The expression of satellite DNA-encoded proteins in the human genome
Abstract
The discovery of dark matter proteins has primarily relied on predicting open reading frames (ORFs) from known RNA molecules, followed by experimental validation. Although this approach has yielded many excellent studies in recent years, its positive output has become increasingly low while costs continue to rise. Meanwhile, whether large portions of the genomic dark matter-such as satellite DNA-encode proteins remains unknown. In this study, we employed 6-frame in silico translation to directly predict ORFs (istORFs) from genomic DNA sequences and their corresponding amino acid sequences (isteins), and then searched for signature peptides and matching RNA sequences in proteomics and ribo-seq databases. Unexpectedly, the positive rate was remarkably high. We identified a large number of satellite DNA-derived ORFs; among the 1,000 highest-copy-number isteins, 415 had detectable signature peptides in mass spectrometry datasets via Pepquery, and 401 showed matching translation signals in ribo-seq data. The MESSS gene family, derived from a novel form of Sat2/3, comprises over 10,000 predicted ORFs with a combined coding region exceeding 6 Mb. Using a specific antibody, we detected MESSS expression in multiple cell lines. These findings provide initial evidence that at least some satellite DNA sequences possess coding capacity and are capable of expressing proteins. We also analyzed conserved isteins across multiple primate and mouse T2T genomes and found that even among highly conserved ORFs, many had not been previously discovered or annotated. Based on these results, we propose a series of hypotheses that await future validation.
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