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Journal articles on the topic 'RNA: DNA hybrides'

Author: Grafiati

Published: 25 May 2024

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1

Yang, Xuan, Binyuan Zhai, Shunxin Wang, Xiangfei Kong, Yingjin Tan, Lin Liu, Xiao Yang, Taicong Tan, Shuxian Zhang, and Liangran Zhang. "RNA-DNA hybrids regulate meiotic recombination." Cell Reports 37, no. 10 (December 2021): 110097. http://dx.doi.org/10.1016/j.celrep.2021.110097.

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2

Kamath-Loeb, Ashwini S., Amnon Hizi, John Tabone, Marjorie S. Solomon, and Lawrence A. Loeb. "Inefficient Repair of RNA . DNA Hybrids." European Journal of Biochemistry 250, no. 2 (December 1997): 492–501. http://dx.doi.org/10.1111/j.1432-1033.1997.0492a.x.

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3

Waldron, Denise. "RNA–DNA hybrids: double-edged swords." Nature Reviews Genetics 18, no. 1 (November 21, 2016): 3. http://dx.doi.org/10.1038/nrg.2016.153.

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4

Hall, Kathleen B. "NMR spectroscopy of DNA/RNA hybrids." Current Opinion in Structural Biology 3, no. 3 (June 1993): 336–39. http://dx.doi.org/10.1016/s0959-440x(05)80103-4.

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5

Kim, Joung Sug, Junghyun Park, Jang Hyeon Choi, Seungjae Kang, and Nokyoung Park. "RNA–DNA hybrid nano-materials for highly efficient and long lasting RNA interference effect." RSC Advances 13, no. 5 (2023): 3139–46. http://dx.doi.org/10.1039/d2ra06249f.

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A new RNAi approach was developed using an X-RDNA and Ri-Dgel. The nanostructured materials of dsRNA–DNA hybrids showed higher efficient and longer lasting RNA interference effect compared with conventional dsRNA.

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6

Di, Lin, Yusi Fu, Yue Sun, Jie Li, Lu Liu, Jiacheng Yao, Guanbo Wang, et al. "RNA sequencing by direct tagmentation of RNA/DNA hybrids." Proceedings of the National Academy of Sciences 117, no. 6 (January 27, 2020): 2886–93. http://dx.doi.org/10.1073/pnas.1919800117.

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Transcriptome profiling by RNA sequencing (RNA-seq) has been widely used to characterize cellular status, but it relies on second-strand complementary DNA (cDNA) synthesis to generate initial material for library preparation. Here we use bacterial transposase Tn5, which has been increasingly used in various high-throughput DNA analyses, to construct RNA-seq libraries without second-strand synthesis. We show that Tn5 transposome can randomly bind RNA/DNA heteroduplexes and add sequencing adapters onto RNA directly after reverse transcription. This method, Sequencing HEteRo RNA-DNA-hYbrid (SHERRY), is versatile and scalable. SHERRY accepts a wide range of starting materials, from bulk RNA to single cells. SHERRY offers a greatly simplified protocol and produces results with higher reproducibility and GC uniformity compared with prevailing RNA-seq methods.

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7

Paull, Tanya T. "RNA–DNA hybrids and the convergence with DNA repair." Critical Reviews in Biochemistry and Molecular Biology 54, no. 4 (July 4, 2019): 371–84. http://dx.doi.org/10.1080/10409238.2019.1670131.

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8

Huang, Yuegao, Congju Chen, and Irina M. Russu. "Structural Energetics of Two RNA-DNA Hybrids." Biophysical Journal 96, no. 3 (February 2009): 578a. http://dx.doi.org/10.1016/j.bpj.2008.12.3022.

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9

Vydzhak, Olga, Brian Luke, and Natalie Schindler. "Non-coding RNAs at the Eukaryotic rDNA Locus: RNA–DNA Hybrids and Beyond." Journal of Molecular Biology 432, no. 15 (July 2020): 4287–304. http://dx.doi.org/10.1016/j.jmb.2020.05.011.

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10

Aguilera, Andrés, and Belén Gómez-González. "DNA–RNA hybrids: the risks of DNA breakage during transcription." Nature Structural & Molecular Biology 24, no. 5 (May 2017): 439–43. http://dx.doi.org/10.1038/nsmb.3395.

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11

Ozdemir, Ahmet Y., Timur Rusanov, Tatiana Kent, Labiba A. Siddique, and Richard T. Pomerantz. "Polymerase θ-helicase efficiently unwinds DNA and RNA-DNA hybrids." Journal of Biological Chemistry 293, no. 14 (February 14, 2018): 5259–69. http://dx.doi.org/10.1074/jbc.ra117.000565.

