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dc.contributor.authorNadel, Julie
dc.contributor.authorAthanasiadou, Rodoniki
dc.contributor.authorLemetre, Christophe
dc.contributor.authorWijetunga, N. Ari
dc.contributor.authorÓ Broin, Pilib
dc.contributor.authorSato, Hanae
dc.contributor.authorZhang, Zhengdong
dc.contributor.authorJeddeloh, Jeffrey
dc.contributor.authorMontagna, Cristina
dc.contributor.authorGolden, Aaron
dc.contributor.authorSeoighe, Cathal
dc.contributor.authorGreally, John M.
dc.identifier.citationNadel, Julie; Athanasiadou, Rodoniki; Lemetre, Christophe; Wijetunga, N. Ari; Ó Broin, Pilib; Sato, Hanae; Zhang, Zhengdong; Jeddeloh, Jeffrey; Montagna, Cristina; Golden, Aaron; Seoighe, Cathal; Greally, John M. (2015). Rna:dna hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships. Epigenetics & Chromatin 8 ,
dc.description.abstractBackground: RNA:DNA hybrids represent a non-canonical nucleic acid structure that has been associated with a range of human diseases and potential transcriptional regulatory functions. Mapping of RNA:DNA hybrids in human cells reveals them to have a number of characteristics that give insights into their functions. Results: We find RNA:DNA hybrids to occupy millions of base pairs in the human genome. A directional sequencing approach shows the RNA component of the RNA:DNA hybrid to be purine-rich, indicating a thermodynamic contribution to their in vivo stability. The RNA:DNA hybrids are enriched at loci with decreased DNA methylation and increased DNase hypersensitivity, and within larger domains with characteristics of heterochromatin formation, indicating potential transcriptional regulatory properties. Mass spectrometry studies of chromatin at RNA:DNA hybrids shows the presence of the ILF2 and ILF3 transcription factors, supporting a model of certain transcription factors binding preferentially to the RNA:DNA conformation. Conclusions: Overall, there is little to indicate a dependence for RNA:DNA hybrids forming co-transcriptionally, with results from the ribosomal DNA repeat unit instead supporting the intriguing model of RNA generating these structures in trans. The results of the study
dc.publisherSpringer Nature
dc.relation.ispartofEpigenetics & Chromatin
dc.rightsAttribution-NonCommercial-NoDerivs 3.0 Ireland
dc.subjectrna:DNA hybrid
dc.subjectDNA methylation
dc.subjecttranscription factor
dc.subjectnon-coding rna
dc.subjectmass spectrometry
dc.subjectr-loop formation
dc.subjectclass switch sequences
dc.subjectfactor-binding sites
dc.subjecthuman ribosomal DNA
dc.subjectactivated t-cells
dc.subjectchip-seq data
dc.subjectrna/DNA hybrids
dc.subjectstranded rna
dc.subjectpause sites
dc.titleRna:dna hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships

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