Genomic gems: SINE RNAs regulate mRNA production

Abstract

Mammalian short interspersed elements (SINEs) are abundant retrotransposons that have long been considered junk DNA; however, RNAs transcribed from mouse B2 and human Alu SINEs have recently been found to control mRNA production at multiple levels. Upon cell stress B2 and Alu RNAs bind RNA polymerase II (Pol II) and repress transcription of some protein-encoding genes. Bi-directional transcription of a B2 SINE establishes a boundary that places the growth hormone locus in a permissive chromatin state during mouse development. Alu RNAs embedded in Pol II transcripts can promote evolution and proteome diversity through exonization via alternative splicing. Given the diverse means by which SINE encoded RNAs impact production of mRNAs, this genomic junk is proving to contain hidden gems.

Figure 1

SINE RNAs control the heat shock response in mouse and human cells. A) Pol III transcribed SINE RNAs increase upon heat shock. B) During heat shock, mouse B2 RNA or human Alu RNA enters complexes at the promoters of repressed genes. TFIIF facilitates dissociation of B1 RNA from Pol II. C) Heat shock activated genes are resistant to repression by B2 RNA and Alu RNA.

Figure 2

A B2 SINE serves as a boundary element to regulate transcription during pituitary development in mouse cells. Bidirectional transcription of a B2 SINE upstream of the growth hormone locus facilitates a change in chromatin structure from a repressive heterochromatic state to a permissive euchromatic state.

Figure 3

Alu RNA exonization promotes proteome diversity. A) Shown is an example in which embedded Alu RNA is exonized via alternative splicing into an mRNA. B) Alu RNA indirect repeats embedded in an mRNA can become double stranded and undergo A-to-I editing, resulting in Alu exonization.