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12

Kolasa, Kimberly A., Janet R. Morrow, and Arun P. Sharma. "Trivalent lanthanide ions do not cleave RNA in DNA-RNA hybrids." Inorganic Chemistry 32, no. 19 (September 1993): 3983–84. http://dx.doi.org/10.1021/ic00071a002.

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13

Wang, Isabel X., Christopher Grunseich, Jennifer Fox, Joshua Burdick, Zhengwei Zhu, Niema Ravazian, Markus Hafner, and Vivian G. Cheung. "Human proteins that interact with RNA/DNA hybrids." Genome Research 28, no. 9 (August 14, 2018): 1405–14. http://dx.doi.org/10.1101/gr.237362.118.

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14

Pires, Vanessa Borges, Nina Lohner, Tina Wagner, Carolin B. Wagner, Maya Wilkens, Mona Hajikazemi, Katrin Paeschke, Falk Butter, and Brian Luke. "RNA-DNA hybrids prevent resection at dysfunctional telomeres." Cell Reports 42, no. 2 (February 2023): 112077. http://dx.doi.org/10.1016/j.celrep.2023.112077.

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15

Shiels, Jerome C., Bozidar Jerkovic, Anne M. Baranger, and Philip H. Bolton. "RNA–DNA Hybrids Containing Damaged DNA are Substrates for RNase H." Bioorganic & Medicinal Chemistry Letters 11, no. 19 (October 2001): 2623–26. http://dx.doi.org/10.1016/s0960-894x(01)00527-3.

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16

Crossley, Magdalena P., Michael J. Bocek, Stephan Hamperl, Tomek Swigut, and Karlene A. Cimprich. "qDRIP: a method to quantitatively assess RNA–DNA hybrid formation genome-wide." Nucleic Acids Research 48, no. 14 (June 16, 2020): e84-e84. http://dx.doi.org/10.1093/nar/gkaa500.

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Abstract R-loops are dynamic, co-transcriptional nucleic acid structures that facilitate physiological processes but can also cause DNA damage in certain contexts. Perturbations of transcription or R-loop resolution are expected to change their genomic distribution. Next-generation sequencing approaches to map RNA–DNA hybrids, a component of R-loops, have so far not allowed quantitative comparisons between such conditions. Here, we describe quantitative differential DNA–RNA immunoprecipitation (qDRIP), a method combining synthetic RNA–DNA-hybrid internal standards with high-resolution, strand-specific sequencing. We show that qDRIP avoids biases inherent to read-count normalization by accurately profiling signal in regions unaffected by transcription inhibition in human cells, and by facilitating accurate differential peak calling between conditions. We also use these quantitative comparisons to make the first estimates of the absolute count of RNA–DNA hybrids per cell and their half-lives genome-wide. Finally, we identify a subset of RNA–DNA hybrids with high GC skew which are partially resistant to RNase H. Overall, qDRIP allows for accurate normalization in conditions where R-loops are perturbed and for quantitative measurements that provide previously unattainable biological insights.

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17

Figiel, Małgorzata, Hyongi Chon, Susana M. Cerritelli, Magdalena Cybulska, Robert J. Crouch, and Marcin Nowotny. "The Structural and Biochemical Characterization of Human RNase H2 Complex Reveals the Molecular Basis for Substrate Recognition and Aicardi-Goutières Syndrome Defects." Journal of Biological Chemistry 286, no. 12 (December 22, 2010): 10540–50. http://dx.doi.org/10.1074/jbc.m110.181974.

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RNase H2 cleaves RNA sequences that are part of RNA/DNA hybrids or that are incorporated into DNA, thus, preventing genomic instability and the accumulation of aberrant nucleic acid, which in humans induces Aicardi-Goutières syndrome, a severe autoimmune disorder. The 3.1 Å crystal structure of human RNase H2 presented here allowed us to map the positions of all 29 mutations found in Aicardi-Goutières syndrome patients, several of which were not visible in the previously reported mouse RNase H2. We propose the possible effects of these mutations on the protein stability and function. Bacterial and eukaryotic RNases H2 differ in composition and substrate specificity. Bacterial RNases H2 are monomeric proteins and homologs of the eukaryotic RNases H2 catalytic subunit, which in addition possesses two accessory proteins. The eukaryotic RNase H2 heterotrimeric complex recognizes RNA/DNA hybrids and (5′)RNA-DNA(3′)/DNA junction hybrids as substrates with similar efficiency, whereas bacterial RNases H2 are highly specialized in the recognition of the (5′)RNA-DNA(3′) junction and very poorly cleave RNA/DNA hybrids in the presence of Mg2+ ions. Using the crystal structure of the Thermotoga maritima RNase H2-substrate complex, we modeled the human RNase H2-substrate complex and verified the model by mutational analysis. Our model indicates that the difference in substrate preference stems from the different position of the crucial tyrosine residue involved in substrate binding and recognition.

