Recently, more accessible transcriptomic approaches have provided a new and deeper understanding of envi- ronmental toxicity. The present study focuses on the transcriptomic profiles of green microalgae Chlamydomonas reinhardtii exposed to new industrially promising material, TiO2 nanotubes (NTs), as an example of a widely used one-dimensional nanomaterial. The first algal in vitro assay included 2.5 and 7.5 mg/L TiO2 NTs, resulting in a dose-dependent negative effect on biological endpoints. At a working concentration of 7.5 mg/L, RNA - sequencing showed a mainly negative effect on the cells. In summary, the results indicated metabolic disrup- tion, such as ATP loss, damage to mitochondria and chloroplasts, loss of solutes due to permeated membranes, and cell wall damage. Moreover, apoptosis-induced transcripts were detected. Interestingly, reactivation of transposons was observed. In signalling and transcription pathways, including chromatin remodelling and locking, the annotated genes were downregulated.