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I am trying to find out what controls what exons are spliced out, and I keep coming across the term cis regulator, but I cannot seem to find a clear explanation of what happens...

Thank you in advance :)

EDIT: to clarify, I have tried to read the Wikipedia article on alternative splicing and I get the main idea (some exons being cut out of the mRNA with the introns to produce the mature mRNA, I think...) but I don't understand the 'mechanism' section, I.e. What controls which exons will be cut out? And what enzymes 'splice' the mRNA- how do they do it in the right place, and stick the mRNA together again?

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    $\begingroup$ Just to be clear, do you want to know how alternative splicing works? Have you tried reading the Wikipedia article on it? Can you tell us, what you don't understand more specifically? Actually this is pretty broad... $\endgroup$
    – Chris ♦
    Mar 11, 2015 at 14:20
  • $\begingroup$ @Chris thank you for your reply! I have tried reading the Wikipedia article- I get the main idea of alternative splicing (some exons being cut out of the mRNA with the introns to produce the mature mRNA, I think...) but I don't understand the 'mechanism' section, I.e. What controls which exons will be cut out? And what enzymes 'splice' the mRNA- how do they do it in the right place, and stick the mRNA together again? $\endgroup$
    – Meep
    Mar 11, 2015 at 14:24
  • $\begingroup$ Can you add this comment into your question? It would make it much clearer. $\endgroup$
    – Chris ♦
    Mar 11, 2015 at 14:39

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21joanna12, look into snRNPs. These are parts of the splicosomal apparatus and some of them (the U1 and U2, U11 and U12 snRNPs) are also the guideposts that bind near the splice junctions at the end of introns. These help guide the splicing apparatus to the splice sites. There are also proteins that bind RNA and interact with the splicing apparatus to switch alternative splicing, such as SP proteins.
https://en.wikipedia.org/wiki/SnRNP
https://en.wikipedia.org/wiki/SR_protein
https://en.wikipedia.org/wiki/Exonic_splicing_enhancer

Here's a recent review that might serve as an entry into the literature: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4232567/

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  • $\begingroup$ I'm a little familiar with U1 - U6 because I just read a paper on splice switching oligos to control splicing of a defective dystrophin gene to skip a frame shift mutation. But I haven't heard of U11 or U12. I still don't understand how cells select specific alternative splicing patterns to produce a specific protein. Could the pool of miRNAs produced by a cell affect alternative splicing in a manner similar to splice switching oligos just by binding to certain splice sites and forcing the spliceosome to find a different site? $\endgroup$
    – user137
    Mar 11, 2015 at 15:46
  • $\begingroup$ There are two sorts of spliceosomes. The major spliceosome uses the U1 and U2 snRNPs and the minor splicosome uses the U11 and U12 snRNPs. It is binding of the splice-regulatory proteins that influence where the splices occur. I have not heard of RNA directly influencing splicing patterns. I'm very aware of the DMD splice switching using Morpholino oligos - it has great potential as therapeutics for genetic diseases. $\endgroup$
    – Jon D. Moulton
    Mar 11, 2015 at 19:37
  • $\begingroup$ The oligo-based methods of altering splicing can take two different approaches. The most common strategy is to use an oligo to block the binding site of a guidepost snRNP (U1 or U2, U11 or U12). The other approach is to block the binding site of a regulatory protein, preventing that protein from docking with the pre-mRNA. It is the latter approach that is interfering with the mechanics of alternative splicing. The former method, blocking snRNP binding, can cause skipping of an exon that is never skipped by "normal" alternative splicing mechanisms. $\endgroup$
    – Jon D. Moulton
    Mar 11, 2015 at 22:05
  • $\begingroup$ And if that exon contains a frameshift or bad stop codon, skipping it can create a protein that retains enough function to still work. Now if we can just get some good delivery methods for getting the oligos into cells. $\endgroup$
    – user137
    Mar 11, 2015 at 22:39
  • $\begingroup$ user137, the arginine-rich peptides, such as (RXR)4, are pretty good. Moulton HM, Moulton JD. Morpholinos and Their Peptide Conjugates: Therapeutic Promise and Challenge for Duchenne Muscular Dystrophy. Biochim Biophys Acta. 2010 Feb 16. [Epub ahead of print]. sciencedirect.com/science/article/pii/S0005273610000520 $\endgroup$
    – Jon D. Moulton
    Mar 12, 2015 at 14:23
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A review by Penalva and Sánchez explains one example of how alternate splicing is regulated at the molecular level. There are other possible mechanisms that I am only vaguely aware of.

https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/12966139/

Sex determination in Drosophila melanogaster is largely controlled by a cascade of alternate splicing events.

In a brief (and admittedly incomplete) summary, the product(s) of one gene (RNA binding protein) recognize a particular splice site in a downstream transcript. On binding, that site is no longer available as a splice acceptor site and the splicing mechanism is "forced" to work with the next available acceptor site. This leads to the excision of the former exon, which has now become an intron.

This process is represented graphically in the above cited review in Fig 3A where female/functional Sxl product (when present) blocks another RNA-binding protein (U2AF) which is involved in default splicing, and tells it to move on to the next available acceptor site. (I would like to include Fig 3A here but don't know how. Perhaps this will help: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC193869/figure/f3/)

Sex-lethal gene product exists in male- and female-specific forms, produced by (who would have guessed?) alternate splicing of the Sxl transcript. The male-specific transcript has an early stop codon and yields a non-functional protein. The female form modifies splicing of the transformer gene product to produce a female-specific (functional) version of the transformer mRNA. The unmodified (male) version again produces a non-functional protein. The female-specific version of the tra gene product (wait for it!) modifies the splicing of the doublesex transcript to produce a female-specific doublesex protein. The unmodified/default splice dsx transcript produces a male-specific protein. These male- and female-specific proteins lead to male- and female-specific expression of an array of genes further downstream. By the way, the Sxl gene product not only affects the tra transcript but it also modifies the splicing OF ITS OWN TRANSCRIPT to keep Sxl expression going after its initial onset. It also plays a role in setting the overall level of X-chromosome transcription to achieve "dosage compensation".

Hope this helps.

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  • $\begingroup$ the product(s) of one gene recognize a particular splice site in a downstream transcript. On binding, that site is no longer available as a splice acceptor site and the splicing mechanism is "forced" to work with the next available acceptor site. But what determines which splice site is chosen? Suppose pre-mRNA has exons 1,2,3,4. What determines that in one scenario exon 2 will be skipped, whereas in another scenario exon 3? Do we need a different RNA binding protein for each exon of each pre-mRNA molecule? Or can the same RNA binding protein interact with multiple exons, if yes, how? $\endgroup$
    – mercury0114
    Nov 7, 2019 at 12:03

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