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18

Santamarı́a, David, Guillermo de la Cueva, Marı́a Luisa Martı́nez-Robles, Dora B. Krimer, Pablo Hernández, and Jorge B. Schvartzman. "DnaB Helicase Is Unable to Dissociate RNA-DNA Hybrids." Journal of Biological Chemistry 273, no. 50 (December 11, 1998): 33386–96. http://dx.doi.org/10.1074/jbc.273.50.33386.

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19

de Vroom, E., H. C. P. F. Roelen, C. P. Saris, T. N. W. Budding, G. A. van der Marel, and J. H. van Boom. "Preparation of covalently linked DNA-RNA hybrids and arabinocytidine containing DNA fragments." Nucleic Acids Research 16, no. 7 (1988): 2987–3003. http://dx.doi.org/10.1093/nar/16.7.2987.

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20

Zhan, Yilin, and Giovanni Zocchi. "Flexibility of DNA/PNA, DNA/LNA, DNA/RNA hybrids measured with a nanoscale transducer." EPL (Europhysics Letters) 119, no. 4 (August 1, 2017): 48005. http://dx.doi.org/10.1209/0295-5075/119/48005.

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21

Xu, B., and D. A. Clayton. "A persistent RNA-DNA hybrid is formed during transcription at a phylogenetically conserved mitochondrial DNA sequence." Molecular and Cellular Biology 15, no. 1 (January 1995): 580–89. http://dx.doi.org/10.1128/mcb.15.1.580.

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Critical features of the mitochondrial leading-strand DNA replication origin are conserved from Saccharomyces cerevisiae to humans. These include a promoter and a downstream GC-rich sequence block (CSBII) that encodes rGs within the primer RNA. During in vitro transcription at yeast mitochondrial replication origins, there is stable and persistent RNA-DNA hybrid formation that begins at the 5' end of the rG region. The short rG-dC sequence is the necessary and sufficient nucleic acid element for establishing stable hybrids, and the presence of rGs within the RNA strand of the RNA-DNA hybrid is required. The efficiency of hybrid formation depends on the length of RNA synthesized 5' to CSBII and the type of RNA polymerase employed. Once made, the RNA strand of an RNA-DNA hybrid can serve as an effective primer for mitochondrial DNA polymerase. These results reveal a new mechanism for persistent RNA-DNA hybrid formation and suggest a step in priming mitochondrial DNA replication that requires both mitochondrial RNA polymerase and an rG-dC sequence-specific event to form an extensive RNA-DNA hybrid.

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22

Gillespie, F. P., T. H. Hong, and J. M. Eisenstadt. "Transcription and translation of mitochondrial DNA in interspecific somatic cell hybrids." Molecular and Cellular Biology 6, no. 6 (June 1986): 1951–57. http://dx.doi.org/10.1128/mcb.6.6.1951-1957.1986.

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We examined the mitochondrial transcription and translation products of somatic cell hybrids constructed by the fusion of Chinese hamster and mouse cells. The hybrid cell lines OAC-k, OAC-l, and OAC-m contain approximately equal amounts of hamster and mouse mitochondrial DNA and produced mitochondrial rRNA from both parental species in the same ratio. Cell lines OAC-k, OAC-l, and OAC-m also produced poly(A)+ mouse mitochondrial RNA transcripts comparable in complexity and quantity to poly(A)+ RNA from the mouse parent. However, the overall level of poly(A)+ hamster mitochondrial RNA from these hybrids was significantly reduced compared with that from the hamster parent. The hybrid cells also lacked several poly(A)+ RNA species found in the hamster parent, but contained additional minor transcripts. The mitochondrially coded proteins of the OAC-k, OAC-l, and OAC-m cells were predominantly encoded by the mouse mitochondrial DNA.

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23

Gillespie, F. P., T. H. Hong, and J. M. Eisenstadt. "Transcription and translation of mitochondrial DNA in interspecific somatic cell hybrids." Molecular and Cellular Biology 6, no. 6 (June 1986): 1951–57. http://dx.doi.org/10.1128/mcb.6.6.1951.

