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

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

Research output: Contribution to journalArticle

50 Citations (Scopus)

Abstract

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
Volume39
Issue number12
DOIs
StatePublished - Jul 2011
Externally publishedYes

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Transcription Initiation Site
Genes
RNA Polymerase II
DNA
Gene Expression Regulation
Introns
Transcription Factors
Genome
RNA

ASJC Scopus subject areas

  • Genetics

Cite this

Eddy, J., Vallur, A. C., Varma, S., Liu, H. D., Reinhold, W. C., Pommier, Y., & Maizels, N. (2011). G4 motifs correlate with promoter-proximal transcriptional pausing in human genes. Nucleic Acids Research, 39(12), 4975-4983. https://doi.org/10.1093/nar/gkr079

G4 motifs correlate with promoter-proximal transcriptional pausing in human genes. / Eddy, Johanna; Vallur, Aarthy C.; Varma, Sudir; Liu, Hongfang D; Reinhold, William C.; Pommier, Yves; Maizels, Nancy.

In: Nucleic Acids Research, Vol. 39, No. 12, 07.2011, p. 4975-4983.

Research output: Contribution to journalArticle

Eddy, J, Vallur, AC, Varma, S, Liu, HD, Reinhold, WC, Pommier, Y & Maizels, N 2011, 'G4 motifs correlate with promoter-proximal transcriptional pausing in human genes', Nucleic Acids Research, vol. 39, no. 12, pp. 4975-4983. https://doi.org/10.1093/nar/gkr079
Eddy, Johanna ; Vallur, Aarthy C. ; Varma, Sudir ; Liu, Hongfang D ; Reinhold, William C. ; Pommier, Yves ; Maizels, Nancy. / G4 motifs correlate with promoter-proximal transcriptional pausing in human genes. In: Nucleic Acids Research. 2011 ; Vol. 39, No. 12. pp. 4975-4983.
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