Editing Protein isoform (section)

== Mechanism ==
{{main|Alternative splicing}}
[[File:Alternative splicing.jpg|thumb|Different mechanisms of [[RNA splicing]]|320x320px]]
The primary mechanisms that produce protein isoforms are alternative splicing and variable promoter usage, though modifications due to genetic changes, such as [[Mutation|mutations]] and [[Polymorphism (biology)|polymorphisms]] are sometimes also considered distinct isoforms.<ref name=":5">{{cite journal | vauthors = Kornblihtt AR, Schor IE, Alló M, Dujardin G, Petrillo E, Muñoz MJ | title = Alternative splicing: a pivotal step between eukaryotic transcription and translation | language = En | journal = Nature Reviews Molecular Cell Biology | volume = 14 | issue = 3 | pages = 153–65 | date = March 2013 | pmid = 23385723 | doi = 10.1038/nrm3525 | s2cid = 54560052 | hdl = 11336/21049 | hdl-access = free }}</ref>

Alternative splicing is the main [[post-transcriptional modification]] process that produces mRNA transcript isoforms, and is a major molecular mechanism that may contribute to protein diversity.<ref name=":1" /> The [[spliceosome]], a large [[ribonucleoprotein]], is the molecular machine inside the nucleus responsible for RNA cleavage and [[Ligation (molecular biology)|ligation]], removing non-protein coding segments ([[Intron|introns]]).<ref name=":3">{{cite journal | vauthors = Lee Y, Rio DC | title = Mechanisms and Regulation of Alternative Pre-mRNA Splicing | journal = Annual Review of Biochemistry | volume = 84 | issue = 1 | pages = 291–323 | date = 2015-01-01 | pmid = 25784052 | pmc = 4526142 | doi = 10.1146/annurev-biochem-060614-034316 }}</ref>

Because splicing is a process that occurs between [[Transcription (biology)|transcription]] and [[Translation (biology)|translation]], its primary effects have mainly been studied through [[genomics]] techniques—for example, [[Microarray analysis techniques|microarray]] analyses and [[RNA-Seq|RNA sequencing]] have been used to identify alternatively spliced transcripts and measure their abundances.<ref name=":5" /> Transcript abundance is often used as a proxy for the abundance of protein isoforms, though [[proteomics]] experiments using gel electrophoresis and mass spectrometry have demonstrated that the correlation between transcript and protein counts is often low, and that one protein isoform is usually dominant.<ref name=":6">{{cite journal | vauthors = Tress ML, Abascal F, Valencia A | title = Alternative Splicing May Not Be the Key to Proteome Complexity | journal = Trends in Biochemical Sciences | volume = 42 | issue = 2 | pages = 98–110 | date = February 2017 | pmid = 27712956 | doi = 10.1016/j.tibs.2016.08.008 | pmc=6526280}}</ref> One 2015 study states that the cause of this discrepancy likely occurs after translation, though the mechanism is essentially unknown.<ref>{{cite journal | vauthors = Battle A, Khan Z, Wang SH, Mitrano A, Ford MJ, Pritchard JK, Gilad Y | title = Genomic variation. Impact of regulatory variation from RNA to protein | journal = Science | volume = 347 | issue = 6222 | pages = 664–7 | date = February 2015 | pmid = 25657249 | pmc = 4507520 | doi = 10.1126/science.1260793 }}</ref> Consequently, although alternative splicing has been implicated as an important link between variation and disease, there is no conclusive evidence that it acts primarily by producing novel protein isoforms.<ref name=":6" />

Alternative splicing generally describes a tightly regulated process in which alternative transcripts are intentionally generated by the splicing machinery. However, such transcripts are also produced by splicing errors in a process called "noisy splicing," and are also potentially translated into protein isoforms. Although ~95% of multi-exonic genes are thought to be alternatively spliced, one study on noisy splicing observed that most of the different low-abundance transcripts are noise, and predicts that most alternative transcript and protein isoforms present in a cell are not functionally relevant.<ref>{{cite journal | vauthors = Pickrell JK, Pai AA, Gilad Y, Pritchard JK | title = Noisy splicing drives mRNA isoform diversity in human cells | journal = PLOS Genetics | volume = 6 | issue = 12 | pages = e1001236 | date = December 2010 | pmid = 21151575 | pmc = 3000347 | doi = 10.1371/journal.pgen.1001236 | doi-access = free }}</ref>

Other transcriptional and post-transcriptional regulatory steps can also produce different protein isoforms.<ref>{{cite journal | vauthors = Smith LM, Kelleher NL | title = Proteoform: a single term describing protein complexity | language = En | journal = Nature Methods | volume = 10 | issue = 3 | pages = 186–7 | date = March 2013 | pmid = 23443629 | pmc = 4114032 | doi = 10.1038/nmeth.2369 }}</ref> Variable promoter usage occurs when the transcriptional machinery of a cell ([[RNA polymerase]], [[Transcription factor|transcription factors]], and other [[Enzyme|enzymes]]) begin transcription at different promoters—the region of DNA near a gene that serves as an initial binding site—resulting in slightly modified transcripts and protein isoforms.