R-loop induced G-quadruplex in non-template promotes transcription by successive R-loop formation.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
07 07 2020
07 07 2020
Historique:
received:
11
09
2019
accepted:
17
06
2020
entrez:
9
7
2020
pubmed:
9
7
2020
medline:
9
9
2020
Statut:
epublish
Résumé
G-quadruplex (G4) is a noncanonical secondary structure of DNA or RNA which can enhance or repress gene expression, yet the underlying molecular mechanism remains uncertain. Here we show that when positioned downstream of transcription start site, the orientation of potential G4 forming sequence (PQS), but not the sequence alters transcriptional output. Ensemble in vitro transcription assays indicate that PQS in the non-template increases mRNA production rate and yield. Using sequential single molecule detection stages, we demonstrate that while binding and initiation of T7 RNA polymerase is unchanged, the efficiency of elongation and the final mRNA output is higher when PQS is in the non-template. Strikingly, the enhanced elongation arises from the transcription-induced R-loop formation, which in turn generates G4 structure in the non-template. The G4 stabilized R-loop leads to increased transcription by a mechanism involving successive rounds of R-loop formation.
Identifiants
pubmed: 32636376
doi: 10.1038/s41467-020-17176-7
pii: 10.1038/s41467-020-17176-7
pmc: PMC7341879
doi:
Substances chimiques
RNA, Messenger
0
Viral Proteins
0
RNA
63231-63-0
DNA
9007-49-2
bacteriophage T7 RNA polymerase
EC 2.7.7.-
DNA-Directed RNA Polymerases
EC 2.7.7.6
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
3392Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM115631
Pays : United States
Références
Collie, G. W. & Parkinson, G. N. The application of DNA and RNA G-quadruplexes to therapeutic medicines. Chem. Soc. Rev. 40, 5867–5892 (2011).
pubmed: 21789296
Chambers, V. S. et al. High-throughput sequencing of DNA G-quadruplex structures in the human genome. Nat. Biotechnol. 33, 877–881 (2015).
pubmed: 26192317
Hansel-Hertsch, R. et al. G-quadruplex structures mark human regulatory chromatin. Nat. Genet. 48, 1267–1272 (2016).
pubmed: 27618450
Maizels, N. & Gray, L. T. The G4 genome. PLoS Genet. 9, e1003468 (2013).
pubmed: 23637633
pmcid: 3630100
Huppert, J. L. & Balasubramanian, S. G-quadruplexes in promoters throughout the human genome. Nucleic Acids Res. 35, 406–413 (2007).
pubmed: 17169996
Halder, K., Wieland, M. & Hartig, J. S. Predictable suppression of gene expression by 5′-UTR-based RNA quadruplexes. Nucleic Acids Res. 37, 6811–6817 (2009).
pubmed: 19740765
pmcid: 2777418
Holder, I. T. & Hartig, J. S. A matter of location: influence of G-quadruplexes on Escherichia coli gene expression. Chem. Biol. 21, 1511–1521 (2014).
pubmed: 25459072
Agarwal, T., Roy, S., Kumar, S., Chakraborty, T. K. & Maiti, S. In the sense of transcription regulation by G-quadruplexes: asymmetric effects in sense and antisense strands. Biochemistry 53, 3711–3718 (2014).
pubmed: 24850370
Mendoza, O., Bourdoncle, A., Boule, J. B., Brosh, R. M. Jr. & Mergny, J. L. G-quadruplexes and helicases. Nucleic Acids Res. 44, 1989–2006 (2016).
pubmed: 26883636
pmcid: 4797304
Maizels, N. G4-associated human diseases. EMBO Rep. 16, 910–922 (2015).
pubmed: 26150098
pmcid: 4552485
Rigo, R., Palumbo, M. & Sissi, C. G-quadruplexes in human promoters: a challenge for therapeutic applications. Biochim. Biophys. Acta Gen. Subj. 1861, 1399–1413 (2017).
pubmed: 28025083
Siddiqui-Jain, A., Grand, C. L., Bearss, D. J. & Hurley, L. H. Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription. Proc. Natl Acad. Sci. USA 99, 11593–11598 (2002).
pubmed: 12195017
Cogoi, S. & Xodo, L. E. G-quadruplex formation within the promoter of the KRAS proto-oncogene and its effect on transcription. Nucleic Acids Res. 34, 2536–2549 (2006).
pubmed: 16687659
pmcid: 1459413
Sun, D. et al. The proximal promoter region of the human vascular endothelial growth factor gene has a G-quadruplex structure that can be targeted by G-quadruplex-interactive agents. Mol. Cancer Ther. 7, 880–889 (2008).
