Unknown

Dataset Information

0

Zinc-finger transcription factors are associated with guanine quadruplex motifs in human, chimpanzee, mouse and rat promoters genome-wide.


ABSTRACT: Function of non-B DNA structures are poorly understood though several bioinformatics studies predict role of the G-quadruplex DNA structure in transcription. Earlier, using transcriptome profiling we found evidence of widespread G-quadruplex-mediated gene regulation. Herein, we asked whether potential G-quadruplex (PG4) motifs associate with transcription factors (TF). This was analyzed using 220 position weight matrices [designated as transcription factor binding sites (TFBS)], representing 187 unique TF, in >75,000 genes in human, chimpanzee, mouse and rat. Results show binding sites of nine TFs, including that of AP-2, SP1, MAZ and VDR, occurred significantly within 100 bases of the PG4 motif (P < 1.24E-10). PG4-TFBS combinations were conserved in 'orthologously' related promoters across all four organisms and were associated with >850 genes in each genome. Remarkably, seven of the nine TFs were zinc-finger binding proteins indicating a novel characteristic of PG4 motifs. To test these findings, transcriptome profiles from human cell lines treated with G-quadruplex-specific molecules were used; 66 genes were significantly differentially expressed across both cell-types, which also harbored conserved PG4 motifs along with one/more of the nine TFBS. In addition, genes regulated by PG4-TFBS combinations were found to be co-regulated in human tissues, further emphasizing the regulatory significance of the associations.

SUBMITTER: Kumar P 

PROVIDER: S-EPMC3185432 | BioStudies | 2011-01-01T00:00:00Z

REPOSITORIES: biostudies

Similar Datasets

2014-01-01 | S-EPMC5154493 | BioStudies
1000-01-01 | S-EPMC3592403 | BioStudies
1000-01-01 | S-EPMC1522027 | BioStudies
2019-01-01 | S-EPMC6323897 | BioStudies
2007-01-01 | S-EPMC2047340 | BioStudies
2007-01-01 | S-EPMC2246259 | BioStudies
2019-01-01 | S-EPMC6370388 | BioStudies
1000-01-01 | S-EPMC3676070 | BioStudies
2014-01-01 | S-EPMC4224337 | BioStudies
2013-01-01 | S-EPMC3700821 | BioStudies