Alternatively Spliced Genes
149
site is U1snRNP-dependent, and TIA-1
may function by facilitating U1-snRNP
binding to the 5
0
splice site.
Human Y-box binding protein (YB-1)
was
initially
identiFed
as
a
transcrip-
tion factor interacting with single-stranded
DNA in response to cold shock. YB-1 con-
tains a Fve-stranded ß-barrel known as the
‘‘COLD’’ domain and accessory domains
rich in basic amino acids and aromatic
groups. This domain arrangement in YB-1
protein with speciFc interaction domain
containing ß-sheets and a basic domain
providing generic RNA binding is remi-
niscent of the modular structure of the SR
proteins. YB-1 stimulates the splicing of
the human CD44 alternative exon v4 by in-
teracting with the A/C-rich element in the
exonic splicing enhancer. Another protein,
DEAD-box RNA helicase p72, has been re-
ported to affect the splicing of alternative
exons containing AC-rich exon enhancer
elements. The mechanism of YB-1 or other
proteins interacting with the A/C-rich type
of ESEs in splicing activation remains to
be elucidated.
HnRNP proteins hnRNPA1 A1 and PTB
are among the best characterized splicing
repressors. HnRNP A1 can interact with
either ESSs or ISSs to prevent exon recog-
nition by SR proteins or U2 assembly.
A model has been proposed for interac-
tions between hnRNP A1 and ESS based
on studies on HIV Tat exon 3 splicing.
In this model, the high-afFnity binding of
hnRNPA1 to ESS promotes nucleation of
multiple A1 along the exon. The formation
of this inhibition zone can be blocked by
S±2/AS±, but not by another SR protein
SC35, providing an explanation for differ-
ential antagonism between hnRNP A1 and
different SR proteins. Two different mod-
els have been proposed for the function of
hnRNPA1 in splicing silencing mediated
by ISSs. In the case of HIV Tat intron
2 splicing, the interaction of hnRNP A1
with an alternative branch point sequence
blocks the recognition of the branch site
by U2snRNP. In the second model, the
cooperative binding of hnRNP A1 to two
intronic elements flanking the alternative
exon inhibits exon inclusion by a looping-
out mechanism during autoregulation of
hnRNP A1 gene splicing.
PTB interacts with U/C-rich elements
in ISSs in a number of genes including
n-src, ±G±R2, GABA
A
R
γ
2, tropomyosin,
NMDA R1 exon 5, clathrin light chain
B, caspase-2, and calcitonin/CGRP genes.
Depletion of PTB using an RNA inter-
ference approach demonstrates that PTB
is a negative regulator of exon deFnition
in cultured cells. PTB-binding sites are
frequently located in the intronic regions
upstream of the regulated 3
0
splice sites,
although functionally active PTB-binding
sites are also found in intronic elements
downstream of the alternatively spliced ex-
ons (such as in c-src and caspase-2 genes).
Mechanisms
by
which
PTB
represses
splicing are not clear yet. One model
for repression by PTB is via competition
with U2A± binding to the polypyrimidine
tract to block early spliceosome forma-
tion. This model is based on studies of
alternative splicing of GABA
A
R
γ
2, NMDA
R1 exon 5, and clathrin light chain B
genes. In these genes, the high-afFnity
PTB binding to the long polypyrimidine
tracts immediately upstream of the neural-
speciFc exons represses the inclusion of
these exons in nonneural tissues. A sim-
ilar repression mechanism may be used
in suppressing the inclusion of muscle-
speciFc exons in rat
α
-or
β
-tropomyosin.
PTB exists in a range of different tissues
as an abundant splicing repressor. The
repressor activity of PTB may be mod-
ulated by other regulatory proteins. Two
tissue-speciFc PTB-related proteins have
previous page 149 Encyclopedia of Molecular Cell Biology and Molecular Medicine read online next page 151 Encyclopedia of Molecular Cell Biology and Molecular Medicine read online Home Toggle text on/off