Biology Reference
In-Depth Information
model and the Affymetrix microarray probesets partially overlap with the
RNA-Seq signal (indicating that they can be used to assess the expression
levels of the gene), a better measure of gene expression is achieved when
counting the RNA-Seq reads along the entire gene. This is clearly shown
in
Fig. 10.5
A, where the RNA-Seq signal extends up to 5 kb upstream of
the annotated TSS for THb/ZIP, or even
200 kb for TR
b
(
Figs. 10.3
A
and
10.5
B). If read count was restricted to the annotated region, a lot of
signal could actually be missed, potentially introducing biases comparable
to those found in microarray analysis. In this context, using RNA-PET to
define precise gene boundaries would prove particularly helpful in achiev-
ing better differential analysis of RNA-Seq data.
In addition, when using RNA-Seq derivatives (
Wang et al., 2009
), frag-
ments spanning multiple exons can be easily mapped to the genome or trans-
criptome, giving precise data about the expression levels of the various
alternative transcripts (
Fig. 10.3
B). Furthermore, beyond the strict defini-
tion of exon boundaries, RNA-PET can provide important data about
TH effect on alternative TSS and TTS usage (
Fig. 10.4
B). The best-case sce-
nario for accurately measuring gene expression with RNA-Seq requires
high quality gene models.
4. TR INTERACTOME
4.1. Whole genome TR mapping
Recent advances provide the technologies to go beyond the simple
measurement of transcripts abundance, making it possible to investigate
the detailed molecular mechanisms involved in the transcriptional dynamics
of TR mediated regulatory cascades.
Upon binding to T
3
RE, TR recruits cofactors that will modify the
transcriptional permissiveness of chromatin (
Wong, Shi, & Wolffe, 1995
).
Although T
3
RE are located near TH regulated genes (
Ranjan et al.,
1994
), recent experimental evidence on the regulation of gene expression
by transcription factors involves loop-mediated physical interactions be-
tween regulatory factors bound to DNA at distant enhancers and the core
transcriptional machinery located at the TSS of regulated genes
(
Fullwood, Liu, et al., 2009
). In fact, in a manner similar to other transcrip-
tion factors, TR could regulate the expression of target genes over long ge-
nomic distances (up to several tens of kilobases, unpublished data), although
some TR-binding site are located nearby TH-responsive genes.
