INTRON

'Introns' are sections of DNA colinear to the mRNA sequence that will be spliced out after transcription, but before the mRNA is translated. Introns are common in eukaryotic RNAs of all types, but are found in prokaryotic tRNA and rRNA genes only. The regions of a gene that remain in spliced mRNA are called exons. The number and length of introns varies widely among species and among genes within the same species. For example, the pufferfish ''Takifugu rubripes'' has little intronic DNA. Genes in mammals and flowering plants, on the other hand, often have numerous introns, which can be much longer than the nearby exons.

Contents

Introduction

Classification of introns

Intron evolution

Identification

See also

References

External links

Introduction

Introns sometimes allow for alternative splicing of a gene, so that several different proteins that share some sections in common can be produced from a single gene. The control of mRNA splicing, and hence of which alternative is produced, is performed by a wide variety of signal molecules.
Introns also sometimes contain "old code," sections of a gene that were probably once translated into protein but which are now discarded.
It was generally assumed that the sequence in any given intron is junk DNA with no function. More recently, this is being questioned however; it is known that introns contain several short sequences that are important for efficient splicing. The exact mechanism for these ''intronic splicing enhancers'' is not well understood, but it is thought that they serve as binding sites on the transcript for proteins that stabilize the spliceosome. It is also possible that RNA secondary structure formed by intronic sequences may have an effect on splicing, and in alternative splicing, an exonic sequence in one product is intronic in another. "Old code" sequences, on the other hand, in most cases indeed seem to be "evolutionary kipple".
The discovery of introns led to the Nobel Prize in Physiology or Medicine in 1993 for Phillip Allen Sharp and Richard J. Roberts. The term ''intron'' was introduced by American biochemist Walter Gilbert in 1978:

"The notion of the cistron [...] must be replaced by that of a transcription unit containing regions which will be lost from the mature messenger - which I suggest we call introns (for intragenic regions) - alternating with regions which will be expressed - exons." (Gilbert 1978)

Some introns such as Group I and Group II introns are actually ribozymes that are capable of catalyzing their own splicing out of the primary RNA transcript. This self splicing was discovered by Thomas Cech who shared the 1989 Nobel Prize in Chemistry with Sidney Altman for the discovery of the catalytic properties of RNA.Intron also can be the regulator of gene expresion.

Classification of introns

Four classes of introns are known to exist:

★ Nuclear introns

★ Group I intron

★ Group II intron

★ Group III intron
Sometimes group III introns are also identified as group II introns, because of their similarity in structure and function.
Nuclear or spliceosomal introns are spliced by the spliceosome and a series of snRNAs (small nuclear RNAs). There are certain splice signals (or consensus sequences) which abet the splicing (or identification) of these introns by the spliceosome.
Group I, II and III introns are self splicing introns and are relatively rare compared to spliceosomal introns.
Group II and III introns are similar and have a conserved secondary structure. The lariat pathway is used in their splicing. They perform functions similar to the spliceosome and may be evolutionarily related to it. Group I introns are the only class of introns whose splicing requires a free guanine nucleoside. They possess a secondary structure different from that of group II and III introns. They are found in most bacteria and protozoa.

Intron evolution

There are two competing theories attempting to explain the origin and evolution of spliceosomal introns (Other classes of introns such as self-splicing and tRNA introns are not subject to much debate, but see ^[1] for the former). These are popularly called as the Introns-Early (IE) or the Introns-Late (IL) views.
The 'IE model', championed by Walter Gilbert^[2], proposes that introns are extremely old and numerously present in the earliest ancestors of prokaryotes and eukaryotes (the progenote). In this model introns were subsequently lost from prokaryotic organisms, allowing them to attain growth efficiency. A central prediction of this theory is that the early introns were mediators that facilitated the recombination of exons that represented the protein domains. Such a model would directly lead to the evolution of new genes.
The 'IL model' proposes that introns were more recently inserted into original intron-less contiguous genes after the divergence of eukaryotes and prokaryotes. In this model, introns probably had their origin in parasitic transposable elements. This model is based on the observation that the spliceosomal introns are restricted to eukaryotes alone. However, there is considerable debate on the presence of introns in the early prokaryote-eukaryote ancestors and the subsequent intron loss-gain during eukaryotic evolution. It is also suggested that the evolution of introns and more generally the intron-exon structure is largely independent of the coding-sequence evolution^[3].

Identification

Nearly all eukaryotic nuclear introns begin with GU and end with AG (the GU-AG rule).
This mainly occurs in eukaryotic mRNA.

See also

'Structure:'

★ Exon

★ Splice site

★ Twintron
'Splicing:'

★ alternate splicing

★ Minor spliceosome
'Others:'

★ Eukaryotic chromosome fine structure

★ Intein

★ Noncoding DNA

★ Selfish DNA

References

★ Why genes in pieces, Gilbert, Walter, , , Nature, 1978

★ The evolution of spliceosomal introns: patterns, puzzles and progress, , Scott William, Roy, Nature Reviews Genetics, 2006

★ Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements., , J. Peter, Gogarten, BMC Evolutionary Biology, 2006

★ Large-Scale Trends in the Evolution of Gene Structures within 11 Animal Genomes, , Mark, Yandell, PLoS Comput. Biol., 2006 Supporting Information
1. Gogarten JP, Hilario E. "Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements." ''BMC Evol Biol.'' 2006 Nov 13; 6: 94. PMID 17101053
2. Fedorov A, Cao X, Saxonov S, de Souza SJ, Roy SW, Gilbert W. "Intron distribution difference for 276 ancient and 131 modern genes suggests the existence of ancient introns." ''Proc Natl Acad Sci U S A.'' 2001 Nov 6; 98(23): 13177-82. PMID 11687643.

3. Yandell M, Mungall CJ, Smith C, Prochnik S, Kaminker J, Hartzell G, Lewis S, Rubin GM. "Large-scale trends in the evolution of gene structures within 11 animal genomes." ''PLoS Comput Biol.'' 2006 Mar; 2(3): e15. PMID 16518452

External links

★ Intron finding tool for plant genomic sequences