Nanopore signal deviations from pseudouridine modifications in RNA are sequence-specific: quantification requires dedicated synthetic controls.

Autor: Makhamreh A; Department of Bioengineering, Northeastern University, Boston, MA, USA., Tavakoli S; Department of Bioengineering, Northeastern University, Boston, MA, USA., Fallahi A; Department of Bioengineering, Northeastern University, Boston, MA, USA., Kang X; Department of Bioengineering, Northeastern University, Boston, MA, USA., Gamper H; Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA., Nabizadehmashhadtoroghi M; Department of Mechanical Engineering, Northeastern University, Boston, MA, USA., Jain M; Department of Bioengineering, Northeastern University, Boston, MA, USA.; Department of Physics, Northeastern University, Boston, MA, USA., Hou YM; Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA., Rouhanifard SH; Department of Bioengineering, Northeastern University, Boston, MA, USA. s.rouhanifard@northeastern.edu., Wanunu M; Department of Bioengineering, Northeastern University, Boston, MA, USA. wanunu@neu.edu.; Department of Physics, Northeastern University, Boston, MA, USA. wanunu@neu.edu.

Publikováno v: Scientific reports [Sci Rep] 2024 Sep 28; Vol. 14 (1), pp. 22457. Date of Electronic Publication: 2024 Sep 28.

mRNA psi profiling using nanopore DRS reveals cell type-specific pseudouridylation.

Autor: McCormick CA; Dept. of Bioengineering, Northeastern University, Boston, MA., Qiu Y; Dept. of Bioengineering, Northeastern University, Boston, MA., Fanari O; Dept. of Bioengineering, Northeastern University, Boston, MA., Liu Y; Dept. of Bioengineering, Northeastern University, Boston, MA., Bloch D; Dept. of Bioengineering, Northeastern University, Boston, MA., Klink IN; Dept. of Bioengineering, Northeastern University, Boston, MA., Meseonznik M; Dept. of Bioengineering, Northeastern University, Boston, MA., Jain M; Dept. of Bioengineering, Northeastern University, Boston, MA.; Dept. of Physics, Northeastern University, Boston, MA., Wanunu M; Dept. of Bioengineering, Northeastern University, Boston, MA.; Dept. of Physics, Northeastern University, Boston, MA., Rouhanifard SH; Dept. of Bioengineering, Northeastern University, Boston, MA.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 May 30. Date of Electronic Publication: 2024 May 30.

Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess neuronal epitranscriptome plasticity.

Autor: Fanari O; Dept. of Bioengineering, Northeastern University, Boston, MA.; These authors contributed equally., Tavakoli S; Dept. of Bioengineering, Northeastern University, Boston, MA.; These authors contributed equally., Akeson S; Dept. of Bioengineering, Northeastern University, Boston, MA., Makhamreh A; Dept. of Bioengineering, Northeastern University, Boston, MA., Nian K; Dept. of Bioengineering, Northeastern University, Boston, MA., McCormick CA; Dept. of Bioengineering, Northeastern University, Boston, MA., Qiu Y; Dept. of Bioengineering, Northeastern University, Boston, MA., Bloch D; Dept. of Bioengineering, Northeastern University, Boston, MA., Jain M; Dept. of Bioengineering, Northeastern University, Boston, MA.; Dept. of Physics, Northeastern University, Boston, MA., Wanunu M; Dept. of Bioengineering, Northeastern University, Boston, MA.; Dept. of Physics, Northeastern University, Boston, MA., Rouhanifard SH; Dept. of Bioengineering, Northeastern University, Boston, MA.; Lead contact.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 Apr 11. Date of Electronic Publication: 2024 Apr 11.

Semi-quantitative detection of pseudouridine modifications and type I/II hypermodifications in human mRNAs using direct long-read sequencing.

Autor: Tavakoli S; Department of Bioengineering, Northeastern University, Boston, MA, USA., Nabizadeh M; Department of Mechanical Engineering, Northeastern University, Boston, MA, USA., Makhamreh A; Department of Bioengineering, Northeastern University, Boston, MA, USA., Gamper H; Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA., McCormick CA; Department of Bioengineering, Northeastern University, Boston, MA, USA., Rezapour NK; Department of Physics, Northeastern University, Boston, MA, USA., Hou YM; Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA., Wanunu M; Department of Bioengineering, Northeastern University, Boston, MA, USA.; Department of Physics, Northeastern University, Boston, MA, USA., Rouhanifard SH; Department of Bioengineering, Northeastern University, Boston, MA, USA. s.rouhanifard@northeastern.edu.

Publikováno v: Nature communications [Nat Commun] 2023 Jan 19; Vol. 14 (1), pp. 334. Date of Electronic Publication: 2023 Jan 19.

ClampFISH 2.0 enables rapid, scalable amplified RNA detection in situ.

Autor: Dardani I; Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA., Emert BL; Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA., Goyal Y; Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA.; Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.; Center for Synthetic Biology, Northwestern University, Chicago, IL, USA., Jiang CL; Genetics and Epigenetics, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA., Kaur A; Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA., Lee J; Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA., Rouhanifard SH; Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA.; Department of Bioengineering, Northeastern University, Boston, MA, USA., Alicea GM; Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD, USA.; Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA., Fane ME; Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD, USA.; Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA., Xiao M; The Wistar Institute, Philadelphia, PA, USA., Herlyn M; The Wistar Institute, Philadelphia, PA, USA., Weeraratna AT; Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD, USA.; Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA., Raj A; Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA. arjunraj@seas.upenn.edu.; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. arjunraj@seas.upenn.edu.

Publikováno v: Nature methods [Nat Methods] 2022 Nov; Vol. 19 (11), pp. 1403-1410. Date of Electronic Publication: 2022 Oct 24.