Abstract
RNA can bind within the major groove of purine-rich DNA via Hoogsteen base pairing and form a triple helical RNA–DNA structure that anchors the RNA to specific DNA sequences, thereby targeting RNA-associated regulatory proteins to distinct genomic sites. Here we present methods to analyze the potential of a given RNA to form triplexes in vitro and to validate these structures in vivo.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Felsenfeld G, Davies DR, Rich A (1957) Formation of a three-stranded polynucleotide molecule. J Am Chem Soc 79:2023–2024
Goñi JR, de la Cruz X, Orozco M (2004) Triplex-forming oligonucleotide target sequences in the human genome. Nucleic Acids Res 32:354–360
Buske FA, Bauer DC, Mattick JS, Bailey TL (2012) Triplexator: detecting nucleic acid triple helices in genomic and transcriptomic data. Genome Res 22:1372–1381
Schmitz KM, Mayer C, Postepska A, Grummt I (2010) Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes. Genes Dev 24:2264–2269
Zhao Z, Sentürk N, Chen C, Grummt I (2018) LncRNA PAPAS tethered to the rDNA enhancer recruits hypophosphorylated CHD4/NuRD4 to repress rRNA synthesis at elevated temperature. Genes Dev 32:836–848
Grote P, Wittler L, Hendrix D, Koch F, Währisch S, Beisaw A et al (2013) The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. Dev Cell 24:206–214
Mondal T, Subhash S, Vaid R, Enroth S, Uday S, Reinius B et al (2015) MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA-DNA triplex structures. Nat Commun 6:7743
Postepska-Igielska A, Giwojna A, Gasri-Plotnitsky L, Schmitt N, Dold A, Ginsberg D et al (2015) LncRNA Khps1 regulates expression of the proto-oncogene SPHK1 via triplex-mediated changes in chromatin structure. Mol Cell 60:626–636
Blank-Giwojna A, Postepska-Igielska A, Grummt I (2019) LncRNA KHPS1 activates a poised enhancer by triplex-dependent recruitment of epigenetic regulators. Cell Rep 26:2904–2915
O’Leary VB, Ovsepian SV, Carrascosa LG, Buske FA, Radulovic V, Niyazi M et al (2015) PARTICLE, a triplex-forming long ncRNA, regulates locus-specific methylation in response to low-dose irradiation. Cell Rep 11:474–485
Kalwa M, Hänzelmann S, Otto S, Kuo CC, Franzen J, Joussen S et al (2016) The lncRNA HOTAIR impacts on mesenchymal stem cells via triple helix formation. Nucleic Acids Res 44:10631–10643
Paugh SW, Coss DR, Bao J, Laudermilk LT, Grace CR, Ferreira AM et al (2016) MicroRNAs form triplexes with double stranded DNA at sequence-specific binding sites; a eukaryotic mechanism via which microRNAs could directly alter gene expression. PLoS Comput Biol 12(2):e1004744
Li Y, Syed J, Sugiyama H (2016) RNA-DNA triplex formation by long noncoding RNAs. Cell Chem Biol 23:1325–1333
Sentürk Cetin N, Kuo C-C, Ribarska T, Li R, Costa IG, Grummt I (2019) Isolation and genome-wide characterization of cellular DNA:RNA triplex structures. Nucleic Acids Res 47:2306–2321
Maldonado R, Schwartz U, Silberhorn E, Langst G (2019) Nucleosomes stabilize ssRNA-dsDNA triple helices in human cells. Mol Cell 73:1243–1254
Brown WT, Nolin S, Houck G Jr, Ding X, Glicksman A, Li SY, Stark-Houck S, Brophy P, Duncan C, Dobkin C, Jenkins E (1996) Prenatal diagnosis and carrier screening for fragile X by PCR. Am J Med Genet 64:191–195
Acknowledgements
Work in the Grummt lab has been funded by the DFG (GR475/22-2; SFB1036), CellNetworks (EcTop Survey 2014), the Baden-Württemberg Stiftung, and the Deutsches Krebsforschungszentrum (DKFZ).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Postepska-Igielska, A., Blank-Giwojna, A., Grummt, I. (2020). Analysis of RNA–DNA Triplex Structures In Vitro and In Vivo. In: Ørom, U. (eds) RNA-Chromatin Interactions. Methods in Molecular Biology, vol 2161. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0680-3_16
Download citation
DOI: https://doi.org/10.1007/978-1-0716-0680-3_16
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-0679-7
Online ISBN: 978-1-0716-0680-3
eBook Packages: Springer Protocols