Question

How are introns detected for splicing?
USE THIS KEY: Splice sites are marked with specific nucleotide sequences. The intron begins with a FU and ends with an AG. Also, introns have an internal splice sited called a branch site.

Answer 1

Ans-

Intron - RNA sequences between exons that are removed by splicing

Introns have been found in eukaryotic mRNA, tRNA and rRNA, as well as chloroplast, mitochondrial and a phage of E. coli. Eubacteria are the only species in which introns have not been found. In general, genes that are related by evolution have related organizations with conservation of the position at least some introns. Furthermore, conservation of introns is also detected between genes in related species.

The amount and size of introns varies greatly. The mammalian DHFR has 6 exons that total about 2000 bases, yet the gene is 31,000 bases. Likewise, the alpha-collagen has 50 exons that range from 45-249 bases and the gene is about 40,000 bases. Clearly two genes of the same size can have different number of introns, and introns that vary in size.

Some species will have an intron in a gene, but another species may not have an intron in the same gene. An example is the cytochrome oxidase subunit II gene of plant mitochondria where some plant species have an intron in this gene and others do not.

Introns are removed from primary transcripts by cleavage at conserved sequences called splice sites. These sites are found at the 5′ and 3′ ends of introns. Most commonly, the RNA sequence that is removed begins with the dinucleotide GU at its 5′ end, and ends with AG at its 3′ end. These consensus sequences are known to be critical, because changing one of the conserved nucleotides results in inhibition of splicing. Another important sequence occurs at what is called the branch point, located anywhere from 18 to 40 nucleotides upstream from the 3′ end of an intron. The branch point always contains an adenine, but it is otherwise loosely conserved. A typical sequence is YNYYRAY, where Y indicates a pyrimidine, N denotes any nucleotide, R denotes any purine, and A denotes adenine. Rarely, alternate splice site sequences are found that begin with the dinucleotide AU and end with AC; these are spliced through a similar mechanism.

eukaryotic genes with long introns also contain exonic splicing enhancers (ESEs). These sequences, which help position the splicing apparatus, are found in the exons of genes and bind proteins that help recruit splicing machinery to the correct site. Most splicing occurs between exons on a single RNA transcript, but occasionally trans-splicing occurs, in which exons on different pre-mRNAs are ligated together.

The splicing process occurs in cellular machines called spliceosomes, in which the snRNPs are found along with additional proteins. The primary variety of spliceosome is one of the most plentiful structures in the cell, and recently, a secondary type of spliceosome has been identified that processes a minor category of introns. These introns are referred to as U12-type introns because they depend upon the action of a snRNP called U12 (the common introns described above are called U2-type introns). The role of U12-type introns is not yet defined, but their persistence throughout evolution and conservation between homologous genes of widely divergent species suggests an important functional basis.