biomolecules Article Transcriptional Profiling Reveals Ribosome Biogenesis, Microtubule Dynamics and Expression of Specific lncRNAs to be Part of a Common Response to Cell-Penetrating Peptides Tomas Venit 1, Moataz Dowaidar 2 , Maxime Gestin 2, Syed Raza Mahmood 1 , Ülo Langel 2,3 and Piergiorgio Percipalle 1,4,* 1 Science Division, Biology Program, New York University Abu Dhabi (NYUAD), Abu Dhabi P.O. Box 129188, UAE;
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[email protected] (S.R.M.) 2 Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16B, SE-106 91 Stockholm, Sweden;
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[email protected] (Ü.L.) 3 Laboratory of Molecular Biotechnology, Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia 4 Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden * Correspondence:
[email protected]; Tel.: +971-26284389 Received: 29 October 2020; Accepted: 13 November 2020; Published: 17 November 2020 Abstract: Cell-penetrating peptides (CPPs) are short peptides that are able to efficiently penetrate cellular lipid bilayers. Although CPPs have been used as carriers in conjugation with certain cargos to target specific genes and pathways, how rationally designed CPPs per se affect global gene expression has not been investigated. Therefore, following time course treatments with 4 CPPs-penetratin, PepFect14, mtCPP1 and TP10, HeLa cells were transcriptionally profiled by RNA sequencing. Results from these analyses showed a time-dependent response to different CPPs, with specific sets of genes related to ribosome biogenesis, microtubule dynamics and long-noncoding RNAs being differentially expressed compared to untreated controls.