genes are transcribed into pre - mrna and pass through splicing as a post - transcriptional modification to generate mature mrna for translation . splicing is an essential process for gene expression in eukaryotes , eliminating introns and joining the exons , which occurs in the spliceosome , a complex of small nuclear ribonucleoproteins ( snrnps ) and other proteins . this splicing can generate alternative spliced transcripts from pre - mrna and different exon constitutions , resulting in different proteins . the most representative mechanisms are as follows : 1 , extending or shortening the exon by alternative donor and acceptor sites ; 2 , exon skipping ; 3 , mutual exon exclusion ; and 4 , intron retention [ 1 , 3 , 4 ] . these mechanisms allow protein isoforms with different biological characters to be produced from single genes . therefore , complex transcriptomes and proteomes could be derived from a limited number of genes . namely , this process is an important strategy for the complicated regulation of eukaryotes , and most genes ( 92 - 95% ) undergo this process [ 5 , 6 ] . alternative splicing is regulated according to cell type , developmental stage , and disease states [ 1 , 7 , 8 ] . biochemical mechanisms for the recognition of splice sites are not understood clearly according to cellular conditions , but some tissue - specific factors participate in alternative splicing . in addition , quantitative gene expression is controlled by nonsense - mediated decay mechanisms that degrade targeting mrnas , producing nonsense mutations . as many as 50% of genetic diseases of humans are related to mutations in splice site sequences and regulatory elements , such enhancers and silencers , resulting in alternative exon constitution [ 3 , 10 , 11 ] . recently , the splicedisease database , providing information for relationships among gene mutation , splicing defects , and diseases , was reported . especially , aberrent spliced variants are found frequently in cancer , indicating that they could play a role for the survival of cancer cells . alternative splicing of cancer - related genes could affect cell cycle control , signal transduction pathways , apoptosis , angiogenesis , invasion , and metastasis [ 8 , 13 ] . cancer markers allow us to determine the prognosis and therapy for cancer during the remedy of cancer . cancerous cells grow irregularly , create malignant tumors , and move to the other parts of the body . accordingly , alternative transcripts produced by splicing events represent good candidates for cancer biomarkers [ 7 , 8 , 13 ] . in the present review , alternative splicing is an essential post - transcriptional process for creating various protein isoforms from the same gene . alternative splicing is regulated by mutations in genetic regions [ 3 , 7 , 14 ] . most exons are flanked by the intronic dinucleotides gt ( donor site ) and ag ( acceptor site ) , which are recognized by the spliceosome ( fig . however , mutations of these splice sites lead to aberrant splicing , producing exon skipping and different joining of exons to truncated or nonfunctional or dysfunctional proteins . it was reported that mutations of splice sites may play important roles in human disease , and longer proteins also tend to associate to various disease [ 16 , 17 ] . in the case of the pax6 gene , a 5 ' splice site mutation in intron 12 induces exon skipping in relation to autosomal dominant aniridia . in the apc gene , abnormal splicing by a 3 ' splice site mutation in intron 3 causes exon 4 skipping due to a frameshift in hepatoblastoma . a mutation in intron 25 of the abca3 gene creates novel 5 ' splice sites . are gc - ag , gg - ag , gt - tg , gt - cg , at - ag , ga - ag , gt - ac , and ct - ag ( 5'-3 ' splice sites ) [ 21 - 23 ] . mutations at the noncanonical splice site of the sedl gene cause variants in x - linked spondyloepiphyseal dysplasia tarda . additionally , less exon skipping and more intron retention by alternative splice sites are observed in cancer tissue compared to normal tissues from an analysis of expression sequence tags ( ests ) . as a mutation of pre - mrna , a to i rna editing has regulatory roles , such as altering splice sites and sequences necessary for recognition of the spliceosome , resulting in modulation of alternatively spliced transcripts . the last case of alternative splicing is by cis - genomic mutations in regulatory factors , such as branch sites , exonic and intronic splicing enhancers , and silencers [ 7 , 27 ] . pre - mrna has exonic and intronic