Alu and B1 Repeats Have Been Selectively Retained in the Upstream and Intronic Regions of Genes of Specific Functional Classes

ALU and B1 repeats are mobile elements that originated in an initial duplication of the 7SL RNA gene prior to the primate-rodent split about 80 million years ago and currently account for a substantial fraction of the human and mouse genome respectively. Following the primate-rodent split, ALU and B1 elements spread independently in each of the two genomes in a seemingly random manner, and, according to the prevailing hypothesis, negative selection shaped their final distribution in each genome by forcing the selective loss of certain ALU and B1 copies. In this paper, contrary to the prevailing hypothesis, we present evidence that ALU and B1 elements have been selectively retained in the upstream and intronic regions of genes belonging to specific functional classes, while at the same time we found no evidence for selective loss of these elements in any functional class. A subset of the functional links we discovered corresponds to functions where ALU involvement has actually been experimentally validated, whereas the majority of the functional links we report are novel. Finally, the unexpected finding that ALU and B1 elements show similar biases in their distribution across functional classes despite having spread independently in their respective genomes, further supports our claim that the extant instances of ALU and B1 elements are the result of positive selection.

By: Aristotelis Tsirigos; Isidore Rigoutsos

Published in: RC24782 in 2009


This Research Report is available. This report has been submitted for publication outside of IBM and will probably be copyrighted if accepted for publication. It has been issued as a Research Report for early dissemination of its contents. In view of the transfer of copyright to the outside publisher, its distribution outside of IBM prior to publication should be limited to peer communications and specific requests. After outside publication, requests should be filled only by reprints or legally obtained copies of the article (e.g., payment of royalties). I have read and understand this notice and am a member of the scientific community outside or inside of IBM seeking a single copy only.


Questions about this service can be mailed to .