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Background A pool of small RNA fragments (RFs) derived from diverse cellular RNAs has recently emerged as a rich source of functionally relevant molecules. Although their formation and accumulation has been connected to various stress conditions, the knowledge on RFs produced upon viral infections is very limited. Here, we applied the next generation sequencing (NGS) to characterize RFs generated in the hepatitis C virus (HCV) cell culture model (HCV-permissive Huh-7.5 cell line). Results We found that both infected and non-infected cells contained a wide spectrum of RFs derived from virtually all RNA classes. A significant fraction of identified RFs accumulated to similar levels as miRNAs. Our analysis, focused on RFs originating from constitutively expressed non-coding RNAs, revealed three major patterns of parental RNA cleavage. We found that HCV infection induced significant changes in the accumulation of low copy number RFs, while subtly altered the levels of high copy number ones. Finally, the candidate RFs potentially relevant for host-virus interactions were identified. Conclusions Our results indicate that RFs should be considered an important component of the Huh-7.5 transcriptome and suggest that the main factors influencing the RF biogenesis are the RNA structure and RNA protection by interacting proteins. The data presented here significantly complement the existing transcriptomic, miRnomic, proteomic and metabolomic characteristics of the HCV cell culture model. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3891-3) contains supplementary material, which is available to authorized users.

International audience; The NMR spectral densities of a complex motion consisting of combination of anisotropic overall motion and internal motion have been derived. Two approximations of the equations derived for the cases of slow, Jslow(), and fast, Jfast(), internal motions are presented. These equations imply that reduction in spectral density of overall motion can be observed if the maxima of internal and overall motions spectral densities versus temperature are well separated, so for the fast internal motion. Slow intramolecular motion influences the values of spectral densities of the overall motion if one of the two spins performs a motion as for example a proton in double minimum of the 15N-H.....N hydrogen bond. The analysis presented reveals small differences between the temperature dependencies of spectral densities of the isotropic and anisotropic overall motions. The theory is illustrated by the 13C protonated carbon spin-lattice relaxation of -cyclodextrin macromolecule, using the expected motional parameters: DII/D  5 at room temperature and for a fast or slow internal motion.