Biology Reference
In-Depth Information
splice forms with multiple ESTs that also exhibit tissue-specific expression
patterns and may in fact be the major transcript in some tissues.
5. Genome Architecture
Although comparative genomics often focuses solely on gene content
analysis, the study of genes in the context of their genomic order and
chromosomal organization is also important. Whole-genome sequencing
efforts have therefore been particularly insightful for studies of genome
architectures, revealing duplications, deletions, translocations, inversions,
chromosomal splitting and fusion, and even whole-genome duplications.
Initially, the term “synteny” was used to denote genetic linkage of genes
on the same chromosome; however, the emergence of much more
detailed data on genomic gene arrangements has shifted the usage of
the term. Nowadays, local conservation of gene arrangements (which
are in fact orthologous genomic loci) are frequently termed regions of
“microsynteny” or synteny blocks, and the term “macrosynteny” is gen-
erally used to describe longer-range orthologous regions that highlight
major chromosomal rearrangements and themselves span a number of
synteny blocks.
The application of comparative genomics to identify synteny blocks
opens new avenues for exploring the likely chain of events of chromoso-
mal rearrangements and for reconstructing ancestral genomes.
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This can
highlight genomic features that may contribute to genomic instability, as
in the case of inversions and long-range deletions which can be driven by
recombination between regions of high sequence identity, e.g. arising
from transposable element activity or segmental duplications.
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The con-
servation of gene arrangements by purifying selection can also reveal
functional coupling between the genes as, for example, in bacteria, where
genes arranged in clustered modules or operons show significant predic-
tive power of gene functions and pathway membership.
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Such clustering
in eukaryotes, however, appears to be far less common, with only a few
examples such as the HOX gene clusters, where conservation of gene
order has been shown to be important for the tight regulation of gene
expression.
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Less stringent coregulation may affect larger genomic
regions, which may be linked to replication properties, as in the case of
