dc.contributor.author | MC LYSAGHT, AOIFE | |
dc.date.accessioned | 2014-11-25T15:07:20Z | |
dc.date.available | 2014-11-25T15:07:20Z | |
dc.date.issued | 2012 | |
dc.date.submitted | 2012 | en |
dc.identifier.citation | Makino T, McLysaght A, Positionally biased gene loss after whole genome duplication: evidence from human, yeast, and plant., Genome research, 22, 12, 2012, 2427-2435 | en |
dc.identifier.other | Y | |
dc.identifier.uri | http://hdl.handle.net/2262/72191 | |
dc.description | PUBLISHED | en |
dc.description.abstract | Whole genome duplication (WGD) has made a significant contribution to many
eukaryotic genomes including yeast, plants and vertebrates. Following WGD, some
ohnologs (WGD paralogs) remain in the genome arranged in blocks of conserved
gene order and content (paralogons). However the most common outcome is loss of
one of the ohnolog pair. It is unclear what factors, if any, govern gene loss from
paralogons. Recent studies have reported physical clustering (genetic linkage) of
functionally linked (interacting) genes in the human genome and propose a biological
significance for the clustering of interacting genes such as co-expression or
preservation of epistatic interactions. Here we conduct a novel test of a hypothesis
that functionally linked genes in the same paralogon are preferentially retained in cis
after WGD. We compare the number of protein-protein interactions (PPIs) between
linked singletons within a paralogon (defined as cis-PPIs) with that of PPIs between
singletons across paralogon pairs (defined as trans-PPIs). We find that paralogons in
which the number of cis-PPIs is greater than that of trans-PPIs are significantly
enriched in human and yeast. The trend is similar in plants, but it is difficult to assess
statistical significance due to multiple, overlapping WGD events. Interestingly,
human singletons participating in cis-PPIs tend to be classified into "response to
stimulus". We uncover strong evidence of biased gene loss after WGD which further
supports the hypothesis of biologically significant gene clusters in eukaryotic
genomes. These observations give us new insight for understanding the evolution of
genome structure and of protein interaction networks. | en |
dc.description.sponsorship | This work is supported by Science Foundation Ireland. | en |
dc.format.extent | 2427-2435 | en |
dc.language.iso | en | en |
dc.relation.ispartofseries | Genome research; | |
dc.relation.ispartofseries | 22; | |
dc.relation.ispartofseries | 12; | |
dc.rights | Y | en |
dc.subject | gene clusters | en |
dc.subject.lcsh | gene clusters | en |
dc.title | Positionally biased gene loss after whole genome duplication: evidence from human, yeast, and plant. | en |
dc.type | Journal Article | en |
dc.contributor.sponsor | Science Foundation Ireland (SFI) | en |
dc.type.supercollection | scholarly_publications | en |
dc.type.supercollection | refereed_publications | en |
dc.identifier.peoplefinderurl | http://people.tcd.ie/mclysaga | |
dc.identifier.rssinternalid | 85465 | |