Transcription is the process through which DNA molecules in the presence of RNA polymerase synthesize RNA transcript. The primary transcript of a eukaryotic mRNA contains sequences encompassing one gene, however, the sequences encoding the polypeptide may not be in close proximity. Noncoding tracts that break up the coding region of the transcript are called introns and the coding regions are called exons. During the process of splicing, the introns are detached from the primary transcript and the exons are joined together from a continuous sequence that specifies a functional polypeptide
Different Forms of Splicing
Depending on the types of introns, splicing can be divided into four types: Group I, II, Class III and Class IV
There are basically four classes of introns. The first two called group I and group II introns share same key characteristics but differ in the details of their splicing mechanisms. Group I introns are found in some nuclear, mitochondrial, and chloroplast genes coding for rRNAs, mRNA and tRNAs. Group II introns on the other hand are found in the primary transcripts of mitochondrial or chloroplast mRNAs in fungi, algae and plants. Neither group I nor group II requires high-energy cofactor (ATP) for splicing. However, the splicing mechanisms in both the groups require two transesterification reaction steps.
The group I splicing reaction requires a guanine nucleoside or nucleotide cofactor, but the cofactor is not used as a source of energy, instead the 3-prime hydoxyl group of guanosine is used as a nucleophile in the first step of the splicing pathway. The guanosine 3-prime hydroxyl group forms a normal 3- prime-5 prime phosphodiester bond with 5-prime end of the intron. The 3-hydoxyl of the exon that is displaced in this step then acts as a nucleophile in a similar reaction at the 3-prime end of the intron. Finally, the introns are removed and ligation of the exons takes place.
However, in case of group II introns, the pattern is same except for the nucleophile in the first step, which in this case is the 2-prime hydoxyl group of an aldehyde residue within the intron. A branched lariat structure is formed as an intermediate.
It has been found that the splicing of group I and group II does not involve any enzyme i.e., these introns are self-splicing. This was first revealed in studies of the splicing mechanism of the group I rRNA intron from ciliated protozoan Tetrahymena thermophila by Thomas Cech et. al. in 1982.
However, introns that are not self-splicing are not designated with a group number. The third and the largest class of introns are those found in nuclear mRNA primary transcripts. They undergo splicing by similar lariat forming mechanism as the group II introns, however, splicing in this case requires the action of specialized RNA-protein complexes called nuclear ribonucleoproteins (snRNPs). Each snRNP contains one of a class of eukaryotic RNAs 100 to 200 nucleotides long called small nuclear RNAs (snRNAs). Five snRNAs (U1, U2, U4, U5 and U6) are involved in splicing reactions are generally found in abundance in eukaryotic nuclei. The U1 snRNA contains a sequence complementary to sequences near the 5-prime splice site of muclear mRNA introns and the U1 snRNP binds to this region in the primary transcript. Addition of U2, U4, U5 and U6 snRNPs leads to the formation of a complex called the spliceosome within which the actual splicing reaction occurs. ATP is required for the assembly of spliceosome.
The fourth class of introns, found in certain tRNAs is distinguished from the group I and II introns in that the splicing reaction requires ATP and an edonuclease. The splicing endonuclease cleaves the phosphodiester bond at both ends of the intron and the two exons are joined by a mechanism similar to the DNA ligase reaction.
This is one of the typical splicing types where splicing can occur in different patterns so that a particular group of exons forms one mRNA and a different group from the same gene transcript forms another mRNA. This leads to different proteins. This mechanism may be employed to produce variant forms of protein required in different tissues or at different times.
(Web): RNA Synthesis and RNA Processing – https://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=cell&part=A1682
(Web): A mechanism for RNA splicing – https://www.pnas.org/content/77/4/1877.short