Determinants of R-loop formation at convergent bidirectionally transcribed trinucleotide repeats

Kaalak Reddy, Mandy Tam, Richard P. Bowater, Miriam Barber, Matthew Tomlinson, Kerrie Nichol Edamura, Yuh-Hwa Wang, Christopher E. Pearson

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Abstract

R-loops have been described at immunoglobulin class switch sequences, prokaryotic and mitochondrial replication origins, and disease-associated (CAG)n and (GAA)n trinucleotide repeats. The determinants of trinucleotide R-loop formation are unclear. Trinucleotide repeat expansions cause diseases including DM1 (CTG)n, SCA1 (CAG)n, FRAXA (CGG)n, FRAXE (CCG)n and FRDA (GAA)n. Bidirectional convergent transcription across these disease repeats can occur. We find R-loops formed when CTG or CGG and their complementary strands CAG or CCG were transcribed; GAA transcription, but not TTC, yielded R-loops. R-loop formation was sensitive to DNA supercoiling, repeat length, insensitive to repeat interruptions, and formed by extension of RNA:DNA hybrids in the RNA polymerase. R-loops arose by transcription in one direction followed by transcription in the opposite direction, and during simultaneous convergent bidirectional transcription of the same repeat forming double R-loop structures. Since each transcribed disease repeat formed R-loops suggests they may have biological functions.
Original languageEnglish
Pages (from-to)1749-1762
Number of pages14
JournalNucleic Acids Research
Volume39
Issue number5
DOIs
Publication statusPublished - 1 Mar 2011

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