Editing Alternative splicing (section)

===Examples===

====Exon skipping: ''Drosophila'' ''dsx''====
[[File:Dsx splicing.jpg|thumb|Alternative splicing of ''dsx'' pre-mRNA]]
Pre-mRNAs from the ''D. melanogaster'' gene ''[[doublesex|dsx]]'' contain 6 exons. In males, exons 1,2,3,5,and 6 are joined to form the mRNA, which encodes a transcriptional regulatory protein required for male development. In females, exons 1,2,3, and 4 are joined, and a [[polyadenylation]] signal in exon 4 causes cleavage of the mRNA at that point. The resulting mRNA is a transcriptional regulatory protein required for female development.<ref name=Lynch>{{cite journal | vauthors = Lynch KW, Maniatis T | title = Assembly of specific SR protein complexes on distinct regulatory elements of the Drosophila doublesex splicing enhancer | journal = Genes & Development | volume = 10 | issue = 16 | pages = 2089–101 | date = August 1996 | pmid = 8769651 | doi = 10.1101/gad.10.16.2089 | doi-access = free }}</ref>

This is an example of exon skipping. The intron upstream from exon 4 has a [[polypyrimidine tract]] that doesn't match the [[consensus sequence]] well, so that U2AF proteins bind poorly to it without assistance from splicing activators. This 3' splice acceptor site is therefore not used in males. Females, however, produce the splicing activator Transformer (Tra) (see below). The SR protein Tra2 is produced in both sexes and binds to an ESE in exon 4; if Tra is present, it binds to Tra2 and, along with another SR protein, forms a complex that assists U2AF proteins in binding to the weak polypyrimidine tract. U2 is recruited to the associated branchpoint, and this leads to inclusion of exon 4 in the mRNA.<ref name=Lynch/><ref name=Graveley>{{cite journal | vauthors = Graveley BR, Hertel KJ, Maniatis T | title = The role of U2AF35 and U2AF65 in enhancer-dependent splicing | journal = RNA | volume = 7 | issue = 6 | pages = 806–18 | date = June 2001 | pmid = 11421359 | pmc = 1370132 | doi = 10.1017/S1355838201010317 }}</ref>

====Alternative acceptor sites: ''Drosophila'' ''{{vanchor|Transformer}}''====
[[File:transformer splicing.gif|left|thumb|Alternative splicing of the ''Drosophila'' ''Transformer'' gene product.]]
Pre-mRNAs of the ''[[Transformer (gene)|Transformer]]'' (Tra) gene of ''[[Drosophila melanogaster]]'' undergo alternative splicing via the alternative acceptor site mode. The gene Tra encodes a protein that is expressed only in females. The primary transcript of this gene contains an intron with two possible acceptor sites. In males, the upstream acceptor site is used. This causes a longer version of exon 2 to be included in the processed transcript, including an early [[stop codon]]. The resulting mRNA encodes a truncated protein product that is inactive. Females produce the master sex determination protein [[Sex lethal]] (Sxl). The Sxl protein is a splicing repressor that binds to an ISS in the RNA of the Tra transcript near the upstream acceptor site, preventing [[U2AF2|U2AF]] protein from binding to the polypyrimidine tract. This prevents the use of this junction, shifting the spliceosome binding to the downstream acceptor site. Splicing at this point bypasses the stop codon, which is excised as part of the intron. The resulting mRNA encodes an active Tra protein, which itself is a regulator of alternative splicing of other sex-related genes (see ''dsx'' above).<ref name=Black/>

