Biology Reference
In-Depth Information
modules, which we interpret as building blocks in spliceosome maturation. We conclude that Petri net representations of large
biological networks and system invariants, are well-suited as a means for validating the integration of experimental knowledge
into a consistent model. Based on this network model, the design of further experiments is facilitated.
KEYWORDS:
Spliceosome, pathway analysis, Petri net theory, T-invariants, T-clusters, MCTS, regulated splicing, alternative
splicing, signal transduction networks
INTRODUCTION
Splicing is a process of mRNA maturation in which parts (introns) of the pre-mRNA are removed and
which significantly increases the coding capacity of a gene [Graveley, 2001]. Splicing activities have
been observed in many metazoans but also in less complex organisms such as the immunodeficiency virus
or yeast cells. It has been shown that, along with the evolution of metazoans towards higher complexity,
the number of genes increased comparably slowly. This has been attributed to the effect of alternative
splicing (AS) [Brett
et al.
, 2000; Modrek, 2001; Johnson
et al.
, 2003],
i.e.
, the variable recognition of
splicing signals that leads to different mature mRNA sequences from the same gene.
Understanding alternative splicing (AS) is preceded and accompanied by the fundamental mechanism
and function of the spliceosomal protein complex. The mechanism of splicing has been studied for almost
three decades, and many details have been elucidated through experimental work with yeast strains. Many
of the protein factors involved in the splicing of yeast genes exhibit homologous counterparts in the human
spliceosome [Brow, 2002] and are organized in functional subcomplexes named U1, U2, U4, U5, and
U6 snRNPs [Stevens
et al.
, 2001, Will and L uhrmann, 2001]. The spliceosome itself belongs to the
most complex machineries that exist in eukaryotic cells, involving more than 150 proteins [Zhou
et al.
,
2002; Jurica and Moore, 2003; Chen
et al.
, 2007]. It constitutes an important regulatory unit that on the
one side offers many potential targets for control by external stimuli, and on the other side emits itself
regulatory effects through realization of specific AS patterns.
The outcome of different splicing events indicates that the maturation of RNAs is a complicated process
that can be influenced by events as simple as mutations in splice sites [Venables, 2004], or as subtle as a
few-nucleotides shift of splicing signals [Hiller
et al.
, 2004; Bortfeldt
et al.
, 2008] or as complex as signal
cascades induced by cell external factors [Stamm, 2002]. The frequent occurrence of subtle splice events
(
e.g.
,T
ASS
DB [Hiller
et al.
, 2007]) requires to reconsider and to deeper explore the function and control
of spliceosome assembly. However, compilations of data about the compositions of spliceosomes, the
involved proteins and their interactions, which participate in alternative splicing events, is missing up to
now.
Splicing decisions are controlled by two major determinants - the pre-mRNA sequence and its inherent
signals as well as the protein-complement of the spliceosome where a signal transduction is frequently
maintained via arginine-serine rich domains (RS domains) of the participating proteins [Shen and Green,
2004]. Hence, the dependence of gene expression on developmental stage or tissue type is modulated to
a major extent by a network of protein-protein and protein-RNA interactions that influence the assembly
and localization of active spliceosomes.
One of the major difficulties in the functional characterization of the spliceosome arises from the
dynamic interactions between its subcomplexes and the huge number of proteins organized within those.
Although extensive knowledge has been gathered about the factors involved in spliceosomal activities,
their functional interplay and regulatory impact is not comprehensively understood and even discussed
controversially. For example, it is not clear whether the assembly process occurs mainly co- or post-
transcriptional and whether a stepwise assembly [G ornemann
et al.
, 2005; Behzadnia
et al.
, 2006] rules
out the possibility of a pre-assembled holospliceosome [Stevens
et al.
, 2002; Malca
et al.
, 2003]. In