pubmed: 18413801
pmcid: 2367258
Onel, B. et al. A new G-quadruplex with hairpin loop immediately upstream of the human BCL2 P1 promoter modulates transcription. J. Am. Chem. Soc. 138, 2563–2570 (2016).
pubmed: 26841249
pmcid: 5019542
Fleming, A. M., Ding, Y. & Burrows, C. J. Oxidative DNA damage is epigenetic by regulating gene transcription via base excision repair. Proc. Natl Acad. Sci. USA 114, 2604–2609 (2017).
pubmed: 28143930
Fleming, A. M., Zhu, J., Ding, Y. & Burrows, C. J. 8-Oxo-7,8-dihydroguanine in the context of a gene promoter G-quadruplex is an on-off switch for transcription. ACS Chem. Biol. 12, 2417–2426 (2017).
pubmed: 28829124
pmcid: 5604463
Fleming, A. M., Zhu, J., Ding, Y. & Burrows, C. J. Location dependence of the transcriptional response of a potential G-quadruplex in gene promoters under oxidative stress. Nucleic Acids Res. 47, 5049–5060 (2019).
pubmed: 30916339
pmcid: 6547423
Smestad, J. A. & Maher, L. J. III Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription. BMC Med. Genet. 16, 91 (2015).
pubmed: 26449372
pmcid: 4599794
Broxson, C., Beckett, J. & Tornaletti, S. Transcription arrest by a G quadruplex forming-trinucleotide repeat sequence from the human c-myb gene. Biochemistry 50, 4162–4172 (2011).
pubmed: 21469677
Aguilera, A. & Garcia-Muse, T. R loops: from transcription byproducts to threats to genome stability. Mol. Cell 46, 115–124 (2012).
pubmed: 22541554
Duquette, M. L., Handa, P., Vincent, J. A., Taylor, A. F. & Maizels, N. Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA. Genes Dev. 18, 1618–1629 (2004).
pubmed: 15231739
pmcid: 443523
Wanrooij, P. H. et al. A hybrid G-quadruplex structure formed between RNA and DNA explains the extraordinary stability of the mitochondrial R-loop. Nucleic Acids Res. 40, 10334–10344 (2012).
pubmed: 22965135
pmcid: 3488243
Zhang, J. Y., Zheng, K. W., Xiao, S., Hao, Y. H. & Tan, Z. Mechanism and manipulation of DNA:RNA hybrid G-quadruplex formation in transcription of G-rich DNA. J. Am. Chem. Soc. 136, 1381–1390 (2014).
pubmed: 24392825
Zhao, Y. et al. Real-time detection reveals responsive cotranscriptional formation of persistent intramolecular DNA and intermolecular DNA:RNA hybrid G-quadruplexes stabilized by R-loop. Anal. Chem. 89, 6036–6042 (2017).
pubmed: 28447783
Belotserkovskii, B. P. et al. Mechanisms and implications of transcription blockage by guanine-rich DNA sequences. Proc. Natl Acad. Sci. USA 107, 12816–12821 (2010).
pubmed: 20616059
Belotserkovskii, B. P., Soo Shin, J. H. & Hanawalt, P. C. Strong transcription blockage mediated by R-loop formation within a G-rich homopurine-homopyrimidine sequence localized in the vicinity of the promoter. Nucleic Acids Res. 45, 6589–6599 (2017).
pubmed: 28498974
pmcid: 5499740
Chen, L. et al. R-ChIP using inactive RNase H reveals dynamic coupling of R-loops with transcriptional pausing at gene promoters. Mol. Cell 68, 745–74 (2017).
pubmed: 29104020
pmcid: 5957070
De Magis, A. et al. DNA damage and genome instability by G-quadruplex ligands are mediated by R loops in human cancer cells. Proc. Natl Acad. Sci. USA 116, 816–825 (2019).
pubmed: 30591567
Tippana, R., Xiao, W. & Myong, S. G-quadruplex conformation and dynamics are determined by loop length and sequence. Nucleic Acids Res. 42, 8106–8114 (2014).
pubmed: 24920827
pmcid: 4081081
Kreig, A. et al. G-quadruplex formation in double strand DNA probed by NMM and CV fluorescence. Nucleic Acids Res. 43, 7961–7970 (2015).
pubmed: 26202971
pmcid: 4652765
Hwang, H., Kim, H. & Myong, S. Protein induced fluorescence enhancement as a single molecule assay with short distance sensitivity. Proc. Natl Acad. Sci. USA 108, 7414–7418 (2011).
pubmed: 21502529
Hwang, H. & Myong, S. Protein induced fluorescence enhancement (PIFE) for probing protein-nucleic acid interactions. Chem. Soc. Rev. 43, 1221–1229 (2014).
pubmed: 24056732
pmcid: 4142350
Roy, R., Hohng, S. & Ha, T. A practical guide to single-molecule FRET. Nat. Methods 5, 507–516 (2008).
pubmed: 18511918
pmcid: 3769523
Joo C., Ha T. Single-molecule FRET with total internal reflection microscopy. Cold Spring Harb. Protoc. 2012, pdb.top072058 (2012).