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We examined the mitochondrial transcription and translation products of somatic cell hybrids constructed by the fusion of Chinese hamster and mouse cells. The hybrid cell lines OAC-k, OAC-l, and OAC-m contain approximately equal amounts of hamster and mouse mitochondrial DNA and produced mitochondrial rRNA from both parental species in the same ratio. Cell lines OAC-k, OAC-l, and OAC-m also produced poly(A)+ mouse mitochondrial RNA transcripts comparable in complexity and quantity to poly(A)+ RNA from the mouse parent. However, the overall level of poly(A)+ hamster mitochondrial RNA from these hybrids was significantly reduced compared with that from the hamster parent. The hybrid cells also lacked several poly(A)+ RNA species found in the hamster parent, but contained additional minor transcripts. The mitochondrially coded proteins of the OAC-k, OAC-l, and OAC-m cells were predominantly encoded by the mouse mitochondrial DNA.

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24

Turner, K. B., H. Y. Yi-Brunozzi, R. G. Brinson, J. P. Marino, D. Fabris, and S. F. J. Le Grice. "SHAMS: Combining chemical modification of RNA with mass spectrometry to examine polypurine tract-containing RNA/DNA hybrids." RNA 15, no. 8 (June 17, 2009): 1605–13. http://dx.doi.org/10.1261/rna.1615409.

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25

Tseng, R. W., and N. H. Acheson. "Use of a novel S1 nuclease RNA-mapping technique to measure efficiency of transcription termination on polyomavirus DNA." Molecular and Cellular Biology 6, no. 5 (May 1986): 1624–32. http://dx.doi.org/10.1128/mcb.6.5.1624-1632.1986.

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We devised a strategy to measure the efficiency of transcription termination in vivo by RNA polymerase on polyomavirus DNA. Pulse-labeled nuclear RNA was hybridized with a single-stranded polyomavirus DNA fragment which spans the transcription initiation region. Hybrids were treated with RNase, bound to nitrocellulose filters, eluted with S1 nuclease, and analyzed by gel electrophoresis. The ratio of full-length to less-than-full-length DNA-RNA hybrids was used to calculate transcription termination frequency. We found that 50% of the polymerases terminated per traverse of the L DNA strand during the late phase of infection. The method for mapping in vivo pulse-labeled RNAs which we developed is potentially useful for studying unstable cellular or viral RNAs.

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26

Tseng, R. W., and N. H. Acheson. "Use of a novel S1 nuclease RNA-mapping technique to measure efficiency of transcription termination on polyomavirus DNA." Molecular and Cellular Biology 6, no. 5 (May 1986): 1624–32. http://dx.doi.org/10.1128/mcb.6.5.1624.

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We devised a strategy to measure the efficiency of transcription termination in vivo by RNA polymerase on polyomavirus DNA. Pulse-labeled nuclear RNA was hybridized with a single-stranded polyomavirus DNA fragment which spans the transcription initiation region. Hybrids were treated with RNase, bound to nitrocellulose filters, eluted with S1 nuclease, and analyzed by gel electrophoresis. The ratio of full-length to less-than-full-length DNA-RNA hybrids was used to calculate transcription termination frequency. We found that 50% of the polymerases terminated per traverse of the L DNA strand during the late phase of infection. The method for mapping in vivo pulse-labeled RNAs which we developed is potentially useful for studying unstable cellular or viral RNAs.

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27

Kratochvílová, Irena, Martin Vala, Martin Weiter, Miroslava Špérová, Bohdan Schneider, Ondřej Páv, Jakub Šebera, Ivan Rosenberg, and Vladimír Sychrovský. "Charge transfer through DNA/DNA duplexes and DNA/RNA hybrids: Complex theoretical and experimental studies." Biophysical Chemistry 180-181 (October 2013): 127–34. http://dx.doi.org/10.1016/j.bpc.2013.07.009.

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28

Kim, Nayun, Jang-Eun Cho, Yue C. Li, and Sue Jinks-Robertson. "RNA∶DNA Hybrids Initiate Quasi-Palindrome-Associated Mutations in Highly Transcribed Yeast DNA." PLoS Genetics 9, no. 11 (November 7, 2013): e1003924. http://dx.doi.org/10.1371/journal.pgen.1003924.

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29

Lopata, M. A., B. Sollner-Webb, and D. W. Cleveland. "Surprising S1-resistant trimolecular hybrids: potential complication in interpretation of S1 mapping analyses." Molecular and Cellular Biology 5, no. 10 (October 1985): 2842–46. http://dx.doi.org/10.1128/mcb.5.10.2842-2846.1985.

