Biology Reference
In-Depth Information
retrotransposon itself or hijacked from other protein-coding TEs. This mobiliza-
tion strategy, termed retrotransposition, is an inherently expansive force within
genomes. The total number of elements increases each time a successful retro-
transposition event occurs, and, as a direct consequence, so does the total size of
the host genome. Retrotranspositional activity has played a tremendously impor-
tant role in genome expansion and diversification during evolutionary history,
providing, in the process, abundant material for natural selection to carve out new
functions. It is frequently noted that TEs from various lineages comprise roughly
45-50% of the human genome (Lander
,2001). A considerable fraction of the
remaining half of our genome likely has an origin in mobile element activity as
well, but these elements have since diverged so far from their initial sequences that
they can no longer be readily identified through nucleotide or protein homology to
known element classes.
et al.
B. LINEs and Tiggers (the diversity and complexity of TE repertoire)
Beyond the simple classification scheme of TEs into Class 1 and Class 2 elements,
there exists an ever-growing bestiary of mobile element lineages, with colorful
names ranging from “SPACE INVADERS” to “Tigger.” Identifying and classify-
ing TEs from diverse species has fueled the development of an array of important
software tools as well as the establishment of curated databases. Examples include
Censor (Jurka
, 1996) and RepeatMasker (www.repeatmasker.org) for iden-
tifying elements based on known libraries of elements, and several methods,
including RepeatScout, Recon, RepeatFinder, PILER, and ReAs for the
et al.
ab initio
discovery of elements (Edgar and Myers, 2005; Li
et al.
, 2005; Price
et al.
, 2005;
Quesneville
, 2001). Repbase and dbRIP provide
information about categorized TEs and the polymorphic status of particular
inserts, respectively (Jurka
et al.
, 2005; Volfovsky
et al.
, 2006). As the genome of
any given organism may hold from a few to hundreds of TE varieties, each
of which is diverging independently from its relatives inhabiting the genomes
of other organismal species, TE nomenclature has the potential to be orders of
magnitude more extensive and cumbersome than analogous systems for organ-
isms. The discovery of TEs that propogate in a “copy and paste” manner without
the need for an RNA intermediate served to undermine the basis of the Type1/
Type2 classification scheme (Morgante
et al.
, 2005; Wang
et al.
, 2007). It has,
however, proven challenging to devise a taxonomic system for mobile elements
that manages to reflect the ancestral relationships among elements, while, at the
same time, avoids being too unwieldy for researchers to practically employ on a
regular basis. As a consequence of this challenge, multiple categorization
schemes have been proposed and are simultaneously in use (Wicker
et al.
, 2005; Wicker
et al.
,
2007). The past decade's precipitous increase in sequencing capacity, and the
“tsunami” of data that continues to ensue from it, has lead to the identification of
et al.
