*3.2. Long Non-Coding Antisense RNA Controls mRNA Translation—Importance of Embedded SINE/Alu Repeats*

Carrieri *et al.* determined that a long ncRNA transcript, which is partially antisense to ubiquitin carboxy-terminal hydrolase L1 (Uchl1), is essential for increased translation of uch1 mRNA [36]. Uch1 is a neuron associated protein in mammals and may be involved in neurological disease formation [37,38]. Two segments of the antisense lncRNA are crucial for function: the 5' end of the lncRNA transcript that overlaps the uch1 sense transcript, and SINEB2 and Alu repeat segments located downstream on the antisense lncRNA. By using a bioinformatics approach, 31 antisense lncRNAs have been pinpointed that contain SINE/Alu sequences in their 3' end half regions. These RNAs can potentially base-pair to sense transcripts via their 5' ends to the 3'UTR of mRNAs, in a similar manner as uch1 sense RNA/antisense RNA transcript pairing occurs. However the mechanism by which the SINE sequences act to control translation of uch1 mRNA has not been determined, but a hint comes from data showing the orientation of the SINE in the antisense lncRNA is important in rescue experiments [36]. This implies a possible RNA/RNA base-pairing mechanism. This work may define a separate class of regulatory lncRNAs in mammals that appears to differ from the Alu-containing lncRNAs described by Gong and Maquat [29].

#### *3.3. Point Mutation in LINE-1/Alu Element Embedded in a lncRNA Results in Lethal Brain Disease*

A primate conserved LINE-1 sequence is found embedded in a lncRNA that maps to human chromosome 8p22 [39]. This LINE sequence also overlaps with an Alu sequence. The lncRNA constitutes a unique transcript originating from an intron. This RNA most likely has regulatory functions. A rare single point mutation, A to G in the LINE-1/Alu sequence is associated with brainstem cell atrophy, a genetic abnormality that results in lethal infantile encephalopathy in humans [39]. The LINE-1 is a degenerate retrotransposon and assumed not to be mobile. It was experimentally determined that in patient brain tissues, the expression of the mutant lncRNA was reduced nearly 10-fold relative to unmutated RNA control levels. mRNAs of two genes that map in the same locus as the lnRNA were found to be unchanged. In addition, knockdown experiments against wild-type lncRNA using siRNA showed a significant increase in apoptotic cells.

Several hypotheses have been presented to explain the drastic phenotypic effects of the single base-pair change in the LINE-1/Alu sequence [39]. One is that piRNAs accidentally target the lncRNA transcript via base-pairing with the mutated LINE-1/Alu sequence and induce silencing of the lncRNA. Another involves inadvertent SRP protein recognition of the mutated sequence, which resides in a conserved internal loop of the Alu secondary structure embedded in the lncRNA. This loop is also present in the 7SL RNA secondary structure.

Thus, this is an example of a point mutation in an embedded TE in a lncRNA sequence that produces human disease. What is not known is what exact role the unique lncRNA plays in normal cell functions and the normal function of the embedded LINE-1/Alu sequence, although there may be involvement in regulatory networks during brain development [39].
