1 Introduction

MicroRNAs (miRNAs) are small, non-coding RNA molecules, approximately 22 nucleotides in length, that play crucial roles in the regulation of gene expression. They function primarily by binding to complementary sequences in the 3′ untranslated regions (UTRs) of target messenger RNAs (mRNAs), leading to mRNA degradation or translational repression (Bartel, 2004; Bushati and Cohen, 2007). Through this mechanism, miRNAs are involved in various biological processes, including development, differentiation, proliferation, and apoptosis (Ambros, 2004). The importance of miRNAs as regulatory elements is furthermore emphasized by their involvement in various diseases, particularly cancer, where they can act as either oncogenes or tumor suppressors (Budakoti et al., 2021; Hussen et al., 2021).

MicroRNAs are transcribed as primary miRNAs (pri-miRNAs) and processed into precursor miRNAs (pre-miRNAs), which are typically around 70 nucleotides long and form hairpin structures (Bartel, 2004). The miRNA duplex is generated from this precursor, consisting of a guide strand (mature miRNA) and a passenger strand (mature*). The mature miRNA is incorporated into the RNA-induced silencing complex (RISC) to guide gene silencing, while the mature* strand is usually degraded, although in some cases, it may also be functional (Bartel, 2004; Okamura et al., 2007).

Despite their critical functions, there is a significant discrepancy in the annotation of miRNAs between different model species, notably between rat (Rattus norvegicus) and mouse (Mus musculus). This discrepancy arises due to differences in sequencing efforts and annotation strategies but also through lineage-specific retroposons playing an essential role in the birth of new miRNA genes (Lehnert et al., 2011). Addressing this gap is essential for leveraging the rat as a model organism in biomedical research, particularly given its widespread use in pharmacology and toxicology studies (Jacob and Kwitek, 2002).

In this study, we corrected several incorrect homology assignments and identified and annotated novel rat miRNAs. Expanding the miRNA repertoire of this crucial model organism will enhance its utility, particularly for toxicological applications, where precise regulatory networks are critical for understanding the molecular basis of toxicity and drug responses.