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Although the technique of S1 mapping is a powerful analytical tool for the analysis of RNA, we now report a surprising complication involving a trimolecular hybrid between two RNA species and a single DNA probe molecule which, if unrecognized, can lead to misleading interpretations. We document that such trimolecular hybrids can be efficiently formed under some hybridization conditions and that the probe DNA sequence at the junction of the two RNA molecules can be remarkably stable to digestion with S1. Trimolecular hybrids can arise in any instance whenever a distal region of an end-labeled DNA probe is homologous to a moderately abundant RNA in the sample to be analyzed. This situation presents a serious, potential complication for a variety of S1 analyses, particularly those in which DNA transfection has been utilized to reintroduce in vitro-engineered genes into cultured animal cells.

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30

Lopata, M. A., B. Sollner-Webb, and D. W. Cleveland. "Surprising S1-resistant trimolecular hybrids: potential complication in interpretation of S1 mapping analyses." Molecular and Cellular Biology 5, no. 10 (October 1985): 2842–46. http://dx.doi.org/10.1128/mcb.5.10.2842.

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Although the technique of S1 mapping is a powerful analytical tool for the analysis of RNA, we now report a surprising complication involving a trimolecular hybrid between two RNA species and a single DNA probe molecule which, if unrecognized, can lead to misleading interpretations. We document that such trimolecular hybrids can be efficiently formed under some hybridization conditions and that the probe DNA sequence at the junction of the two RNA molecules can be remarkably stable to digestion with S1. Trimolecular hybrids can arise in any instance whenever a distal region of an end-labeled DNA probe is homologous to a moderately abundant RNA in the sample to be analyzed. This situation presents a serious, potential complication for a variety of S1 analyses, particularly those in which DNA transfection has been utilized to reintroduce in vitro-engineered genes into cultured animal cells.

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31

Balk, Bettina, André Maicher, Martina Dees, Julia Klermund, Sarah Luke-Glaser, Katharina Bender, and Brian Luke. "Telomeric RNA-DNA hybrids affect telomere-length dynamics and senescence." Nature Structural & Molecular Biology 20, no. 10 (September 8, 2013): 1199–205. http://dx.doi.org/10.1038/nsmb.2662.

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32

Gómez-González, Belén, Sonia Barroso, Emilia Herrera-Moyano, and Andrés Aguilera. "Spontaneous DNA-RNA hybrids: differential impacts throughout the cell cycle." Cell Cycle 19, no. 5 (February 16, 2020): 525–31. http://dx.doi.org/10.1080/15384101.2020.1728015.

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33

Wang, Jiou, Aaron R. Haeusler, and Eric AJ Simko. "Emerging role of RNA•DNA hybrids in C9orf72-linked neurodegeneration." Cell Cycle 14, no. 4 (February 16, 2015): 526–32. http://dx.doi.org/10.1080/15384101.2014.995490.

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34

Strzyz, Paulina. "RNA–DNA hybrids: a double-edged sword in genomic stability." Nature Reviews Molecular Cell Biology 17, no. 12 (November 21, 2016): 740. http://dx.doi.org/10.1038/nrm.2016.155.

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35

Palancade, Benoit, and Rodney Rothstein. "The Ultimate (Mis)match: When DNA Meets RNA." Cells 10, no. 6 (June 8, 2021): 1433. http://dx.doi.org/10.3390/cells10061433.

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RNA-containing structures, including ribonucleotide insertions, DNA:RNA hybrids and R-loops, have recently emerged as critical players in the maintenance of genome integrity. Strikingly, different enzymatic activities classically involved in genome maintenance contribute to their generation, their processing into genotoxic or repair intermediates, or their removal. Here we review how this substrate promiscuity can account for the detrimental and beneficial impacts of RNA insertions during genome metabolism. We summarize how in vivo and in vitro experiments support the contribution of DNA polymerases and homologous recombination proteins in the formation of RNA-containing structures, and we discuss the role of DNA repair enzymes in their removal. The diversity of pathways that are thus affected by RNA insertions likely reflects the ancestral function of RNA molecules in genome maintenance and transmission.

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36

E, Beeram. "Mini review on Protein – Protein and DNA/RNA – protein interactions in biology." Asploro Journal of Biomedical and Clinical Case Reports 2, no. 2 (October 29, 2019): 82–83. http://dx.doi.org/10.36502/2019/asjbccr.6165.

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RNase H1 generally processes the RNA- DNA hybrids through non specific interaction between HBD and the ds RNA/DNA hybrid. There are no direct protein- protein interactions between the hybrid and HBD of RNase H1. The DNA binding region is highly conserved compared to RNA binding region and the Kd for RNA/DNA hybrid is less compared to ds RNA than to that of ds DNA [1]. HBD increases the processivity of RNase H1 and mutations in RNA binding region is tolerated compared to DBR. The RNA interacts between ɑ2 and β3 region with in the loop and with the protein in shallower minor groove.

