Long Non-Coding RNAs Associated with Ribosomes in Human Adipose-Derived Stem Cells: From RNAs to Microproteins

Abstract

Ribosome profiling reveals the translational dynamics of mRNAs by capturing a ribosomal footprint snapshot. Growing evidence shows that several long non-coding RNAs (lncRNAs) contain small open reading frames (smORFs) that are translated into functional peptides. The difficulty in identifying bona-fide translated smORFs is a constant challenge in experimental and bioinformatics fields due to their unconventional characteristics. This motivated us to isolate human adipose-derived stem cells (hASC) from adipose tissue and perform a ribosome profiling followed by bioinformatics analysis of transcriptome, translatome, and ribosome-protected fragments of lncRNAs. Here, we demonstrated that 222 lncRNAs were associated with the translational machinery in hASC, including the already demonstrated lncRNAs coding microproteins. The ribosomal occupancy of some transcripts was consistent with the translation of smORFs. In conclusion, we were able to identify a subset of 15 lncRNAs containing 35 smORFs that likely encode functional microproteins, including four previously demonstrated smORF-derived microproteins, suggesting a possible dual role of these lncRNAs in hASC self-renewal.

Identification of Microproteins in Saccharomyces cerevisiae under Different Stress Conditions

“…Small open reading frame-encoded peptides (SEPs) are microproteins of less than 100–150 amino acids (AA), which are widely distributed in different species (yeast, Drosophila, mice, human, plants, etc.) and play crucial roles in transcriptional regulation, metabolism, cell growth and development, tumorigenesis, calcium transport, and stress response. , In prokaryotes, some SEPs of Escherichia coli were found to be differentially expressed under stress conditions (heat shock, oxidative stress, and acid stress) .…”

“…Growing evidence has shown that microproteins can play an essential role in the stress response of prokaryotes and eukaryotes. 4,5 Small open reading frame-encoded peptides (SEPs) are microproteins of less than 100−150 amino acids (AA), which are widely distributed in different species (yeast, 6 Drosophila, 7 mice, 8 human, 9 plants, 10 etc.) and play crucial roles in transcriptional regulation, metabolism, cell growth and development, tumorigenesis, calcium transport, and stress response.…”

A review of Ribosome profiling and tools used in Ribo-seq data analysis

“…Since its discovery, numerous sites of ribosome translation beyond the presently annotated CDS have been revealed [47] . Furthermore, long noncoding RNA’s role in translational regulation has also been elucidated [48] . Despite its advances in translatome study, there are also many challenges that this method may come with.…”

Long noncoding RNA study: Genome-wide approaches

“…Ribo-seq is based on ribosome-protected RNA fragments (RPFs) after translation inhibition to map translation status. 55 …”