Stennett, E. M., Ciuba, M. A., Lin, S. & Levitus, M. Demystifying PIFE: the photophysics behind the protein-induced fluorescence enhancement phenomenon in Cy3. J. Phys. Chem. Lett. 6, 1819–1823 (2015).
pubmed: 26263254
Koh, H. R. et al. Correlating transcription initiation and conformational changes by a single-subunit RNA polymerase with near base-pair resolution. Mol. Cell 70, 695–706 e695 (2018).
pubmed: 29775583
pmcid: 5983381
Boque-Sastre, R., Soler, M. & Guil, S. Detection and characterization of R loop structures. Methods Mol. Biol. 1543, 231–242 (2017).
pubmed: 28349431
Ginno, P. A., Lott, P. L., Christensen, H. C., Korf, I. & Chedin, F. R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters. Mol. Cell 45, 814–825 (2012).
pubmed: 22387027
pmcid: 3319272
Wahba, L., Gore, S. K. & Koshland, D. The homologous recombination machinery modulates the formation of RNA-DNA hybrids and associated chromosome instability. eLife 2, e00505 (2013).
pubmed: 23795288
pmcid: 3679537
Gowrishankar, J., Leela, J. K. & Anupama, K. R-loops in bacterial transcription: their causes and consequences. Transcription 4, 153–157 (2013).
pubmed: 23756343
pmcid: 3977913
Nudler, E. RNA polymerase backtracking in gene regulation and genome instability. Cell 149, 1438–1445 (2012).
pubmed: 22726433
Masse, E. & Drolet, M. R-loop-dependent hypernegative supercoiling in Escherichia coli topA mutants preferentially occurs at low temperatures and correlates with growth inhibition. J. Mol. Biol. 294, 321–332 (1999).
pubmed: 10610761
Masse, E. & Drolet, M. Escherichia coli DNA topoisomerase I inhibits R-loop formation by relaxing transcription-induced negative supercoiling. J. Biol. Chem. 274, 16659–16664 (1999).
pubmed: 10347234
Masse, E. & Drolet, M. Relaxation of transcription-induced negative supercoiling is an essential function of Escherichia coli DNA topoisomerase I. J. Biol. Chem. 274, 16654–16658 (1999).
pubmed: 10347233
Roy, D., Zhang, Z., Lu, Z., Hsieh, C. L. & Lieber, M. R. Competition between the RNA transcript and the nontemplate DNA strand during R-loop formation in vitro: a nick can serve as a strong R-loop initiation site. Mol. Cell. Biol. 30, 146–159 (2010).
pubmed: 19841062
Kuzminov, A. When DNA topology turns deadly - RNA polymerases dig in their R-loops to stand their ground: new positive and negative (super)twists in the replication-transcription conflict. Trends Genet. 34, 111–120 (2018).
pubmed: 29179918
Belotserkovskii, B. P. et al. Transcription blockage by homopurine DNA sequences: role of sequence composition and single-strand breaks. Nucleic Acids Res. 41, 1817–1828 (2013).
pubmed: 23275544
Kim, M. et al. Quantitative analysis and prediction of G-quadruplex forming sequences in double-stranded DNA. Nucleic Acids Res. 44, 4807–4817 (2016).
pubmed: 27095201
pmcid: 4889947
Tateishi-Karimata, H., Kawauchi, K. & Sugimoto, N. Destabilization of DNA G-quadruplexes by chemical environment changes during tumor progression facilitates transcription. J. Am. Chem. Soc. 140, 642–651 (2018).
pubmed: 29286249
Bobrovskyy, M. & Vanderpool, C. K. Diverse mechanisms of post-transcriptional repression by the small RNA regulator of glucose-phosphate stress. Mol. Microbiol. 99, 254–273 (2016).
pubmed: 26411266
Lee, C. Y., McNerney, C. & Myong, S. G-quadruplex and protein binding by single-molecule FRET microscopy. Methods Mol. Biol. 2035, 309–322 (2019).
pubmed: 31444758
pmcid: 6859946
Zhang, Z., Revyakin, A., Grimm, J. B., Lavis, L. D. & Tjian, R. Single-molecule tracking of the transcription cycle by sub-second RNA detection. eLife 3, e01775 (2014).
pubmed: 24473079
pmcid: 3901038