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37

Kojima, Kenji, Misato Baba, Motoki Tsukiashi, Takuto Nishimura, and Kiyoshi Yasukawa. "RNA/DNA structures recognized by RNase H2." Briefings in Functional Genomics 18, no. 3 (June 20, 2018): 169–73. http://dx.doi.org/10.1093/bfgp/ely024.

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Abstract Ribonuclease H (RNase H) [EC 3.1.26.4] is an enzyme that specifically degrades RNA from RNA/DNA hybrids. Since its discovery in 1969, the enzyme has been extensively studied for its catalytic mechanism and physiological role. RNase H has been classified into two major families, Type 1 and Type 2. Type 1 enzymes are designated RNase HI in prokaryotes and RNase H1 in eukaryotes, while Type 2 enzymes are designated RNase HII in prokaryotes and RNase H2 in eukaryotes. Type 2 enzymes are able to cleave the 5′-phosphodiester bond of one ribonucleotide embedded in a DNA double strand. Recent studies have shown that RNase H2 is involved in excision of a single ribonucleotide embedded in genomic DNA and removal of an R-loop formed in cells. It is also involved in double-strand break of DNA and its repair. In this review, we aim to outline the structures recognized by RNase H2.

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38

Suresh, Gorle, and U. Deva Priyakumar. "DNA–RNA hybrid duplexes with decreasing pyrimidine content in the DNA strand provide structural snapshots for the A- to B-form conformational transition of nucleic acids." Phys. Chem. Chem. Phys. 16, no. 34 (2014): 18148–55. http://dx.doi.org/10.1039/c4cp02478h.

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39

Lee, Hyunjee, HyeokJin Cho, Jooyoung Kim, Sua Lee, Jungmin Yoo, Daeho Park, and Gwangrog Lee. "RNase H is an exo- and endoribonuclease with asymmetric directionality, depending on the binding mode to the structural variants of RNA:DNA hybrids." Nucleic Acids Research 50, no. 4 (November 12, 2021): 1801–14. http://dx.doi.org/10.1093/nar/gkab1064.

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Abstract RNase H is involved in fundamental cellular processes and is responsible for removing the short stretch of RNA from Okazaki fragments and the long stretch of RNA from R-loops. Defects in RNase H lead to embryo lethality in mice and Aicardi-Goutieres syndrome in humans, suggesting the importance of RNase H. To date, RNase H is known to be a non-sequence-specific endonuclease, but it is not known whether it performs other functions on the structural variants of RNA:DNA hybrids. Here, we used Escherichia coli RNase H as a model, and examined its catalytic mechanism and its substrate recognition modes, using single-molecule FRET. We discovered that RNase H acts as a processive exoribonuclease on the 3′ DNA overhang side but as a distributive non-sequence-specific endonuclease on the 5′ DNA overhang side of RNA:DNA hybrids or on blunt-ended hybrids. The high affinity of previously unidentified double-stranded (ds) and single-stranded (ss) DNA junctions flanking RNA:DNA hybrids may help RNase H find the hybrid substrates in long genomic DNA. Our study provides new insights into the multifunctionality of RNase H, elucidating unprecedented roles of junctions and ssDNA overhang on RNA:DNA hybrids.

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40

Bansal, M., J. S. Lee, J. W. Kozarich, and J. Stubbe. "Mechanistic analyses of site-specific degradation in DNA-RNA hybrids by prototypic DNA cleavers." Nucleic Acids Research 25, no. 9 (May 1, 1997): 1836–45. http://dx.doi.org/10.1093/nar/25.9.1836.

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41

Bansal, M., J. W. Kozarich, and J. Stubbe. "Effects of hypoxanthine substitution on bleomycin-mediated DNA strand degradation in DNA-RNA hybrids." Nucleic Acids Research 25, no. 9 (May 1, 1997): 1846–53. http://dx.doi.org/10.1093/nar/25.9.1846.

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42

Coutlée, Francois, Linda Bobo, Kumudini Mayur, Robert H. Yolken, and Raphael P. Viscidi. "Immunodetection of DNA with biotinylated RNA probes: A study of reactivity of a monoclonal antibody to DNA-RNA hybrids." Analytical Biochemistry 181, no. 1 (August 1989): 96–105. http://dx.doi.org/10.1016/0003-2697(89)90399-0.

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43

Kapali, Ojashpi Singh, and Vladimir Kuznetsov. "Abstract 407: RNA:DNA hybrid/R-loop determinants variation in distinct basal-like breast cancer cells." Cancer Research 84, no. 6_Supplement (March 22, 2024): 407. http://dx.doi.org/10.1158/1538-7445.am2024-407.

