**5. Mitochondrial noncoding RNAs**

In addition to the canonical mitochondrial genes and the newly proposed MDPs, vertebrate mitogenomes encode several noncoding RNAs [36]. The first discovered mitochondrial long noncoding RNA (lncRNA) was the human L-strand-specific 7S RNA (lncCR-L) [52, 53].

At least eight vertebrate mitochondrial lncRNAs have now been proposed and characterized [54]. Two lncRNAs correspond to the H-strand and L-strand of CR (lncCR-H and lncCR-L) [10, 18, 47, 52, 55, 56], one is an antisense chimer to partial regions of the CytB and COI mRNAs (LIPCAR) [57–59], three are mRNA antisense RNAs (lncND5, lncND6, and lncCytB) [60], and two are chimeric RNAs that involve sense and antisense mtLSUrRNAs (SncmtRNA and ASncmtRNA) [61–63]. So far, LIPCAR, rRNA chimers, and lncCR-H have been associated with human diseases [56, 57, 61, 63–66]. There are apparently a large number of small noncoding RNAs (mitosRNAs) generated from vertebrate mitochondrial transcripts [36, 67–69]. None of these mitosRNAs have been assigned to a specific function funded on experimental evidence. However, in a recent study by Riggs and Podrabsky [70], mitosRNAs were associated to a hypoxia stress response in killifish embryos.

and more than 8 (>320 bp) [5, 14, 15, 18], rendering lncCR-H highly variable in size. Finally, lncCR-H terminates in a short polyA tail at TAS. Thus, lncCR-H has apparently no fixed length in Atlantic cod mitochondria and varies in size between approximately 300 and 500 nt. Interestingly, the TAS motif consists of a perfect palindromic sequence motif (**TTTATACAT**ATGTATAAA). We found lncCR-L to terminate with a polyA tail at the same

**Figure 4.** Schematic view of CR and corresponding noncoding RNAs in Atlantic cod. tRNA genes (tRNAThr, tRNAPro, tRNAPhe), T–P spacer, HTR (heteroplasmic tandem repeat array), TAS (termination associated sequence), and CSB2 (conserved sequence box 2) are indicated. The H-strand-specific lncCR-H is located at the 5′ domain of CR and is the precursor of two enriched small RNAs (above CR map). The L-strand-specific lncCR-L is located at the central domain

Expanding the Coding Potential of Vertebrate Mitochondrial Genomes: Lesson Learned…

http://dx.doi.org/10.5772/intechopen.75883

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The Atlantic cod mitogenomes express a number of small RNAs, revealed by SOLiD small RNA sequencing experiments (our unpublished results). Here, the majority of mitosRNA was identified as mitochondrial tRNA-derived fragments (tRFs; see [69, 70]). Interestingly, most Atlantic cod mitochondrial tRFs correspond to H-strand tRNAs, and some tRFs were differentially expressed during early developmental stages (our unpublished results). Many of the same tRF species detected in Atlantic cod have recently been noted in rainbow trout egg cells [69] and in killifish embryos [70], suggesting a conserved feature at least among some bony

The SOLiD experiments also detected several abundant small RNAs mapping to the mitochondrial CR [17]. We found three small RNA candidates generated from lncCR-L, suggesting this lncRNA to be a precursor for mitosRNA (**Figure 4**). Similarly, two mitosRNA were generated from lncCR-H, one corresponded to a pyrimidine-rich motif and the other to tRF-1 derived from tRNAThr (**Figure 4**). What functions these small RNAs may serve in the

site as lncCR-H but on the opposite strand [10].

of CR and is the precursor of three enriched small RNAs (below CR map).

**5.2. Atlantic cod mitochondrial small RNAs**

fishes.
