Investigation of transcription and translation from sORFs and altORFs in naive B and T cells in M. musculus

Abstract

Identification of transcription and translation from noncoding regions augmented the complexity of the genome, a problem further compounded by novel open reading frames (ORFs) present within noncoding as well as genic regions with as of yet unclear functions. In this study, we investigated two novel ORFs: short ORFs (sORFs) and alternative ORFs (altORFs), within mouse naive B and T cells. We established evidence of transcription for 2721 sORFs and 4251 altORFs and found 3604 sORFs and 2104 altORFs to be translated. We also identified 289 sORFs and 980 altORFs as differentially expressed (DE) between B and T cells. Furthermore, PCA analysis indicated that transcript expression levels of these novel ORFs are significant and sufficient to distinguish between the two cell types. Additionally, differential methylation (DM) analysis of these differentially expressed novel ORFs and protein-coding transcripts allowed us to identify 117, 139 and 1398 DMRs upstream, downstream and within the body of DE sORFs, 199, 257 and 28497 near DE altORFs and 1712,1679 and 24910 near protein-coding transcripts. Moreover, 46 sORFs containing DMRs were identified in the upstream and downstream regions of protein-coding transcripts indicating that expression of DE protein-coding transcripts might be affected by sORFs. Also, we found no evidence of LINE/SINE repeat elements regulating expression of DE sORFs. Here, we present a framework for a systematic investigation of transcription and translation from novel ORFs that could be utilized to ascertain their functions or identify potential diseases variants present within them.