splicing enhancers ( eses , ises ) and silencers ( esss , isss ) that promote exon inclusion and exclusion by regulation of splice site recognition , respectively ( fig . the arginine - serine - rich ( sr ) protein that binds to eses induces splicing via a helping assembly spliceosome by interacting with snrnp . on the contrary , heterogeneous nuclear ribonucleoprotein is bound to eses and ises and inhibits splice site recognition by blocking spliceosome assembly [ 15 , 27 - 29 ] . mutations in regulatory factor could disturb the binding of these spliceosome assembly - related proteins . mutations at nucleotide positions 57 and 58 of the 174-bp - long exon 7 cause exon 7 skipping as a result of aberrant splicing by interrupted ese - specific consensus sequences that are recognized by the sc35 and sf2/asf sr proteins [ 10 , 30 ] . additionally , ron , encoding the tyrosine kinase receptor for macrophage - stimulating protein , has alternative splice transcripts . it is regulated by overexpression of sf2/asf binding to ese and ise in colon and breast cancer . alternative splicing is also known to be affected by epigenetic regulation , such as dna methylation , histone modification , and chromatin structure ( fig . the relationship between chromatin structure and alternative splicing is still in a maze , but association studies are gradually increasing genomewide [ 32 - 34 ] . hisone modifications are enriched in exons rather than introns and related to exon expression , especially h3k36me3 , h3k79me1 , h2bk5me1 , h3k27me1 , h3k27me2 , and h3k27me3 [ 35 , 36 ] . h3k36me3 marking in exons is found in weakly expressed , alternatively spliced exons , indicating that histone modification has a relation to transcription via splicing - related marking mechanisms [ 36 , 37 ] . these histone marks could recruit splicing regulators with chromatin binding proteins and affect mrna splicing . additionally , hisone acethylation could modulate splicing rates to react quickly to changing conditions with increased rna polymerase ii processivity , and spliceosome rearrangements are affected by histone acetylation . nevertheless , although there is little evidence , dna methylation has been reported to have a relationship with splice sites . exon skipping and mutually exclusive exons have significantly lower levels of both cg and mcg in the exonic regions , whereas intron retention has significantly higher levels of cg in both exonic and intronic regions . a dna - binding protein , ccctc - binding factor ( ctcf ) , furthermore , these mechanisms are known to be changed according to cell type and disease states . especially , in cancer , the epigenetic regulation of chromatin structure effects aberrant gene expression by alternative splicing in cancer [ 1 , 7 , 8 ] . taken together , gene expression via alternative splicing is altered by complicated and mutual mechanisms , from genetic to epigenetic regulation . therefore , it casts light on the understanding of cancer mechanisms by an investigation of alternative splicing patterns . a number of studies have been reported that alternative splicing is related closely to development , cellular stress , and various diseases , including cancer , as a crucial contributor to transcriptome and proteome diversity [ 1 , 7 , 8 , 14 ] . in cancer , with increasing genomic instability , sequence substitution and aberrant alternative splicing occur frequently , leading to erroneous and dysfunctional proteins . protein isoforms made from this process are developmentally regulated and preferentially re - expressed in cancer and help the differentiation and survival of cancer cells ( fig . 2 ) . the development of genomewide analysis allows large - scale examination of the relationship between alternative splicing and tumorigenesis [ 40 , 41 ] . every case of alternative splicing is reported in cancer ; among these , the most frequent case is the mutually exclusive exon . for example , overexpression of cd44 , involved in cell proliferation , differentiation , migration , and alternative splicing , by different splice sites of cd44 during tumorigenesis indicates that it could play roles in tumor cell invasion and metastasis [ 42 - 45 ] . tumor suppressor genes , such as p53 and pten ( phosphatase and tensin homolog , deleted on chromosome ten ) , have splicing variants associated to cancer . p53 protein isoforms through alternative splicing have critical roles in many biological processes , indicating that dysregulation effects tumorigenesis . different expression of pten and its