Intron

An intron is a segment within a gene that is transcribed into a precursor RNA molecule but removed during RNA splicing. The sequences joined together after its removal are called exons. The term can refer either to the intervening sequence in DNA or to its RNA counterpart. Introns are especially familiar as components of protein-coding genes, where their removal helps produce mature messenger RNA (mRNA), but they also occur in genes whose products are functional RNAs. (genome.gov)

Relationship to gene structure

In an intron-containing gene, transcription initially produces an RNA containing both exons and introns. Splicing removes the introns and connects the adjoining exons. It normally changes the RNA, not the underlying DNA: the intron remains part of the gene and can be transcribed again. In protein-coding genes, the processed mRNA subsequently directs translation into a protein. (genome.gov)

“Intron” is therefore a description of how a sequence is processed, rather than a synonym for all non-protein-coding DNA. Introns lie within transcription units, whereas intergenic sequences lie between genes. Conversely, an exon need not encode protein: exons can include untranslated portions of mRNA. Intronic sequences may also contain information that regulates transcription or RNA processing, so removal from one RNA product does not imply biological inactivity. (genome.gov)

The distinction can depend on the RNA product being considered. Through alternative splicing, a sequence removed in one transcript may be retained in another. Intron retention describes the persistence of an otherwise removable intron in an RNA product; it can be a regulated event rather than simply a processing error. (nature.com)

Major types

Introns comprise several mechanistically distinct classes, rather than a single uniform category.

These classes differ in RNA structure, recognition signals, and catalytic machinery. Group I and group II introns can act as ribozymes, although proteins often assist their folding and activity in living cells. Some group II introns also encode proteins involved in their splicing and movement to new genomic sites. (nature.com)

Spliceosomal recognition and removal

Spliceosomal introns are identified through combinations of sequence signals, including a 5′ splice site, a branch point, and a 3′ splice site. Many major-class introns also have a pyrimidine-rich region upstream of the 3′ splice site. The common boundary pattern is GU at the beginning and AG at the end of the intron in RNA, corresponding to GT and AG in the DNA coding strand. These short boundary sequences are not sufficient by themselves to determine which sites are used. (ncbi.nlm.nih.gov)

Removal usually involves two chemical steps:

1. The 2′ hydroxyl group of an adenosine at the branch point attacks the bond at the 5′ splice site. This separates the upstream exon from the intron and creates an unusual 2′–5′ linkage within the intron.
2. The newly exposed 3′ hydroxyl group of the upstream exon attacks the bond at the 3′ splice site. The exons are joined, and the intron is released as a lariat, consisting of a loop with a projecting tail. (ncbi.nlm.nih.gov)

Splicing is often coordinated with transcription, allowing recognition and removal to begin while the precursor RNA is still being synthesized. Accurate processing depends on the surrounding RNA sequence and on interactions among RNA and protein components, not merely on finding matching terminal dinucleotides. (ncbi.nlm.nih.gov)

The major and minor spliceosomes use related but distinct RNA components. Minor-class introns are sometimes associated with AU–AC boundaries, but many have GU–AG boundaries. Their classification therefore depends on broader recognition signals and the machinery that removes them, rather than on their terminal bases alone. (nature.com)

Distribution and biological roles

Introns are widespread in eukaryotes, although their abundance differs greatly among organisms and genes. Most human protein-coding genes contain introns; many introns are considerably longer than the adjacent exons. Some eukaryotic genes contain no introns, while others contain numerous intervening sequences. Self-splicing introns also occur in bacteria and in genes of mitochondria and chloroplasts. Introns are therefore not exclusive to nuclear protein-coding genes. (genome.gov)

Introns can participate in gene expression in several ways:

• RNA-product diversification. Alternative selection of splice sites or retention of introns can change the RNA products generated from a gene.
• Regulatory information. Intronic sequences can influence transcription and the recognition of splice sites.
• Intron-mediated enhancement. In some experimental systems, an intron increases expression relative to an otherwise comparable intronless construct.

These effects are context-dependent. For example, reporter experiments in Caenorhabditis elegans found that a single intron near the 5′ end could increase protein expression, whereas an intron near the 3′ end did not produce the same effect. Experiments in Arabidopsis demonstrated increased RNA accumulation that did not require successful splicing of the tested intron. Such findings do not establish that every intron enhances expression or that enhancement always follows the same mechanism. (genome.gov)

Retained introns can introduce premature termination signals into protein-coding transcripts. These RNAs may be removed by cellular surveillance, including nonsense-mediated decay, linking intron processing to control of RNA abundance. (nature.com)

Discovery and evolutionary significance

The recognition of introns emerged from studies of adenovirus RNA in 1977. Researchers found that sequences joined together in mature viral mRNA corresponded to separated regions of the viral DNA. These observations established that an RNA product need not be a continuous copy of one uninterrupted DNA segment. Richard J. Roberts and Phillip A. Sharp received the 1993 Nobel Prize in Physiology or Medicine for discoveries concerning split genes. (pubmed.ncbi.nlm.nih.gov)

The close similarities between group II intron splicing and spliceosomal splicing provide evidence for an evolutionary relationship. Both can use an internal adenosine to form a lariat, and their catalytic systems share structural features. A prominent model proposes that the spliceosomal system developed from an ancestral group II intron-like system. This is an evolutionary explanation supported by mechanistic evidence, not a directly observed historical event. (ncbi.nlm.nih.gov)

Research and interpretation

Introns make it difficult to infer complete RNA and protein products from a genome sequence alone. Correct interpretation requires identifying splice boundaries and determining which combinations of exons occur in particular transcripts. Alternative splicing adds further ambiguity because one gene can produce multiple processed RNAs. (ncbi.nlm.nih.gov)

Intronic mutations can have consequences even when they do not alter a protein-coding exon. Changes affecting splice recognition can cause abnormal intron retention or other processing defects. Primary research has, for example, identified intronic mutations that disrupt removal of a minor intron in LZTR1. The significance of an intronic variant consequently depends on its particular sequence and experimentally supported effects; its location outside a coding exon is not enough to establish that it is harmless or harmful. (nature.com)

References

1. Introngenome.gov
2. Exongenome.gov
3. RNA Processing and Turnover — The Cellncbi.nlm.nih.gov
4. From DNA to RNA — Molecular Biology of the Cellncbi.nlm.nih.gov
5. Synthesis and Processing of RNA — Genomesncbi.nlm.nih.gov
6. Synthesis and Processing of RNA — Genomesncbi.nlm.nih.gov
7. Defective minor spliceosomes induce SMA-associated phenotypes through sensitive intron-containing neural genes in Drosophilanature.com
8. Structural insights into intron catalysis and dynamics during splicingnature.com
9. Article: tRNA splicing endonuclease complexnature.com
10. In vivo measurements reveal a single 5′-intron is sufficient to increase protein expression level in Caenorhabditis elegansnature.com
11. Intron-Mediated Enhancement of Gene Expression Independent of Unique Intron Sequences and Splicingpmc.ncbi.nlm.nih.gov
12. Intron retention is regulated by altered MeCP2-mediated splicing factor recruitmentnature.com