In our approach to study transcription fidelity, we combine the efficiency and high-sensitivity of the novel cre/lox-based genetic assay, developed for the yeast and E. coli cells in our group, as a team effort with three other RBL groups, with the power and precision of biochemical analysis of RNAP mutants, transcription factors and reaction conditions promoting transcription errors in these organisms. We also study in vitro the mechanisms of transcription fidelity in higher eukaryotes. For genetic assay, we create site-directed chromosomal mutants and gene constructs using advanced high-precision methods of gene manipulations based on recombineering developed in collaboration with Don Court's group. Application of the modern NGS RNA sequencing techniques brings our analysis of transcription errors to a genome-wide scale. The use of four biological models, namely E. coli, Bacillus, S. cerevisiae and human triple negative breast cancer (TNBC) cells under normal and stress conditions, allows us to do the cross-species and cross-kingdom study of transcription fidelity helping to unravel conserved and unique features of strategies that various organisms implement to control transcription fidelity. We believe that the experimental strategy and techniques that we use in the current work lay a solid foundation for our future studies on transcription fidelity.
| Imashimizu, Masahiko; Takahashi, Hiroki; Oshima, Taku et al. (2015) Visualizing translocation dynamics and nascent transcript errors in paused RNA polymerases in vivo. Genome Biol 16:98 |
| Penno, Christophe; Sharma, Virag; Coakley, Arthur et al. (2015) Productive mRNA stem loop-mediated transcriptional slippage: Crucial features in common with intrinsic terminators. Proc Natl Acad Sci U S A 112:E1984-93 |
| Parks, Adam R; Court, Carolyn; Lubkowska, Lucyna et al. (2014) Bacteriophage ? N protein inhibits transcription slippage by Escherichia coli RNA polymerase. Nucleic Acids Res 42:5823-9 |
| Imashimizu, Masahiko; Shimamoto, Nobuo; Oshima, Taku et al. (2014) Transcription elongation: Heterogeneous tracking of RNA polymerase and its biological implications. Transcription 5: |
| Afonin, Kirill A; Kasprzak, Wojciech K; Bindewald, Eckart et al. (2014) In silico design and enzymatic synthesis of functional RNA nanoparticles. Acc Chem Res 47:1731-41 |
| Vitiello, Christal L; Kireeva, Maria L; Lubkowska, Lucyna et al. (2014) Coliphage HK022 Nun protein inhibits RNA polymerase translocation. Proc Natl Acad Sci U S A 111:E2368-75 |
| Afonin, Kirill A; Desai, Ravi; Viard, Mathias et al. (2014) Co-transcriptional production of RNA-DNA hybrids for simultaneous release of multiple split functionalities. Nucleic Acids Res 42:2085-97 |
| Imashimizu, Masahiko; Kashlev, Mikhail (2014) Unveiling translocation intermediates of RNA polymerase. Proc Natl Acad Sci U S A 111:7507-8 |
| Ishibashi, Toyotaka; Dangkulwanich, Manchuta; Coello, Yves et al. (2014) Transcription factors IIS and IIF enhance transcription efficiency by differentially modifying RNA polymerase pausing dynamics. Proc Natl Acad Sci U S A 111:3419-24 |
| Imashimizu, Masahiko; Shimamoto, Nobuo; Oshima, Taku et al. (2014) Transcription elongation. Heterogeneous tracking of RNA polymerase and its biological implications. Transcription 5:e28285 |
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