====Exon definition: Fas receptor====
[[File:Fas alternative splicing.jpg|thumb|right|Alternative splicing of the Fas receptor pre-mRNA]]
Multiple isoforms of the [[Fas receptor]] protein are produced by alternative splicing. Two normally occurring isoforms in humans are produced by an exon-skipping mechanism. An mRNA including exon 6 encodes the membrane-bound form of the Fas receptor, which promotes [[apoptosis]], or programmed cell death. Increased expression of Fas receptor in skin cells chronically exposed to the sun, and absence of expression in skin cancer cells, suggests that this mechanism may be important in elimination of pre-cancerous cells in humans.<ref name=Filipowicz>{{cite journal | vauthors = Filipowicz E, Adegboyega P, Sanchez RL, Gatalica Z | title = Expression of CD95 (Fas) in sun-exposed human skin and cutaneous carcinomas | journal = Cancer | volume = 94 | issue = 3 | pages = 814–9 | date = February 2002 | pmid = 11857317 | doi = 10.1002/cncr.10277 | s2cid = 23772719 | doi-access = free }}</ref> If exon 6 is skipped, the resulting mRNA encodes a soluble Fas protein that does not promote apoptosis. The inclusion or skipping of the exon depends on two antagonistic proteins, [[TIA1|TIA-1]] and polypyrimidine tract-binding protein (PTB).
* The 5' donor site in the intron downstream from exon 6 in the pre-mRNA has a weak agreement with the consensus sequence, and is not bound usually by the U1 snRNP. If U1 does not bind, the exon is skipped (see "a" in accompanying figure).
* Binding of TIA-1 protein to an intronic splicing enhancer site stabilizes binding of the U1 snRNP.<ref name=Matlin/> The resulting 5' donor site complex assists in binding of the splicing factor U2AF to the 3' splice site upstream of the exon, through a mechanism that is not yet known (see b).<ref name=Izquierdo2005>{{cite journal | vauthors = Izquierdo JM, Majós N, Bonnal S, Martínez C, Castelo R, Guigó R, Bilbao D, Valcárcel J | display-authors = 6 | title = Regulation of Fas alternative splicing by antagonistic effects of TIA-1 and PTB on exon definition | journal = Molecular Cell | volume = 19 | issue = 4 | pages = 475–84 | date = August 2005 | pmid = 16109372 | doi = 10.1016/j.molcel.2005.06.015 | doi-access = free }}
</ref>
* Exon 6 contains a pyrimidine-rich exonic splicing silencer, ''ure6'', where PTB can bind. If PTB binds, it inhibits the effect of the 5' donor complex on the binding of U2AF to the acceptor site, resulting in exon skipping (see c).

This mechanism is an example of exon definition in splicing. A spliceosome assembles on an intron, and the snRNP subunits fold the RNA so that the 5' and 3' ends of the intron are joined. However, recently studied examples such as this one show that there are also interactions between the ends of the exon. In this particular case, these exon definition interactions are necessary to allow the binding of core splicing factors prior to assembly of the spliceosomes on the two flanking introns.<ref name=Izquierdo2005/>

====Repressor-activator competition: HIV-1 ''tat'' exon 2====

[[File:Tat exon2 splicing.jpg|thumb|left|Alternative splicing of HIV-1 tat exon 2]]
[[HIV]], the [[retrovirus]] that causes [[AIDS]] in humans, produces a single primary RNA transcript, which is alternatively spliced in multiple ways to produce over 40 different mRNAs.<ref name=Zahler2004>{{cite journal | vauthors = Zahler AM, Damgaard CK, Kjems J, Caputi M | title = SC35 and heterogeneous nuclear ribonucleoprotein A/B proteins bind to a juxtaposed exonic splicing enhancer/exonic splicing silencer element to regulate HIV-1 tat exon 2 splicing | journal = The Journal of Biological Chemistry | volume = 279 | issue = 11 | pages = 10077–84 | date = March 2004 | pmid = 14703516 | doi = 10.1074/jbc.M312743200 | doi-access = free }}</ref> Equilibrium among differentially spliced transcripts provides multiple mRNAs encoding different products that are required for viral multiplication.<ref name=Jaquenet2001>{{cite journal | vauthors = Jacquenet S, Méreau A, Bilodeau PS, Damier L, Stoltzfus CM, Branlant C | title = A second exon splicing silencer within human immunodeficiency virus type 1 tat exon 2 represses splicing of Tat mRNA and binds protein hnRNP H | journal = The Journal of Biological Chemistry | volume = 276 | issue = 44 | pages = 40464–75 | date = November 2001 | pmid = 11526107 | doi = 10.1074/jbc.M104070200 | doi-access = free }}</ref> One of the differentially spliced transcripts contains the ''tat'' gene, in which exon 2 is a cassette exon that may be skipped or included. The inclusion of tat exon 2 in the RNA is regulated by competition between the splicing repressor hnRNP A1 and the SR protein SC35. Within exon 2 an exonic splicing silencer sequence (ESS) and an exonic splicing enhancer sequence (ESE) overlap. If A1 repressor protein binds to the ESS, it initiates [[cooperative binding]] of multiple A1 molecules, extending into the 5' donor site upstream of exon 2 and preventing the binding of the core splicing factor U2AF35 to the polypyrimidine tract. If SC35 binds to the ESE, it prevents A1 binding and maintains the 5' donor site in an accessible state for assembly of the spliceosome. Competition between the activator and repressor ensures that both mRNA types (with and without exon 2) are produced.<ref name=Zahler2004/>