Do Alu repeats shape the primate transcriptome?

@article{citeulike:2319729, abstract = {BACKGROUND:Of all repetitive elements in the human genome, Alus are unusual in being enriched near genes expressed across a broad range of tissues. This has led to the proposal that Alus might be modifying the expression breadth of neighbouring genes, possibly be providing CpG islands, modifying transcription factor binding or altering chromatin structure. Here we ask whether Alus might have increased expression breadth of genes in their vicinity. Results: Contrary to the modification hypothesis, we find that those genes that have always had broad expression are richest in Alus, while those more likely to have become more broadly expressed have lower enrichment. This result is consistent with a model in which Alus accumulate near broadly expressed genes but donat affect their expression breadth. This model is consistent with the finding that expression breadth of mouse genes predicts Alu density near their human orthologs. Alus were, however, found to be related to some alternative measures of transcription profile divergence, although evidence is contradictory as to whether Alus associate with lowly or highly diverged genes. If Alu have any effect it is not by provision of CpG islands as they are especially rare near transcriptional start sites. Previously reported Alu enrichment for genes serving certain cellular functions, suggested to be evidence of functional importance of Alus, appears to be partly a by-product of the association with broadly expressed genes. Conclusions: The abundance of Alu near broadly expressed genes is better explained by their preferential preservation near housekeeping genes rather than a modifying effect on expression of genes.}, author = {Urrutia, Araxi and Ocana, Leandro B. and Hurst, Laurence }, citeulike-article-id = {2319729}, doi = {10.1186/gb-2008-9-2-r25}, journal = {Genome Biology}, keywords = {alu, genome-evolution, retrotransposition, retrotransposon}, number = {2}, posted-at = {2008-05-19 17:31:45}, priority = {2}, title = {Do Alu repeats shape the primate transcriptome?}, url = {http://dx.doi.org/10.1186/gb-2008-9-2-r25}, volume = {9}, year = {2008} }

TY - JOUR ID - citeulike:2319729 L3 - citeulike-article-id:2319729 TI - Do Alu repeats shape the primate transcriptome? JF - Genome Biology VL - 9 IS - 2 N2 - BACKGROUND:Of all repetitive elements in the human genome, Alus are unusual in being enriched near genes expressed across a broad range of tissues. This has led to the proposal that Alus might be modifying the expression breadth of neighbouring genes, possibly be providing CpG islands, modifying transcription factor binding or altering chromatin structure. Here we ask whether Alus might have increased expression breadth of genes in their vicinity. Results: Contrary to the modification hypothesis, we find that those genes that have always had broad expression are richest in Alus, while those more likely to have become more broadly expressed have lower enrichment. This result is consistent with a model in which Alus accumulate near broadly expressed genes but donat affect their expression breadth. This model is consistent with the finding that expression breadth of mouse genes predicts Alu density near their human orthologs. Alus were, however, found to be related to some alternative measures of transcription profile divergence, although evidence is contradictory as to whether Alus associate with lowly or highly diverged genes. If Alu have any effect it is not by provision of CpG islands as they are especially rare near transcriptional start sites. Previously reported Alu enrichment for genes serving certain cellular functions, suggested to be evidence of functional importance of Alus, appears to be partly a by-product of the association with broadly expressed genes. Conclusions: The abundance of Alu near broadly expressed genes is better explained by their preferential preservation near housekeeping genes rather than a modifying effect on expression of genes. KW - alu KW - genome-evolution KW - retrotransposition KW - retrotransposon AU - Urrutia, Araxi AU - Ocana, Leandro AU - Hurst, Laurence PY - 2008/// UR - http://dx.doi.org/10.1186/gb-2008-9-2-r25 ER -