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Abstract Introduction: Despite progress in treatment methods and diagnosis, breast cancer remains one of the world's leading cancers causes of death. Among the various subtypes, basal-like breast cancer (BLBC) is highly diverse, low differentiated, most aggressive form with poor prognosis. Co-translational R-loops are created by combining G-rich RNA with complementary C-rich DNA (RNA: DNA hybrid), which creates a three-stranded nucleic acid structure. R-loops are often associated with genome instability and aggressiveness of cancers. However, their role in the diversity of BLBC remains controversial and poorly understood. This study aims to characterize RNA: DNA hybrid variations in BLBC from a cellular, genetic, and biochemical perspective. Methods: This study investigates the variation of RNA: DNA hybrid formation in stable BLBC cells. We utilize a panel of stable basal-like cell lines (MDAMB231, MDAMB436, SUM149PT) and proliferative non-cancer cells (MCF10A). They represent different genetic and cell lineages in BLBC development which allows us to study R-loop distribution in different basal lineage cells. Luminal breast cancer cells (MCF7) were used in comparative analysis. To detect RNA: DNA hybrids, we optimized Immunofluorescence (IF) specificity using RNase III and H enzymes. Predictions from Quantitative Model of R-loop Forming Sequences (QmRLFS) identify RLFS in specific gene regulatory regions. This design allows us to define R-loop position and boundaries, and optimize primers for the DRIP-qPCR which quantifies RNA: DNA hybrid enrichment in transcription regulatory sites for several breast cancer-associated genes such as BRCA1, TP53, PTEN, and AURKA. The expression of these genes was detected using RTqPCR. Results: Our IF and computational image analyses demonstrated that RNA: DNA hybrids are present not only luminal cells (as found by others), but also in the studied BLBC cells. The non-cancer proliferative cells (MCF10A) show low RNA: DNA hybrid signals bolstering our experimental technique. Variation of the RNA: DNA hybrid signals were distinct in various BLBC cells which was supported by the DRIP-qPCR and RTqPCR findings. The R-loop formation data variations was referred to the cell line contexts and the studied genes responsible for tumor suppression, DNA damage/repair signaling and impair apoptosis in breast cancer. Conclusion: Our study suggests that RNA: DNA hybrids are formed and distributed heterogeneously in the genomes and gene regions of stable BLBC cell lines, while in basal proliferative (non-cancer) cells hybrid signals are weak. A subset of the RNA: DNA hybrids might be particularly significant at certain gene loci contributing to tumor progression, indicating their significance in BLBC pathogenesis. This study provides insights into the cellular and molecular basis of the BLBC heterogeneity and implicates the RNA:DNA hybrid as a potential diagnostic and therapeutic markers. Citation Format: Ojashpi Singh Kapali, Vladimir Kuznetsov. RNA:DNA hybrid/R-loop determinants variation in distinct basal-like breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 407.

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Meng, Xiangzhou, Hung Quang Dang, and Geoffrey M. Kapler. "Developmentally Programmed Switches in DNA Replication: Gene Amplification and Genome-Wide Endoreplication in Tetrahymena." Microorganisms 11, no. 2 (February 16, 2023): 491. http://dx.doi.org/10.3390/microorganisms11020491.

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Locus-specific gene amplification and genome-wide endoreplication generate the elevated copy number of ribosomal DNA (rDNA, 9000 C) and non-rDNA (90 C) chromosomes in the developing macronucleus of Tetrahymena thermophila. Subsequently, all macronuclear chromosomes replicate once per cell cycle during vegetative growth. Here, we describe an unanticipated, programmed switch in the regulation of replication initiation in the rDNA minichromosome. Early in development, the 21 kb rDNA minichromosome is preferentially amplified from 2 C to ~800 C from well-defined origins, concurrent with genome-wide endoreplication (2 C to 8–16 C) in starved mating Tetrahymena (endoreplication (ER) Phase 1). Upon refeeding, rDNA and non-rDNA chromosomes achieve their final copy number through resumption of just the endoreplication program (ER Phase 2). Unconventional rDNA replication intermediates are generated primarily during ER phase 2, consistent with delocalized replication initiation and possible formation of persistent RNA-DNA hybrids. Origin usage and replication fork elongation are affected in non-rDNA chromosomes as well. Despite the developmentally programmed 10-fold reduction in the ubiquitous eukaryotic initiator, the Origin Recognition Complex (ORC), active initiation sites are more closely spaced in ER phases 1 and 2 compared to vegetative growing cells. We propose that initiation site selection is relaxed in endoreplicating macronuclear chromosomes and may be less dependent on ORC.

