Splice site mutation
A splice site mutation is a genetic mutation that inserts, deletes or changes a number of nucleotides in the specific site at which splicing of an intron takes place during the processing of precursor messenger RNA into mature messenger RNA. The deletion of the splicing site results in one or more introns remaining in mature mRNA and may lead to the production of aberrant proteins. When a splice site mutation occurs, the mRNA transcript possesses information from these introns that normally should not be included. Introns are supposed to be removed, while the exons are expressed. The mutation must occur at the specific site at which intron splicing occurs: within non-coding sites in a gene, directly next to the location of the exon. The mutation can be an insertion, deletion, frame shift, etc. The splicing process itself is controlled by the given sequences, known as splice-donor and splice-acceptor sequences, which surround each exon. Mutations in these sequences may lead to retention of large segments of intronic DNA by the mRNA, or to entire exons being spliced out of the mRNA. These changes could result in production of a nonfunctional protein.[1]
Several genetic diseases may be the result of splice site mutations. For example, mutations that cause the incorrect splicing of β-globin mRNA are responsible of some cases of β-thalassemia. Another Example is TTP (thrombotic thrombocytopenic purpura). TTP is caused by deficiency of ADAMTS-13. A splice site mutation of ADAMTS-13 gene can therefore cause TTP. It is estimated that 15% of all point mutations causing human genetic diseases occur within a splice site.[2]
Background
In 1993, Dr. Richard J. Roberts and Dr. Phillip A. Sharp received the Nobel Prize in Physiology or Medicine for their discovery of "split genes".[4] Using the model adenovirus in their research, they were able to discover splicing--the fact that pre-mRNA is processed into mRNA once introns were removed from the RNA segment. These two scientists discovered the existence of splice sites, thereby changing the face of genomics research. They also discovered that the splicing of the messenger RNA can occur in different ways, opening up the possibility for a mutation to occur.
Technology
Today, many different types of technologies exist in which splice sites can be located and analyzed for more information. The Human Splicing Finder is an online database stemming from the Human Genome Project data. The genome database identifies thousands of mutations related to medical and health fields, as well as providing critical research information regarding splice site mutations. The tool specifically searches for pre-mRNA splicing errors, the calculation of potential splice sites using complex algorithms, and correlation with several other online genomic databases, such as the Ensembl genome browser.[5]
Role in Disease
Epilepsy
Some types of epilepsy may be brought on due to a splice site mutation.
In addition to a mutation in a stop codon, a splice site mutation on the 3' strand was found in a gene coding for cystatin B in Progressive Myoclonus Epilepsy[6] patients. This combination of mutations was not found in unaffected individuals. By comparing sequences with and without the splice site mutation, investigators were able to determine that a G-to-C nucleotide transversion occurs at the last position of the first intron. This transversion occurs in the region that codes for the cystatin B gene. Individuals suffering from Progressive Myoclonus Epilepsy possess a mutated form of this gene, which results in decreased output of mature mRNA, and subsequently decreases in protein expression.
A study has also shown that a type of Childhood Absence Epilepsy (CAE) causing febrile seizures may be linked to a splice site mutation in the sixth intron of the GABRG2 gene. This splice site mutation was found to cause a nonfunctional GABRG2 subunit in affected individuals.[7] According to this study, a point mutation was the culprit for the splice-donor site mutation, which occurred in intron 6. A nonfunctional protein product is produced, leading to the also nonfunctional subunit.
Parathyroid Deficiency
When a splice site mutation occurs in intron 2 of the gene that produces the parathyroid hormone, a parathyroid deficiency can prevail. In one particular study, a G to C substitution in the splice site of intron 2 produces a skipping effect in the messenger RNA transcript. The exon that is skipped possesses the initiation start codon to produce parathyroid hormone.[8] Such failure in initiation causes the deficiency.
Analysis
Splice site mutations can be analyzed using information theory .[9]
References
- ^ Understanding Cancer Genomics: Splice Site Mutations. National Cancer Institute.
- ^ Carvalho, Gisah A; Weiss, Roy E; Refetoff, Samuel (June 22, 1998). "Complete Thyroxine-Binding Globulin (TBG) Deficiency Produced by a Mutation in Acceptor Splice Site Causing Frameshift and Early Termination of Translation (TBG-Kankakee)". The Journal of Clinical Endocrinology and Metabolism. 83 (10): 3604–3608. doi:10.1210/jcem.83.10.5208.
- ^ Understanding Cancer Genomics. National Cancer Institute.
- ^ http://www.nobelprize.org/nobel_prizes/medicine/laureates/1993/press.html.
{{cite web}}: Missing or empty|title=(help) - ^ Human Splice Finder. http://www.umd.be/HSF/.
{{cite web}}: External link in|website=|title=(help); Missing or empty|url=(help) - ^ Pennacchio, Len A.; Lehesjoki, Anna-Elina; Stone, Nancy E.; Wilour, Virginia L. (Mar 22, 1996). "Mutations in the Gene Encoding Cystatin B in Progressive Myoclonus Epilepsy (EPM1)" (PDF). Science. 271 (5256): 1731–1734. doi:10.1126/science.271.5256.1731. Retrieved 2014-09-14.
- ^ Kananura, Colette; Haug, Karsten; Sander, Thomas; Runge, Uwe; Gu, Wenli; Hallmann, Kerstin; Rebstock, Johannes; Heils, Armin; Steinlein, Ortrud (July 2002). "A Splice-Site Mutation in GABRG2 Associated With Childhood Absence Epilepsy and Febrile Convulsions". Arch Neurol. 59: 1137–1141. doi:10.1001/archneur.59.7.1137. Retrieved 2014-09-11.
{{cite journal}}: Unknown parameter|displayauthors=ignored (|display-authors=suggested) (help) - ^ Parkinson, David B.; Thakker, Rajesh V. (1992). "A donor splice site mutation in the parathyroid hormone gene is associated with autosomal recessive hypoparathyroidism" (PDF). Nature Genetics. 1 (2): 149–152. doi:10.1038/ng0592-149. PMID 1302009.
- ^ Hum Mutat. 1998;12(3):153-71. Information analysis of human splice site mutations. Rogan PK, Faux BM, Schneider TD. http://www.ncbi.nlm.nih.gov/pubmed/9711873 http://alum.mit.edu/www/toms/paper/rfs/