Exons ligation

Figure 10.13 Phosphoryl-transfer reactions. The figure shows (a) nucleotide polymerization, (b) nucleic acid hydrolysis, (c) first cleavage of an exon-intron junction by group I ribozyme (d) and by a group II ribozyme, (e) strand transfer during transposition and (f) exon ligation during RNA splicing. (From Yang et al., 2006. Copyright 2006, with permission from Elsevier.)...

Figure 2 Details of two successive trans-esterification reactions. In the first step, the 2 -OH group of the branch point adenosine nucleophilically attacks the phosphate at the junction of the S exon and intron (S splice site), resulting in the formation of a new S -2 phosphodiester bond between the first nucleotide of the intron and the branch point adenosine (lariat structure formation) and breakage of an old 3 -S phosphodiester bond between the last nucleotide of the S exon and the first nucleotide of the intron (cut-off S exon formation). In the second step, the 3 -OH group of the cut-off S exon nucleophilically attacks the phosphate at the junction of the intron and 3 exon, ligating the two exons (mRNA formation) and releasing the lariat intron. The phosphates at the S splice site (red) and at the 3 splice site (green) and the branch point adenosine and its 2 -OH group are pictured. The lines represent the intron and boxes depict exons (El and E2).

Mayas RM, Maita H, Staley JP. Exon ligation is proofread by the DExD/H-box ATPase Prp22p. Nat. Struct. Mol. Biol. 2006 13 482-490. 

After transcription, during RNA processing, introns are removed and the exons are ligated together to form the mamre mRNA that appears in the cytoplasm. 

The mechanisms whereby introns are removed from the primary transcript in the nucleus, exons are ligated to form the mRNA molecule, and the mRNA molecule is transported to the cytoplasm are being elucidated. Four different splicing reaction mechanisms have been described. The one most frequently used in eukaryotic cells is described below. Although the sequences of nu-... 

Fig. 12 The spliceosome splicing reaction. In the first step, the 2 -OH of an adenosine residue that is conserved in the intron attacks the phosphorus at the 5 splice site and generates an intron-3 -exon 2 intermediate and a free 5 exon 1. In the second step, the free 3 -OH of the 5 exon attacks the phosphorus at the 3 splice site to produce ligated exons and an excised intron...

Most cellular genes are composed of intron and exon sequences. During maturation of the RNA transcript, the introns are excised and the exons are ligated together. This processing step also facilitates export of RNA from the nucleus into the cytoplasm for protein translation. At least one intron and one exon are almost always included in the therapeutic expression cassette to ensure that the engineered transcript is processed in the same manner as the natural cellular transcript. 

Fig. 8.2.2 Principle of genomic quantification by multiplex ligation-dependent probe amplification (MLPA). Synthetic oligonuleotides are designed to bind to exon 1 (oligo 1a and 1b) and 2 (2a and 2b). After specific hybridisation, the oligos are ligated. The ligation products undergo quantitative polymerase chain reaction using universal primers X and Y...

Fig. S. In vitro transcription of a cloned DNA fragment from Anabaena azollae containing a self-splicing intron. (A) Restriction map of a 2.7-kb insert in pBSM13—. Arrows indicate direction of transcription from the T3 and T7 promoters in the vector. tRNA exon (solid) and intron (hatched) sequences are indicated. (B) Plasmid DNA truncated by Ps/I (P), SlpI (S), Dral (D), and Hindi) (H) (in the 3 exon), downstream of the T3 promoter. After transcription with T3 RNA polymerase, products were fractionated on a 3% polyacrylamide-8 M urea gel the autoradiogram is shown. Scale at left indicates position of Haelll restriction fragments of phage 0X174 DNA in nucleotides. Labels indicate positions expected for the unspliced run-off transcript (Pre), ligated exons (LE), and linear intron (LI). (From Xu et at. Copyright 1990 by the AAAS.)...

In group II introns, the attacking nucleophile in the first step is either the 2 -OH group of an adenosine located close to the intron terminus (Fig. Id) or a water molecule (analogous to Fig. lb). The second step is similar to that of group I introns and involves attack of the 5 -exon terminus on the 3 -splice site and ligation of the two exons. 

The 3 -OH terminus of exon 1 then attacks the phosphodiester bond between the intron and exon 2. Exons 1 and 2 become joined, and the intron is released in lariat form. Again, this reaction is a transesterilication. Splicing is thus accomplished by two transesterification reactions rather than by hydrolysis followed by ligation. The first reaction... 

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