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Characterization of long G4-rich enhancer-associated genomic regions engaging in a novel loop:loop 'G4 Kissing' interaction.

Publication ,  Journal Article
Williams, JD; Houserova, D; Johnson, BR; Dyniewski, B; Berroyer, A; French, H; Barchie, AA; Bilbrey, DD; Demeis, JD; Ghee, KR; Hughes, AG ...
Published in: Nucleic Acids Research
June 2020

Mammalian antibody switch regions (∼1500 bp) are composed of a series of closely neighboring G4-capable sequences. Whereas numerous structural and genome-wide analyses of roles for minimal G4s in transcriptional regulation have been reported, Long G4-capable regions (LG4s)-like those at antibody switch regions-remain virtually unexplored. Using a novel computational approach we have identified 301 LG4s in the human genome and find LG4s prone to mutation and significantly associated with chromosomal rearrangements in malignancy. Strikingly, 217 LG4s overlap annotated enhancers, and we find the promoters regulated by these enhancers markedly enriched in G4-capable sequences suggesting G4s facilitate promoter-enhancer interactions. Finally, and much to our surprise, we also find single-stranded loops of minimal G4s within individual LG4 loci are frequently highly complementary to one another with 178 LG4 loci averaging >35 internal loop:loop complements of >8 bp. As such, we hypothesized (then experimentally confirmed) that G4 loops within individual LG4 loci directly basepair with one another (similar to characterized stem-loop kissing interactions) forming a hitherto undescribed, higher-order, G4-based secondary structure we term a 'G4 Kiss or G4K'. In conclusion, LG4s adopt novel, higher-order, composite G4 structures directly contributing to the inherent instability, regulatory capacity, and maintenance of these conspicuous genomic regions.

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Published In

Nucleic Acids Research

DOI

EISSN

1362-4962

ISSN

0305-1048

Publication Date

June 2020

Volume

48

Issue

11

Start / End Page

5907 / 5925

Related Subject Headings

  • Sequence Deletion
  • Segmental Duplications, Genomic
  • Saccharomyces cerevisiae
  • Nucleic Acid Conformation
  • Humans
  • Guanine
  • Genomics
  • Genome, Human
  • Genetic Variation
  • Gene Rearrangement
 

Citation

APA
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ICMJE
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Williams, J. D., Houserova, D., Johnson, B. R., Dyniewski, B., Berroyer, A., French, H., … Borchert, G. M. (2020). Characterization of long G4-rich enhancer-associated genomic regions engaging in a novel loop:loop 'G4 Kissing' interaction. Nucleic Acids Research, 48(11), 5907–5925. https://doi.org/10.1093/nar/gkaa357
Williams, Jonathan D., Dominika Houserova, Bradley R. Johnson, Brad Dyniewski, Alexandra Berroyer, Hannah French, Addison A. Barchie, et al. “Characterization of long G4-rich enhancer-associated genomic regions engaging in a novel loop:loop 'G4 Kissing' interaction.Nucleic Acids Research 48, no. 11 (June 2020): 5907–25. https://doi.org/10.1093/nar/gkaa357.
Williams JD, Houserova D, Johnson BR, Dyniewski B, Berroyer A, French H, et al. Characterization of long G4-rich enhancer-associated genomic regions engaging in a novel loop:loop 'G4 Kissing' interaction. Nucleic Acids Research. 2020 Jun;48(11):5907–25.
Williams, Jonathan D., et al. “Characterization of long G4-rich enhancer-associated genomic regions engaging in a novel loop:loop 'G4 Kissing' interaction.Nucleic Acids Research, vol. 48, no. 11, June 2020, pp. 5907–25. Epmc, doi:10.1093/nar/gkaa357.
Williams JD, Houserova D, Johnson BR, Dyniewski B, Berroyer A, French H, Barchie AA, Bilbrey DD, Demeis JD, Ghee KR, Hughes AG, Kreitz NW, McInnis CH, Pudner SC, Reeves MN, Stahly AN, Turcu A, Watters BC, Daly GT, Langley RJ, Gillespie MN, Prakash A, Larson ED, Kasukurthi MV, Huang J, Jinks-Robertson S, Borchert GM. Characterization of long G4-rich enhancer-associated genomic regions engaging in a novel loop:loop 'G4 Kissing' interaction. Nucleic Acids Research. 2020 Jun;48(11):5907–5925.
Journal cover image

Published In

Nucleic Acids Research

DOI

EISSN

1362-4962

ISSN

0305-1048

Publication Date

June 2020

Volume

48

Issue

11

Start / End Page

5907 / 5925

Related Subject Headings

  • Sequence Deletion
  • Segmental Duplications, Genomic
  • Saccharomyces cerevisiae
  • Nucleic Acid Conformation
  • Humans
  • Guanine
  • Genomics
  • Genome, Human
  • Genetic Variation
  • Gene Rearrangement