One of the most exciting areas around noncoding sequences are the discoveries being made around ALU elements expressed in the brain. This article is a good review of the current research. A 2006 paper by Hasler and Strub "ALU elements as regulators of gene expression" in the journal Nucleic Acids Research explains that ALU elements arose exclusively in the primate lineage and are implicated in shaping the evolution of the primate brain.
ALUs have been shown to be involved in alternative splicing. They have also been shown to edit mRNAs in other ways as well. The paper talks about a process called exonization where a previously intronic sequence is recruited into the coding region of a gene. When this area includes an ALU element, there is potential for this exon to be alternatively spliced. Computational studies have confirmed that this does indeed happen.
Since ALUs evolved very recently, they all share much similarity. This makes it easier to do bioinformatic studies on them. Also, the fact that they are exclusive to the primate lineage is exciting because they may be the secret that sets humans apart.
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