Promoter G-quadruplexes and transcription factors cooperate to shape the cell type-specific transcriptome

Sara Lago (), Matteo Nadai, Filippo M. Cernilogar, Maryam Kazerani, Helena Domíniguez Moreno, Gunnar Schotta () and Sara N. Richter ()
Additional contact information
Sara Lago: University of Padua
Matteo Nadai: University of Padua
Filippo M. Cernilogar: Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich
Maryam Kazerani: Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich
Helena Domíniguez Moreno: Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich
Gunnar Schotta: Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich
Sara N. Richter: University of Padua

Nature Communications, 2021, vol. 12, issue 1, 1-13

Abstract: Abstract Cell identity is maintained by activation of cell-specific gene programs, regulated by epigenetic marks, transcription factors and chromatin organization. DNA G-quadruplex (G4)-folded regions in cells were reported to be associated with either increased or decreased transcriptional activity. By G4-ChIP-seq/RNA-seq analysis on liposarcoma cells we confirmed that G4s in promoters are invariably associated with high transcription levels in open chromatin. Comparing G4 presence, location and transcript levels in liposarcoma cells to available data on keratinocytes, we showed that the same promoter sequences of the same genes in the two cell lines had different G4-folding state: high transcript levels consistently associated with G4-folding. Transcription factors AP-1 and SP1, whose binding sites were the most significantly represented in G4-folded sequences, coimmunoprecipitated with their G4-folded promoters. Thus, G4s and their associated transcription factors cooperate to determine cell-specific transcriptional programs, making G4s to strongly emerge as new epigenetic regulators of the transcription machinery.

Date: 2021
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-021-24198-2 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-24198-2

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-021-24198-2

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().