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Plant spliceosomal introns: not only cut and paste.

Morello L, Breviario D - Curr. Genomics (2008)

Bottom Line: Furthermore, some introns also contain promoter sequences for alternative transcripts.Nevertheless, such regulatory roles do not require long conserved sequences, so that introns are relatively free to evolve faster than exons: this feature makes them important tools for evolutionary studies and provides the basis for the development of DNA molecular markers for polymorphisms detection.A survey of introns functions in the plant kingdom is presented.

View Article: PubMed Central - PubMed

Affiliation: Istituto Biologia e Biotecnologia Agraria, Via Bassini 15, 20133 Milano, Italy.

ABSTRACT
Spliceosomal introns in higher eukaryotes are present in a high percentage of protein coding genes and represent a high proportion of transcribed nuclear DNA. In the last fifteen years, a growing mass of data concerning functional roles carried out by such intervening sequences elevated them from a selfish burden carried over by the nucleus to important active regulatory elements. Introns mediate complex gene regulation via alternative splicing; they may act in cis as expression enhancers through IME (intron-mediated enhancement of gene expression) and in trans as negative regulators through the generation of intronic microRNA. Furthermore, some introns also contain promoter sequences for alternative transcripts. Nevertheless, such regulatory roles do not require long conserved sequences, so that introns are relatively free to evolve faster than exons: this feature makes them important tools for evolutionary studies and provides the basis for the development of DNA molecular markers for polymorphisms detection. A survey of introns functions in the plant kingdom is presented.

No MeSH data available.


A model illustrating Eukaryotes intron-mediated gene expression versatility. g stays for genes that code for proteins (p). r stays for regulatory elements. The n outside the bracket stays for node which means a DNA locus transcriptionally active. The node is part of a vast gene network, with multiple nodes, that may change anytime during cell life and metabolism. This model should make it appreciable that the presence of introns in Eukaryotes may contribute to the increase of products and regulatory factors without altering the number of the coding genes (four in this example). Eukaryotes versatile expression has been gained in the course of evolution through the occurrence of different events such as the inclusion in protein coding genes of intervening sequences capable of self-splicing (groupI and II introns), exon shuffling, reversal splicing and the entry of the nuclear spliceosome. This latter has contributed to release those sequence constraints present in self-splicing introns. As a consequence, spliceosomal introns increased their sequence variability and may have acquired novel trans-acting regulatory functions. On the opposite, Prokaryotes have maintained their linearity of expression, substantially supported by monocistronic RNAs and few products endowed with simple-circuited regulatory functions.
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Figure 1: A model illustrating Eukaryotes intron-mediated gene expression versatility. g stays for genes that code for proteins (p). r stays for regulatory elements. The n outside the bracket stays for node which means a DNA locus transcriptionally active. The node is part of a vast gene network, with multiple nodes, that may change anytime during cell life and metabolism. This model should make it appreciable that the presence of introns in Eukaryotes may contribute to the increase of products and regulatory factors without altering the number of the coding genes (four in this example). Eukaryotes versatile expression has been gained in the course of evolution through the occurrence of different events such as the inclusion in protein coding genes of intervening sequences capable of self-splicing (groupI and II introns), exon shuffling, reversal splicing and the entry of the nuclear spliceosome. This latter has contributed to release those sequence constraints present in self-splicing introns. As a consequence, spliceosomal introns increased their sequence variability and may have acquired novel trans-acting regulatory functions. On the opposite, Prokaryotes have maintained their linearity of expression, substantially supported by monocistronic RNAs and few products endowed with simple-circuited regulatory functions.

Mentions: The reason why, despite massive losses in some branches of the tree, introns have been maintained in the course of evolution, to the extent that a significant proportion of intron positions is conserved across the millions of years separating plants from animals [10], could hardly be explained without a functional role. Similarly, regulatory roles are likely to be played by a large part of noncoding DNA, mainly intergenic sequences and antisense sequences, that have been recently found to be transcriptionally active in both bacterial and eukaryotic cells [11]. This genomic DNA that definitively codes for a large amount of transcripts of unknown function (TUF) [12] has gained the captivating name, of “the dark matter” of the genome. Between 60 to 70% of the human genome has recently been estimated to be transcribed in one or both strands [13]. To this regard, it has been proposed that introns and other ncRNAs, have evolved to constitute a network of controlling molecules that co-ordinately regulate gene expression through multiple interactions with other molecules such as DNA, RNA and proteins. This network would represent the real gain with respect to the linearity of genetic information that is assembled in the genomes of prokaryotes. The network could explain why the increase in organism complexity can occur without an exponential increase in the number of protein coding sequences [14] (Fig. 1).