alternatively spliced transcripts are found to vary in different tissue types . the pten splice variants retained in intron 3 region and intron 5 region have been found in breast cancer . in the case of the apc gene , aberrant splice skipping of exon 4 , created by insertion of t in intron 4 , is involved in colon cancer . an alternative 5 ' splice site in bcl - x results in 2 isoforms , long and short ( bcl - x ( l ) , bcl - x ( x ) ) , which have contrasting functions related to apoptosis and are overexpressed in various tumors [ 49 , 50 ] . although specific roles of vascular endothelial growth factor ( vegf ) isoforms are not known exactly , among the isoforms of vegf4 involved in formation of new vessels , vegf165 and vegf165b , created by an alternative 3 ' splice site , have different expression in cancer [ 51 , 52 ] . over 40 different mdm2 transcripts are identified in normal and cancer by alternative 5 ' and 3 ' splice sites . they mostly lose the p53 binding domain and promote tumor progression and affect prognosis independently [ 53 , 54 ] . increasing number of reports have demonstrated the expression of aberrant and abnormal splice variants in cancer cells or tissues . however , it is not enough evidence for a functional relationship between alternative splicing and cancer . hallmarks of the initiation and early growth of cancers during tumor progression using large - scale analyses of splicing variants in the cancer est database are needed as new rna prognosis markers . cancer is an uncontrolled state and irregularly altered genetically and epigenetically compared to normal regulation ( fig . many studies have made an effort to identify specific features and regulation mechanims of various diseases , including cancer . it is important and necessary to identify cancer markers to be able to distinguish between cancer and normal cells . cancer markers could be very helpful in understanding tumorigenesis and developing tumor targets for therapeutic intervention . however , there still remain unsolved problems in spite of a number of studies [ 7 , 14 , 45 , 64 ] . from this point of view , alternatively spliced transcripts by mutation and cryptic splice site altered expression levels in cancer have emerged as strong candidates of cancer biomarker at the mrna and protein level . as written previously , some alternative transcripts of several genes , cd44 , p53 , pten , bcl - x , vegf4 , and mdm2 , have been discovered ( see also table 1 ) [ 43 , 46 , 49 , 50 , 52 , 54 ] . recently , the discovery of biomarkers has improved by genomewide analysis [ 13 , 65 , 66 ] . it could be expected to provide valuable information for the association between alternative splice variants and cancers . thus , novel candidate variants could contribute to the development of diagnostic , prognostic , and therapeutic markers . rna splicing is a core mechanism to generate mature mrna for translation , and alternative splicing is an indispensable mechanism , stratgically leading to protein diversity for complicated regulation in eukaryotes . in cancer , alternative splicing is more flexible , leading various proteins with aberrant functions to promote growth and the spread of cancer cells . these alternative transcripts could be used not only as diagnostic biomarkers but also prognostic and theraputic biomarkers . therefore , studies on genetic and epigenetic regulation in relation to alternative splice variants in cancer could open new windows of research in answering unsolved questions of tumorigenesis .
most genes are processed by alternative splicing for gene expression , resulting in the complexity of the transcriptome in eukaryotes . 
 it allows a limited number of genes to encode various proteins with intricate functions . 
 alternative splicing is regulated by genetic mutations in cis - regulatory factors and epigenetic events . furthermore , 
 splicing events occur differently according to cell type , developmental stage , and various diseases , including cancer . 
 genome instability and flexible proteomes by alternative splicing could affect cancer cells to grow and survive , leading to metastasis . 
 cancer cells that are transformed by aberrant and uncontrolled mechanisms could produce alternative splicing to maintain and spread them continuously . 
 splicing variants in various cancers represent crucial roles for tumorigenesis . 
 taken together , the identification of alternative spliced variants as biomarkers to distinguish between normal and cancer cells could cast light on tumorigenesis .