Molecular Biology

SINEs of Repression

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Science  21 Mar 2008:
Vol. 319, Issue 5870, pp. 1590
DOI: 10.1126/science.319.5870.1590b

Mammalian genomes are packed to overflowing with a menagerie of repetitive DNA elements, many of which are derived from defunct transposons. Short interspersed elements (SINEs)—relic retrotransposons—are maintained in both mouse and human genomes. A clue to the basis for the persistence of these apparently “parasitic” DNA regions in the mouse comes from the observation that the noncoding (nc) RNA transcribed from B2 SINEs in response to heat shock can act to repress specific protein-coding genes by binding to and repressing RNA polymerase II (pol II).

The predominant SINEs in humans are Alu elements, similar in part to mouse B1 SINEs but evolutionarily unrelated to the other predominant mouse SINE, B2. Mariner et al. show that human Alu ncRNA, like mouse B2 ncRNA, can repress specific genes in response to heat shock, and that, like B2 RNA, it achieves this by binding to the RNA pol II pre-initiation complex, probably preventing appropriate interaction with promoter DNA. Human Alu RNA has a similar effect in mouse cells, and conversely, mouse B2 RNA in human cells. The mouse B1 SINE RNA is related to a processed short cytoplasmic RNA fragment of Alu (corresponding to the 5' half of Alu ncRNA) and both can bind RNA pol II. Although neither can repress transcription in vitro, it is quite possible they also have related regulatory functions. Thus it would seem that humans do not have either of the B1 or B2 SINE family of repeats because the Alu repeats can by themselves carry out the function of both of the mouse SINE RNAs, and possibly supplanted them during evolution. — GR

Mol. Cell 29, 499 (2008).

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