Plant spliceosomal introns: not only cut and paste.

Morello L, Breviario D - Curr. Genomics (2008)

A model illustrating Eukaryotes intron-mediated gene expression versatility. g stays for genes that code for proteins (p). r stays for regulatory elements. The n outside the bracket stays for node which means a DNA locus transcriptionally active. The node is part of a vast gene network, with multiple nodes, that may change anytime during cell life and metabolism. This model should make it appreciable that the presence of introns in Eukaryotes may contribute to the increase of products and regulatory factors without altering the number of the coding genes (four in this example). Eukaryotes versatile expression has been gained in the course of evolution through the occurrence of different events such as the inclusion in protein coding genes of intervening sequences capable of self-splicing (groupI and II introns), exon shuffling, reversal splicing and the entry of the nuclear spliceosome. This latter has contributed to release those sequence constraints present in self-splicing introns. As a consequence, spliceosomal introns increased their sequence variability and may have acquired novel trans-acting regulatory functions. On the opposite, Prokaryotes have maintained their linearity of expression, substantially supported by monocistronic RNAs and few products endowed with simple-circuited regulatory functions.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2682935&req=5

Figure 1: A model illustrating Eukaryotes intron-mediated gene expression versatility. g stays for genes that code for proteins (p). r stays for regulatory elements. The n outside the bracket stays for node which means a DNA locus transcriptionally active. The node is part of a vast gene network, with multiple nodes, that may change anytime during cell life and metabolism. This model should make it appreciable that the presence of introns in Eukaryotes may contribute to the increase of products and regulatory factors without altering the number of the coding genes (four in this example). Eukaryotes versatile expression has been gained in the course of evolution through the occurrence of different events such as the inclusion in protein coding genes of intervening sequences capable of self-splicing (groupI and II introns), exon shuffling, reversal splicing and the entry of the nuclear spliceosome. This latter has contributed to release those sequence constraints present in self-splicing introns. As a consequence, spliceosomal introns increased their sequence variability and may have acquired novel trans-acting regulatory functions. On the opposite, Prokaryotes have maintained their linearity of expression, substantially supported by monocistronic RNAs and few products endowed with simple-circuited regulatory functions.
Mentions: The reason why, despite massive losses in some branches of the tree, introns have been maintained in the course of evolution, to the extent that a significant proportion of intron positions is conserved across the millions of years separating plants from animals [10], could hardly be explained without a functional role. Similarly, regulatory roles are likely to be played by a large part of noncoding DNA, mainly intergenic sequences and antisense sequences, that have been recently found to be transcriptionally active in both bacterial and eukaryotic cells [11]. This genomic DNA that definitively codes for a large amount of transcripts of unknown function (TUF) [12] has gained the captivating name, of “the dark matter” of the genome. Between 60 to 70% of the human genome has recently been estimated to be transcribed in one or both strands [13]. To this regard, it has been proposed that introns and other ncRNAs, have evolved to constitute a network of controlling molecules that co-ordinately regulate gene expression through multiple interactions with other molecules such as DNA, RNA and proteins. This network would represent the real gain with respect to the linearity of genetic information that is assembled in the genomes of prokaryotes. The network could explain why the increase in organism complexity can occur without an exponential increase in the number of protein coding sequences [14] (Fig. 1).

Bottom Line: Furthermore, some introns also contain promoter sequences for alternative transcripts.Nevertheless, such regulatory roles do not require long conserved sequences, so that introns are relatively free to evolve faster than exons: this feature makes them important tools for evolutionary studies and provides the basis for the development of DNA molecular markers for polymorphisms detection.A survey of introns functions in the plant kingdom is presented.

View Article: PubMed Central - PubMed

Affiliation: Istituto Biologia e Biotecnologia Agraria, Via Bassini 15, 20133 Milano, Italy.

ABSTRACT
Spliceosomal introns in higher eukaryotes are present in a high percentage of protein coding genes and represent a high proportion of transcribed nuclear DNA. In the last fifteen years, a growing mass of data concerning functional roles carried out by such intervening sequences elevated them from a selfish burden carried over by the nucleus to important active regulatory elements. Introns mediate complex gene regulation via alternative splicing; they may act in cis as expression enhancers through IME (intron-mediated enhancement of gene expression) and in trans as negative regulators through the generation of intronic microRNA. Furthermore, some introns also contain promoter sequences for alternative transcripts. Nevertheless, such regulatory roles do not require long conserved sequences, so that introns are relatively free to evolve faster than exons: this feature makes them important tools for evolutionary studies and provides the basis for the development of DNA molecular markers for polymorphisms detection. A survey of introns functions in the plant kingdom is presented.

No MeSH data available.