Possible Formation of Mitochondrial-RNA Containing Chimeric or Trimeric RNA Implies a Post-Transcriptional and Post-Splicing Mechanism for RNA Fusion

Abstract

Human cells are known to express many chimeric RNAs, i.e. RNAs containing two genes' sequences. Wondering whether there also is trimeric RNA, i.e. an RNA containing three genes' sequences, we wrote simple computer code to screen human expression sequence tags (ESTs) deposited in different public databases, and obtained hundreds of putative trimeric ESTs. We then used NCBI Blast and UCSC Blat browsers to further analyze their sequences, and identified 61 trimeric and two tetrameric ESTs (one EST containing four different sequences). We also identified 57 chimeric, trimeric or teterameric ESTs that contained both mitochondrial (mt) RNA and nuclear RNA (nRNA), i.e. were mtRNA-nRNA fusions. In some trimeric ESTs, the downstream partner was fused to the poly-A tail of the upstream partner, which, together with the mtRNA-nRNA fusions, suggests a possible new mechanism for RNA fusion that occurs after both transcription and splicing have been terminated, and possibly outside the nucleus, in contrast to the two current hypothetical mechanisms, trans-splicing and transcriptional-slippage, that occur in the nucleus. The mt-sequences in the mtRNA-nRNA fusions had pseudogenes in the nucleus but, surprisingly, localized mainly in chromosomes 1 and 5. In some mtRNA-nRNA fusions, as well as in some ESTs that were derived only from mtRNA, the mt-sequences might be cis- or trans-spliced. Actually, we cloned a new cis-spliced mtRNA, coined as 16SrRNA-s. Hence, mtDNA may not always be intron-less. Fusion of three or more RNAs to one, fusion of nRNA to mtRNA, and cis- or trans-splicing of mtRNA should all enlarge the cellular RNA repertoire, in turn enlarging the cellular functions. Therefore, future experimental verification of the existence of these novel classes of fusion RNAs and spliced mtRNAs in human cells should significantly advance our understanding of biology and medicine.

Codon expansion and systematic transcriptional deletions produce tetra-, pentacoded mitochondrial peptides

“…However, at least one detected RNA read bridges the two regions. Hence the reads in Figure 2 (besides the latter) can be explained by two independent regions of the regular nuclear genome: chimaeric transcripts have been described for the nuclear genome (Fang et al 2012) and the human mitochondrion (Yang et al 2013). The alternative is that the reads match indeed a contiguous region of the human mitogenome, assuming systematic mononucleotide deletions after trinucleotides.…”

Isoforms of wild type proteins often appear as low molecular weight bands on SDS‐PAGE

“…Transcription of a gene can be initiated from or completed at different sites in the genomic DNA resulting in different pre‐mRNA variants. One pre‐mRNA may be alternatively cis‐spliced to form different mature mRNAs, while two pre‐mRNAs can be alternatively trans‐spliced to form a chimeric mRNA [1]. These mechanisms eventually yield different protein isoforms that differ in sequence from the wild type (wt) protein.…”

Unbiased Mitoproteome Analyses Confirm Non-canonical RNA, Expanded Codon Translations

“…Some transcripts result from fusion of RNA transcribed from DNA regions that are not contiguous [146], [147]. This can result from reverse-transcription artifacts during cDNA production [148].…”