Abstract
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. 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.
Highlights
Identifiable repeat elements cover a very large fraction of the human and mouse genomes, and even though they are quite diverse at the sequence level, they can be assigned to a fairly small number of families [1]
Alu and B elements belong to the Short Interspersed Nuclear Element (SINE) family, members of which exist in several mammalian genomes, where they have spread in great copy numbers [2,3,4]
We extend previous work by studying and comparing the distributions of extant instances of both Alu and B1 elements, as well as related B2 and B4 elements in both upstream and intronic regions of known proteincoding genes, in order to contribute to the understanding of the evolutionary history of these elements
Summary
Identifiable repeat elements cover a very large fraction of the human and mouse genomes, and even though they are quite diverse at the sequence level, they can be assigned to a fairly small number of families [1]. Alu and B elements belong to the Short Interspersed Nuclear Element (SINE) family, members of which exist in several mammalian genomes, where they have spread in great copy numbers [2,3,4]. The most abundant class or repeat elements in the human genome, originated in the duplication and subsequent fusion of the 7SL RNA gene at the beginning of the radiation of primates [5,6]. Following the primate-rodent split, copies of Alu and B1 elements have amplified and duplicated independently in the two genomes while accumulating mutations [4,7]. The extent of the acquired mutations is such that extant instances of archetypal Alu and B1 elements bear little resemblance to one another or to the original 7SL RNA gene
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