Search

Tremendous progress has been made over the last century characterizing the structure, function, and evolutionary dynamics of protein-coding genes. Over the last three decades, biologists have sequenced the genomes of a variety of organisms, and it quickly became apparent that a relatively small portion of most genomes encode protein-coding genes. We now know that the non-protein-coding space contains repetitive sequences along with non-coding RNAs. Many of these non-coding RNAs encode housekeeping transcripts such as: ribosomal RNAs, transfer RNAs, small nucleolar RNAs, and small nuclear RNAs. However, the remaining transcripts include regulatory RNAs that have become the focus of intense investigation over the past two decades. These include the microRNAs and the small interfering RNAs which both act to knock down gene expression. More recently, a class of transcripts called long non-coding RNAs (lncRNAs) have been interrogated. One well described, functional lncRNA is the telomerase RNA which is necessary for genome stability via the maintenance of chromosome ends following DNA replication (Dew-Budd et al. 2020). While lncRNAs have been known for more than two decades, their functions have remained enigmatic; there are few functionally characterized lncRNAs. However, lncRNAs that have been characterized, especially in mammalian systems, appear to fine tune a plethora of developmental and regulatory processes, along with responses to environmental cues. LncRNAs are frequently expressed at low levels and in specific tissues; they are often poorly conserved among closely related species (Palos et al. 2021). As high-throughput RNA-sequencing becomes more widely available and used, researchers have employed the resulting data to identify lncRNAs en masse. For mammals, a variety of high-quality resources have been used to generate informative annotations to allow for improved hypothesis generation. These resources include GENCODE (Frankish et al. 2021), coupled with lnc