G4 motifs correlate with promoter-proximal transcriptional pausing in human genes

Johanna Eddy, Aarthy C. Vallur, Sudir Varma, Hongfang Liu, William C. Reinhold, Yves Pommier, Nancy Maizels

Research output: Contribution to journalArticlepeer-review

66 Scopus citations


The RNA Pol II transcription complex pauses just downstream of the promoter in a significant fraction of human genes. The local features of genomic structure that contribute to pausing have not been defined. Here, we show that genes that pause are more G-rich within the region flanking the transcription start site (TSS) than RefSeq genes or non-paused genes. We show that enrichment of binding motifs for common transcription factors, such as SP1, may account for G-richness upstream but not downstream of the TSS. We further show that pausing correlates with the presence of a GrIn1 element, an element bearing one or more G4 motifs at the 5′-end of the first intron, on the non-template DNA strand. These results suggest potential roles for dynamic G4 DNA and G4 RNA structures in cis-regulation of pausing, and thus genome-wide regulation of gene expression, in human cells.

Original languageEnglish (US)
Pages (from-to)4975-4983
Number of pages9
JournalNucleic acids research
Issue number12
StatePublished - Jul 2011

ASJC Scopus subject areas

  • Genetics


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