Biology Reference
In-Depth Information
Brown, 1992; Cai, Das, & Brown, 2007; Das et al., 2006; Das, Heimeier,
Buchholz, & Shi, 2009; Shi & Brown, 1993; Wang & Brown, 1991,
1993
). Among them, only a small fraction has been characterized as direct
response gene (
Das et al., 2009; Furlow & Brown, 1999; Ranjan, Wong,
& Shi, 1994
). The identification of the TH-induced transcriptional regula-
tory programs needs now to be addressed in a physiological context at the
level of the whole genome to understand how TH regulates metamorphosis.
Such ambitious studies depend on the exploitation of a sequenced amphib-
ian genome. While
Xenopus leavis (X. laevis)
is the most used model,
Xenopus
tropicalis (X. tropicalis)
is by far a more appropriate model because its genome
sequence is in a large part already accessible (
Hellsten et al., 2010
). Now
next-generation sequencing (NGS)-based transcriptome sequencing, tran-
scription factor binding, and epigenetic analyses (chromatin modification)
have dramatically changed how fundamental questions in biology are
addressed (
Hawkins, Hon, & Ren, 2010; Metzker, 2010; Sboner, Mu,
Greenbaum, Auerbach, & Gerstein, 2011
). NGS is well suited to provide
all the primary data required for functional genomic analyses with an
unprecedented resolution enabling the detection of even subtle differ-
ences. This review emphasizes the particular contribution of NGS-based
technologies to functional genomics research with a special focus on gene
regulation by TH.
2. XENOPUS TROPICALIS GENOMIC SEQUENCE AND
ANNOTATION: CURRENT STATE
2.1. A fragmented genome assembly
The sequencing of
X. tropicalis
genome has been an ongoing project for
nearly 10 years. It was initiated by the JGI in late 2003, and the first public
version (3.0) was released in October 2004. The draft assembly version 4.1
released in 2005 had been in use for over 5 years before its publication
(
Hellsten et al., 2010
). A new assembly (version 7.1) quickly followed
and was made available to download on the XenBase Web site in
2011(
Bowes et al., 2008
). These assemblies have been an invaluable resource
for the scientific community. In fact, as opposed to
X. laevis
, which is
pseudotetraploid and has a genome of about 3.1 Gbp,
X. tropicalis
has a rel-
atively small genome (1.7 Gbp) and much less genetic redundancy. This is
expected since it is a diploid species, making it a very appropriate model to
probe,
for example, the TH-induced gene regulatory networks. This
