Splicing, alternative

Splicing occurs in a large protein-nucleic acid complex, termed the spUceosome. Components of the spliceosome are, apart from the pre-mRNA, a number of proteins and small RNAs, termed the Ul, U2, U4, U5 and U6. The RNAs found in the spUceo-some are bound to specific proteins. The complexes are termed snRNPs (small nuclear ribonucleoprotein). Depending upon the type of RNA bound, there are Ul, U2, U5 and U4/U6 snRNPs. 

Based on the observation of self splicing by the 23S RNA of Tetrahymena, it is assumed that the cleavage and rejoining of the phosphodiester bond is catalyzed by the RNA components of the spliceosome. The proteins of the spliceosome are believed to be important for the recognition of the 5 and 3 splice sites and for the formation of a defined structure in the spliceosome. Thus, the proteins of the spliceosome play a decisive role in the choice of the splice site and the effeciency of splicing. 

The signal sequences that determine the location of splicing are shown in Fig. 1.47. Decisive are sequences at the border between exon and intron, foimd as conserved sequences at the 5 (donor site) and 3 (acceptor site) of the splice site. The intron is removed in the form of a lasso. Donor and acceptor sites are then precisely joined together. 

The occurrence of several exons and intron in a gene opens the possibility of alternative splicing. 

Starting with a single pre-mRNA several alternative mRNAs via the rejoining of various exons can be formed, each coding for proteins with different activities and functions. The creation of different proteins due to alternative splicing is a commonly used tool for cell- and tissue-specific expression of proteins. By the formation of variable spliced proteins, a tissue-specific constitutive protein pattern can be created. An example for this is shown in Fig. 1.48. Alternative splicing can also be used to rapidly and flexibly adjust the expression of specific proteins in response to a transduced external signal. 

Besides regulating and maintaining the splicing process itself, the choice of exons for the final transcript is also of vital importance [11,12]. 

Naturally, a whole cornucopia of accessory factors regulates splicing and splice site selection [18]. In addition to cis-elements within the RNA, several families of RNA factors control which alternative splicing path is chosen. Well-studied examples include serine-rich (SR) proteins and heterologous nuclear ribonuclear particles (hnRNPs) [19, 20]. SR proteins bind to exonic splicing enhancers (ESEs) or intronic splicing enhancers (ISEs) and aid in recruiting the spliceosome itself. 

In contrast, hnRNPs mainly interact with silencer sequences to prevent splicing or promote exon skipping. 

Until fairly recently, splicing had not attracted much attention within the community of chemical biologists as useful inhibitors were lacking. Because researchers working on splicing itself had successfully used molecular genetics and small RNA tools for their studies, it seemed nobody was actively looking for 

TIGR Gene Indices http //www.tigr.org/tdb/tgi.shtml Organism specific EST and gene sequences 

UniGene http //w w w. ncbi. nlm. nih. go v/UniGene/ Unified clusters of EST and full-length mRNA sequences 

WUSTL http //genome.wustl.edu/gsc/ Human and model organism sequences, EST 

EASED http //eased.bioinf.mdc-berhn.de/ Extended alternatively spliced EST 

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KhGH A natural, stmctural variant of hGH called 20-K hGH has been reported to occur in the pituitary as well as in the bloodstream (12,13). This variant, which lacks the 15 amino acid residues from Glu-32 to Gln-46, arises from an alternative splicing of the messenger ribonucleic acid (mRNA) (14). This variant shares many but not all of the biological properties of hGH. 

NMD A receptors are selectively activated by A/-methyl-D-aspartate (NMD A) (182). NMD A receptor activation also requires glycine or other co-agonist occupation of an allosteric site. NMDAR-1, -2A, -2B, -2C, and -2D are the five NMD A receptor subunits known. Two forms of NMDAR-1 are generated by alternative splicing. NMDAR-1 proteins form homomeric ionotropic receptors in expression systems and may do so m situ in the CNS. Functional responses, however, are markedly augmented by co-expression of a NMDAR-2 and NMDAR-1 subunits. The kinetic and pharmacological properties of the NMD A receptor are influenced by the particular subunit composition. 

AMP-activated protein kinases are heterotrimeric complexes comprised of catalytic a subunits and regulatory (3 and y subunits (Table 1). Each subunit is encoded by at least two genes, some of which can also be subject to alternate splicing, leading to a diverse array of possible heterotrimeric combinations. 

The ACHE gene includes sites for alternative splicing of its pre-mRNA product both at the 5 and the 3 ends. Three different carboxy termini exist the synaptic or S variant also called as tailed , the erythrocytic or E variant and the readthrough or R variant. These join the two different N-termini to yield variants with the common or the extended N-terminus. 

Mashorer E, Soreq H (2006) Virtues and woes of AChE alternative splicing in stress-related neuropathologies. Trends Neurosci 29(4) 216-224... 

GDNF Family - GDNF, NRTN, ARTN, and PSPN RET Alternative splicing results in three isoforms Required for enteric neuron development, kidney development, and spermatogenesis... 

The insulin-binding domain of the INSR is located within a cystein-rich region of the a-subunits. Alternative splicing of exon 11 generates two isoforms of the a-subunit which differ in their C-terminus and in their tissue distribution (type A leukocytes type B liver type A and B skeletal muscle and fat). The isoforms differ in their affinity to insulin (A > B), but then-relevance for normal and impaired insulin action is not entirely clear [1,2]. 

In mammalia, seven different members encoded by distinct genes have been identified, all of which are activated by a distinct set of cytokines. Diversity in signaling is provided by variants of STAT proteins derived from either alternative splicing of RNA transcripts or proteolytic processing (e.g., STATs 1,3,4, and 5) and the ability of certain STATs to form both homodimers and heterodimers with each other. In response to inteiferon-y monomeric STAT1 dimerizes, while upon interferon-a stimulation a heterotrimeric complex consisting of STAT 1 and STAT2 with associated... 

Phospholipase D is widely distributed in bacteria, fungi, plants and animals, and is present in almost all mammalian cells [3]. In mammals, it occurs as alternatively spliced products of two genes (PLD1 andPLD2) (Fig. 3). Most mammalian cells express different levels of both isoforms. Both PLD1 and PLD2 have four conserved sequences (I-IV), and sequences I and IV contain the HXKX4D (HKD) motif that is characteristic of the PLD superfamily, which includes bacterial endonucleases, phospholipid synthases, viral envelope... 

Welling A, Ludwig A, Zimmer S et al (1997) Alternatively spliced IS 6 segments of the alpha 1C gene determine the tissue-specific dihydropyridine sensitivity of cardiac and vascular smooth muscle L-type Ca2+ channels. Circ Res 81 526-532... 

Alternative Splicing Alzheimer s Disease Ames Test Amiloride... 

Fig. 2 cDNA structure of human tropoelastin. The alternating hydrophobic and hydrophilic domains are generally encoded by different exons, shown in white and black, respectively. The arrows indicate the six exons that are subject to alternative splicing in a cassette-like fashion. Reproduced from [8] with permission from John Wiley and Sons, copyright 1998... 

Human genes do more work than those of the roundworm or fruit fly (eg, alternative splicing is used more frequently). 

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