Term
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Definition
| Process where exons are ligated and introns are removed. |
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Term
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Definition
| "A series of transesterification reactions (transfer of -OH groups, this is how splicesome actually catalyzes)" Lariat initiated by formation of A-G bond. |
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Term
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Definition
Very large complex (more than 200 different proteins in it and have snRNAs and snurps)
Splice sites (regions where exons are ligated) are RECOGNIZED by snurps (small nuclear RiboNucleoprotein Particles) so snurps play a CRUCIAL role in defining what is an intron and what is an exon.
U1 snurp-binds the 5' site then the 3' site
U2-binds the branch site and forms part of the catalytic center. |
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Term
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Definition
nomenclature is different, front = 3' SS, back = 5' SS.
AGGU 5' Splice site
AGGA 3' Splice site |
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Term
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Definition
Where adenosine base is located.
Transesterification reaction takes place here (A-G, lagate removal of structure--intron)
A particular Adenosine gets defined as a branch point (close to 3' branch site) IF IT IS ADJACENT TO A PYRIMIDINE TRACT.
20 nucleotides to pyrimidine tract which is 50 nucleotides to 3' splice site. |
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Term
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Definition
Boundaries are defined by splice sites.
U1 first binds to 5', U2 binds to branch site with U2 auxiliary factors (verify if A is the right one).
All other Snurps come in (U4, U5, and U6), these snurps define your 3' splice site and you will have removal of introns by transesterification process.
The result is a mature mRNA and lariat (removed intron). Spliceosome gets recycled. |
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Term
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Definition
| Series of C & U bases, about 100 of them or so. |
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Term
| Alternative Splicing (Overview) |
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Definition
1) Humans have about 25k genes in our genome but the number of proteins we have is more than 100k.
2) Genes are capable of coding for more than 1 protein by process of alternative splicing
3) Eukaryotic genomes codes through discontinuous coding sequences, exons, separated by non-coding sequences, or introns.
GOVERNED BY trans factors (protein)-affects where U1 binds and defines your selection. You get extended exons.
4) Alternative patterns of RNA splicing result from
*TWO POINTS TO REMEMBER*
a) tissue-specific adaptive
b) developmental
c) hormonal
controls mechanism.
*2ND POINT*
Faulty splicing can cause/contribute to disease. |
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Term
| Alternative Splicing (More Specific) |
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Definition
Most introns require CIS elements comprising of
1) a conserved 5' splice site (AG GUpu) 2) a branch point (BP) sequence (CupuApy) followed by a polypyrimidine tract
3) a 3' splice site (pyAG puN)
Additional sequences exist in the pre-mRNA as auxiliary CIS-ELEMENTS that recruit TRANS-ACTING FACTORS to promote splicing.
*KEY WORD*
REGULATION of alternative splicing is often the result of dynamic antahonism between TRANS-acting PROTEINS binding to cis-ELEMENTS (mRNA sequence). |
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Term
| Modes of Alternative RNA processing |
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Definition
Unspliced RNA-->
1) Selective Splicing (e.g.: exon 1&3&4 are ligated, exon 2 is skipped)
2) Exon Skipping (similar to selective skipping except SS skips invariably, we see SS in developmental, exon skipping is the result of environmental conditions--either OR).
3) Alternative 5' splice site (since splice sites are small, we can have 3-5 more splice sites downstream)
4) Alternate 3' splice site
5) Alternate poly(A) site (addition of extra A sites before all the exons are translates, sequence gets truncated prematurely) |
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Term
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Definition
Auxiliary CIS-elements can promote or repress splice site usage depending on location.
1) If it is present on the exon and enhances splicing, it's called ESEs (exonic splicing enhancers) or silencers (ESSs)
2) ISEs and ISSs
TRANS factors(proteins) interact with cis elements |
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Term
| Examples of trans factors |
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Definition
(proteins)
1) SR Proteins (slicing enhancers), ENHANCE SPLICING OF EXON OR UTILIZATION OF ALTERNATIVE SITE.
2) heterogeneous nuclear ribonucleoprotein (hnRNP) (silencer) |
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Term
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Definition
Ser-Arg Domain. SR Proteins are TRANS-factors that bind to RNA on cis-element that regulate alternative splicing.
Usually Determines alternative splicing (whether to include an exon or not)
*HAVE TO REMEMBER IT HAS TWO DOMAINS*
-RNA BINDING DOMAIN (RBD) -NH3 end
-SERINE ARGININE DOMAIN (RS) -repeating Ser and Arg COOH end
-SERINES in RS domain are HIGHLY PHOSPHORYLATED (signaling cascade such as kinases that can ultimately phosphorylate/active your SR domain, will bind to cis element and enhance splicing)!!!--Ergo, splicing factors can also be regulated via signal transduction pathways |
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Term
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Definition
PKCGammaI-proapoptotic
PKCGammaVIII-anti-apoptotic
The latter has an addition of 93 bp due to an alternative splice site. |
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Term
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Definition
Tropomyosin
Depending on type of tissue different exons are expressed. |
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Term
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Definition
| 3A and 3B (Don't need to memorize) Depending on whether you are in the fetal or adult stage, you will either have inclusion or exclusion of that exon. |
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Term
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Definition
| Example: Presence of insulin will produce one gene over another. |
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Term
| Pre-mRNA alternative splicing and Disease |
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Definition
1)Mutations in the pre-mRNA causing NMD
2)Mutations in regulatory sequences-"cis-elements"
3)Exon usage
4)Introduction of cryptic 5' and 3' splice spites (due to insertion, addition, deletion, etc)
5)SR protein levels and phosphorylation states (signal transduction) |
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Term
| B-Thalassemia (do not need to memorize) |
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Definition
| Mutation of BP that produces a stop codon, a shift that causes premature splicing |
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Term
| Spinal muscular atrophy (SMA) |
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Definition
| degeneration of alpha motonuerons in the brainstem and spinal cord as a RESULT of mutation in cis-element. C->T Base change encodes for SMN2 instead of SMN1. Base change on SMN2 exon corresponds to SF2/ASF binding site (we have change of ESE and introduction of ESS hnRNP site). |
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Term
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Definition
1)Frontotemporal dementia (FTDP)
2)Glucose uptake in skeletal musckle regulated by PKC (protein kinase C) isozyme
One exon is perptually skipped. Change of ratio of 3R instead of 4R is the underlying cause of FTDP. |
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Term
| Introduction of cryptic 5' or 3' splice site |
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Definition
Hutchinson-Gilford progeria syndrome (HGPS) -- growth retardation and premature aging.
Mutations causing HGPS have been identified in LMNA gene because of a mutation that INTRODUCES A ADDITIONAL 5' SPLICE SITE. Resulting protein is called PROGERIN which acts in a dominant fashion to generate HGPS phenotype. |
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Term
| SR protein levels and phosphorylation states |
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Definition
Fibronectin gene (ECM glycoprotein).
Increased levels of 9GB (an ESE) altered splicing patterns. |
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Term
| Mutations affecting multiple functions of splicing |
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Definition
BRCA-1 (Breast cancer gene 1)
Expression of BRCA is reduced or undetectable in carcinomas because of an inherited mutations that disrupts ESE binding-SF2/ASF. |
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Term
| Aberrant splicing caused by disease states |
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Definition
1) Diabetes and various cancer can cause altered expression of a large number of SR proteins
2) You can have silent mutation until an external stimulus activates it-growth factors etc changes in disease states.
3) Atherosclerosis influences several genes in metabolism |
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