A competitive formation of DNA:RNA hybrid G-quadruplex is responsible to the mitochondrial transcription termination at the DNA replication priming site

Nucleic Acids Research, Sep 2014

Human mitochondrial DNA contains a distinctive guanine-rich motif denoted conserved sequence block II (CSB II) that stops RNA transcription, producing prematurely terminated transcripts to prime mitochondrial DNA replication. Recently, we reported a general phenomenon that DNA:RNA hybrid G-quadruplexes (HQs) readily form during transcription when the non-template DNA strand is guanine-rich and such HQs in turn regulate transcription. In this work, we show that transcription of mitochondrial DNA leads to the formation of a stable HQ or alternatively an unstable intramolecular DNA G-quadruplex (DQ) at the CSB II. The HQ is the dominant species and contributes to the majority of the premature transcription termination. Manipulating the stability of the DQ has little effect on the termination even in the absence of HQ; however, abolishing the formation of HQs by preventing the participation of either DNA or RNA abolishes the vast majority of the termination. These results demonstrate that the type of G-quadruplexes (HQ or DQ) is a crucial determinant in directing the transcription termination at the CSB II and suggest a potential functionality of the co-transcriptionally formed HQ in DNA replication initiation. They also suggest that the competition/conversion between an HQ and a DQ may regulate the function of a G-quadruplex-forming sequence.

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A competitive formation of DNA:RNA hybrid G-quadruplex is responsible to the mitochondrial transcription termination at the DNA replication priming site

Ke-wei Zheng 0 Ren-yi Wu 0 Yi-de He 0 Shan Xiao 0 Jia-yu Zhang 0 Jia-quan Liu 0 Yu-hua Hao 0 Zheng Tan 0 0 State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences , Beijing 100101, P.R. China Human mitochondrial DNA contains a distinctive guanine-rich motif denoted conserved sequence block II (CSB II) that stops RNA transcription, producing prematurely terminated transcripts to prime mitochondrial DNA replication. Recently, we reported a general phenomenon that DNA:RNA hybrid Gquadruplexes (HQs) readily form during transcription when the non-template DNA strand is guaninerich and such HQs in turn regulate transcription. In this work, we show that transcription of mitochondrial DNA leads to the formation of a stable HQ or alternatively an unstable intramolecular DNA Gquadruplex (DQ) at the CSB II. The HQ is the dominant species and contributes to the majority of the premature transcription termination. Manipulating the stability of the DQ has little effect on the termination even in the absence of HQ; however, abolishing the formation of HQs by preventing the participation of either DNA or RNA abolishes the vast majority of the termination. These results demonstrate that the type of G-quadruplexes (HQ or DQ) is a crucial determinant in directing the transcription termination at the CSB II and suggest a potential functionality of the co-transcriptionally formed HQ in DNA replication initiation. They also suggest that the competition/conversion between an HQ and a DQ may regulate the function of a G-quadruplex-forming sequence. - Mitochondria are cytoplasmic organelles within eukaryotic cells that carry their own genomic materials apart from those in the nucleus. Human mitochondrial DNA (mtDNA) codes 37 genes in a double-stranded closed circular molecule of 16.5 kb. It contains a distinctive guaninerich (G-rich) motif (GGGGGAGGGGGGGTTTG) denoted conserved sequence block II (CSB II) that directs premature termination of transcription (1). The prematurely terminated transcript serves as a primer to initiate mtDNA replication (1,2). The transition from transcription to primer formation was once proposed by the cleavage of RNA transcript by the mitochondrial RNA processing (RNase MRP) endonuclease (3,4). However, this model is challenged by the fact that the majority of the RNase MRP is localized to the nucleolus (5). The termination is irrespective of the type of RNA polymerase involved and occurs in transcriptions with the mitochondrial RNA polymerase and cofactors or T7 RNA polymerase (68). This fact suggests that the transcription termination is primarily determined by the sequence or structural feature of the CSB II (1). A recent work suggested that the premature termination of transcription at the CSB II is stimulated by G-quadruplex structures formed in RNA transcript (6). G-quadruplexes are four-stranded structures formed by G-rich nucleic acids, in which four G-tracts are held together by Hoogsteen hydrogen bonds in a multi-layered stack of G-quartets (911). G-quadruplex formation is stabilized by K+ and Na+, but not by Li+ (12), and involves the 7-nitrogen (N7) in four of the eight Hoogsteen hydrogen bonds in a G-quartet (13). In that work, it was found that transcription using 7-deaza-GTP in place of the normal guanosine triphosphate (GTP) to inhibit RNA from forming G-quadruplex dramatically reduced the CSB II-dependent transcription termination. The termination was more efficient in K+ than in Li+ solution. Single or double GA mutation in the G5AG7 core of the CSB II reduced the termination, but those outside of the G5AG7 did not. All these facts are suggestive of an involvement of G-quadruplex structures that required the participation of RNA within the G5AG7 tract. A 30-nt RNA oligonucleotide (GAAGCGGGGGAGGGGGGGUUUGGUGGAAAU) covering the CSB II plus the 5 nt upstream and 12 nt downstream of the CSB II formed intramolecular RNA G-quadruplex in an overnight incubation in a K+ or Na+ solution as examined by native gel electrophoresis. It was thus concluded that a predominant unimolecular G-quadruplex uni-G4 whose formation requires guanines within CSB II was the most important quadruplex species to mediate the transcription pretermination (6). One key question remaining unaddressed in that work is that whether the G-quadruplex seen in the incubation actually forms in transcription, which is important for establishing a definitive connection between the structure and the transcription termination. Recently, we found that DNA bearing two or more G-tracts on the non-template strand readily forms DNA:RNA hybrid G-quadruplex (HQ) structures in transcription by recruiting G-tracts from both the non-template DNA strand and RNA transcript. This is a general phenomenon instead of being characteristic of specific sequences. Such HQs can in turn modulate gene expression under both in vitro and in vivo conditions (14). We further showed that putative (...truncated)


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Ke-wei Zheng, Ren-yi Wu, Yi-de He, Shan Xiao, Jia-yu Zhang, Jia-quan Liu, Yu-hua Hao, Zheng Tan. A competitive formation of DNA:RNA hybrid G-quadruplex is responsible to the mitochondrial transcription termination at the DNA replication priming site, Nucleic Acids Research, 2014, pp. 10832-10844, 42/16, DOI: 10.1093/nar/gku764