in PMC

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