Editing Alternative splicing (section)

===Regulatory elements and proteins===

[[File:Splicing repression.jpg|thumb|left|Splicing repression]]
Splicing is regulated by [[trans-acting]] proteins (repressors and activators) and corresponding [[cis-acting]] regulatory sites (silencers and enhancers) on the pre-mRNA. However, as part of the complexity of alternative splicing, it is noted that the effects of a splicing factor are frequently position-dependent. That is, a splicing factor that serves as a splicing activator when bound to an intronic enhancer element may serve as a repressor when bound to its splicing element in the context of an exon, and vice versa.<ref name="Lim">{{cite journal | vauthors = Lim KH, Ferraris L, Filloux ME, Raphael BJ, Fairbrother WG | title = Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 108 | issue = 27 | pages = 11093–8 | date = July 2011 | pmid = 21685335 | pmc = 3131313 | doi = 10.1073/pnas.1101135108 | bibcode = 2011PNAS..10811093H | doi-access = free }}</ref> The secondary structure of the pre-mRNA transcript also plays a role in regulating splicing, such as by bringing together splicing elements or by masking a sequence that would otherwise serve as a binding element for a splicing factor.<ref>{{cite journal | vauthors = Warf MB, Berglund JA | title = Role of RNA structure in regulating pre-mRNA splicing | journal = Trends in Biochemical Sciences | volume = 35 | issue = 3 | pages = 169–78 | date = March 2010 | pmid = 19959365 | pmc = 2834840 | doi = 10.1016/j.tibs.2009.10.004 }}</ref><ref name="ncbi.nlm.nih.gov">{{cite journal | vauthors = Reid DC, Chang BL, Gunderson SI, Alpert L, Thompson WA, Fairbrother WG | title = Next-generation SELEX identifies sequence and structural determinants of splicing factor binding in human pre-mRNA sequence | journal = RNA | volume = 15 | issue = 12 | pages = 2385–97 | date = December 2009 | pmid = 19861426 | pmc = 2779669 | doi = 10.1261/rna.1821809 }}</ref> Together, these elements form a "splicing code" that governs how splicing will occur under different cellular conditions.<ref name=Wang>{{cite journal | vauthors = Wang Z, Burge CB | title = Splicing regulation: from a parts list of regulatory elements to an integrated splicing code | journal = RNA | volume = 14 | issue = 5 | pages = 802–13 | date = May 2008 | pmid = 18369186 | pmc = 2327353 | doi = 10.1261/rna.876308 | format = Free full text }}</ref><ref name=Barash>{{cite journal | vauthors = Barash Y, Calarco JA, Gao W, Pan Q, Wang X, Shai O, Blencowe BJ, Frey BJ | display-authors = 6 | title = Deciphering the splicing code | journal = Nature | volume = 465 | issue = 7294 | pages = 53–9 | date = May 2010 | pmid = 20445623 | doi = 10.1038/nature09000 | s2cid = 2398858 | bibcode = 2010Natur.465...53B }}</ref>

There are two major types of cis-acting RNA sequence elements present in pre-mRNAs and they have corresponding trans-acting [[RNA-binding protein]]s. Splicing ''silencers'' are sites to which splicing repressor proteins bind, reducing the probability that a nearby site will be used as a splice junction. These can be located in the intron itself (intronic splicing silencers, ISS) or in a neighboring exon ([[exonic splicing silencer]]s, ESS). They vary in sequence, as well as in the types of proteins that bind to them. The majority of splicing repressors are [[heterogeneous nuclear ribonucleoprotein]]s (hnRNPs) such as hnRNPA1 and polypyrimidine tract binding protein (PTB).<ref name=Matlin/><ref name=Wang/> Splicing ''enhancers'' are sites to which splicing activator proteins bind, increasing the probability that a nearby site will be used as a splice junction. These also may occur in the intron (intronic splicing enhancers, ISE) or exon ([[exonic splicing enhancer]]s, ESE). Most of the activator proteins that bind to ISEs and ESEs are members of the [[SR protein]] family. Such proteins contain RNA recognition motifs and arginine and serine-rich (RS) domains.<ref name=Matlin/><ref name=Wang/>

[[File:Splicing activation.jpg|thumb|left|Splicing activation]]

In general, the determinants of splicing work in an inter-dependent manner that depends on context, so that the rules governing how splicing is regulated form a splicing code.<ref name=Barash/> The presence of a particular cis-acting RNA sequence element may increase the probability that a nearby site will be spliced in some cases, but decrease the probability in other cases, depending on context. The context within which regulatory elements act includes cis-acting context that is established by the presence of other RNA sequence features, and trans-acting context that is established by cellular conditions. For example, some cis-acting RNA sequence elements influence splicing only if multiple elements are present in the same region so as to establish context. As another example, a cis-acting element can have opposite effects on splicing, depending on which proteins are expressed in the cell (e.g., neuronal versus non-neuronal PTB). The adaptive significance of splicing silencers and enhancers is attested by studies showing that there is strong selection in human genes against mutations that produce new silencers or disrupt existing enhancers.<ref name="Ke">{{cite journal | vauthors = Ke S, Zhang XH, Chasin LA | title = Positive selection acting on splicing motifs reflects compensatory evolution | journal = Genome Research | volume = 18 | issue = 4 | pages = 533–43 | date = April 2008 | pmid = 18204002 | pmc = 2279241 | doi = 10.1101/gr.070268.107 }}</ref><ref>{{cite journal | vauthors = Fairbrother WG, Holste D, Burge CB, Sharp PA | title = Single nucleotide polymorphism-based validation of exonic splicing enhancers | journal = PLOS Biology | volume = 2 | issue = 9 | pages = E268 | date = September 2004 | pmid = 15340491 | pmc = 514884 | doi = 10.1371/journal.pbio.0020268 | doi-access = free }}</ref>