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Nava, Giulia Maria, Lavinia Grasso, Sarah Sertic, Achille Pellicioli, Marco Muzi Falconi, and Federico Lazzaro. "One, No One, and One Hundred Thousand: The Many Forms of Ribonucleotides in DNA." International Journal of Molecular Sciences 21, no. 5 (March 2, 2020): 1706. http://dx.doi.org/10.3390/ijms21051706.

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In the last decade, it has become evident that RNA is frequently found in DNA. It is now well established that single embedded ribonucleoside monophosphates (rNMPs) are primarily introduced by DNA polymerases and that longer stretches of RNA can anneal to DNA, generating RNA:DNA hybrids. Among them, the most studied are R-loops, peculiar three-stranded nucleic acid structures formed upon the re-hybridization of a transcript to its template DNA. In addition, polyribonucleotide chains are synthesized to allow DNA replication priming, double-strand breaks repair, and may as well result from the direct incorporation of consecutive rNMPs by DNA polymerases. The bright side of RNA into DNA is that it contributes to regulating different physiological functions. The dark side, however, is that persistent RNA compromises genome integrity and genome stability. For these reasons, the characterization of all these structures has been under growing investigation. In this review, we discussed the origin of single and multiple ribonucleotides in the genome and in the DNA of organelles, focusing on situations where the aberrant processing of RNA:DNA hybrids may result in multiple rNMPs embedded in DNA. We concluded by providing an overview of the currently available strategies to study the presence of single and multiple ribonucleotides in DNA in vivo.

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Jang, Yumi, Zeinab Elsayed, Rebeka Eki, Shuaixin He, Kang-Ping Du, Tarek Abbas, and Mihoko Kai. "Intrinsically disordered protein RBM14 plays a role in generation of RNA:DNA hybrids at double-strand break sites." Proceedings of the National Academy of Sciences 117, no. 10 (February 24, 2020): 5329–38. http://dx.doi.org/10.1073/pnas.1913280117.

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Accumulating evidence suggests participation of RNA-binding proteins with intrinsically disordered domains (IDPs) in the DNA damage response (DDR). These IDPs form liquid compartments at DNA damage sites in a poly(ADP ribose) (PAR)-dependent manner. However, it is greatly unknown how the IDPs are involved in DDR. We have shown previously that one of the IDPs RBM14 is required for the canonical nonhomologous end joining (cNHEJ). Here we show that RBM14 is recruited to DNA damage sites in a PARP- and RNA polymerase II (RNAPII)-dependent manner. Both KU and RBM14 are required for RNAPII-dependent generation of RNA:DNA hybrids at DNA damage sites. In fact, RBM14 binds to RNA:DNA hybrids. Furthermore, RNA:DNA hybrids and RNAPII are detected at gene-coding as well as at intergenic areas when double-strand breaks (DSBs) are induced. We propose that the cNHEJ pathway utilizes damage-induced transcription and intrinsically disordered protein RBM14 for efficient repair of DSBs.

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Hu, Yan, Henrietta W. Bennett, Na Liu, Martin Moravec, Jessica F. Williams, Claus M. Azzalin, and Megan C. King. "RNA–DNA Hybrids Support Recombination-Based Telomere Maintenance in Fission Yeast." Genetics 213, no. 2 (August 12, 2019): 431–47. http://dx.doi.org/10.1534/genetics.119.302606.

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Happ, C. Scalfi, E. Happ, A. M. Gronenborn, and G. M. Clore. "Synthesis and1-NMR Studies of DNA-RNA Hybrids for Structural Analysis." Nucleosides and Nucleotides 7, no. 5-6 (October 1988): 733–36. http://dx.doi.org/10.1080/07328318808056320.

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Arbona, Maria, Juan Bautista Cuenca, and Rosa Frutos. "Stress response in Drosophila subobscura: DNA-RNA hybrids and transcriptional activity." Biology of the Cell 75, no. 3 (January 1992): 187–95. http://dx.doi.org/10.1016/0248-4900(92)90140-v.

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Krstulović, Luka, Ivana Stolić, Marijana Jukić, Teuta Opačak-Bernardi, Kristina Starčević, Miroslav Bajić, and Ljubica Glavaš-Obrovac. "New quinoline-arylamidine hybrids: Synthesis, DNA/RNA binding and antitumor activity." European Journal of Medicinal Chemistry 137 (September 2017): 196–210. http://dx.doi.org/10.1016/j.ejmech.2017.05.054.

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