The evolution mechanism of intron length

Zhang, Qiang; Li, Hong; Zhao, Xiaoqing; Xue, Hui; Zheng, Yinggan; Meng, Hu; Jia, Yafei; Bo, Suling

doi:10.1016/j.ygeno.2016.07.004

Cited by 16 publications

(8 citation statements)

References 33 publications

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“…Within two years of their discovery in 1977, introns were found to affect gene expression positively. Indeed, distributions of the length and matching rate of optimally matched intron segments are consistent with sequence features of miRNA and siRNA [17] . These results indicate that the interaction between intron sequences and mRNA sequences is a kind of functional RNA-RNA interaction [17] .…”

Section: Datasupporting

confidence: 56%

“…Indeed, distributions of the length and matching rate of optimally matched intron segments are consistent with sequence features of miRNA and siRNA [17] . These results indicate that the interaction between intron sequences and mRNA sequences is a kind of functional RNA-RNA interaction [17] . In molecular genetics, an open reading frame (ORF) is the part of a reading frame that can be translated.…”

Section: Datasupporting

confidence: 56%

See 1 more Smart Citation

Predicting gene expression levels from DNA sequences and post-transcriptional information with transformers

Pipoli

Cappelli²,

Palladini³

et al. 2022

Computer Methods and Programs in Biomedicine

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Section: Datasupporting

confidence: 56%

Section: Datasupporting

confidence: 56%

Predicting gene expression levels from DNA sequences and post-transcriptional information with transformers

Pipoli

Cappelli²,

Palladini³

et al. 2022

Computer Methods and Programs in Biomedicine

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“…The reason for a trend of intron length increase during evolution has not yet been completely elucidated. The hypothesis is that introns can grow by progressive addition of new “structure units” at their 3′ end [ 33 ]. In addition, the spontaneous duplication of DNA segments, apparently by accidental replication, was described [ 34 ].…”

Section: Discussionmentioning

confidence: 99%

Imaging Intron Evolution

Panaro

Calvello

Miniero

et al. 2022

MPs

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Intron evolution may be readily imaged through the combined use of the “dot plot” function of the NCBI BLAST, aligning two sequences at a time, and the Vertebrate “Multiz” alignment and conservation tool of the UCSC Genome Browser. With the NCBI BLAST, an ideal alignment of two highly conserved sequences generates a diagonal straight line in the plot from the lower left corner to the upper right corner. Gaps in this line correspond to non-conserved sections. In addition, the dot plot of the alignment of a sequence with the same sequence after the removal of the Transposable Elements (TEs) can be observed along the diagonal gaps that correspond to the sites of TE insertion. The UCSC Genome Browser can graph, along the entire sequence of a single gene, the level of overall conservation in vertebrates. This level can be compared with the conservation level of the gene in one or more selected vertebrate species. As an example, we show the graphic analysis of the intron conservation in two genes: the mitochondrial solute carrier 21 (SLC25A21) and the growth hormone receptor (GHR), whose coding sequences are conserved through vertebrates, while their introns show dramatic changes in nucleotide composition and even length. In the SLC25A21, a few short but significant nucleotide sequences are conserved in zebrafish, Xenopus and humans, and the rate of conservation steadily increases from chicken/human to mouse/human alignments. In the GHR, a less conserved gene, the earlier indication of intron conservation is a small signal in chicken/human alignment. The UCSC tool may simultaneously display the conservation level of a gene in different vertebrates, with reference to the level of overall conservation in Vertebrates. It is shown that, at least in SLC25A21, the sites of higher conservation are not always coincident in chicken and zebrafish nor are the sites of higher vertebrate conservation.

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“…Zhang et al [76] proposed an interesting theory on the mechanism of evolution of intron length. The authors showed that introns could achieve gene expression and regulation by interacting with corresponding mRNA sequences.…”

Section: Intron Featuresmentioning

confidence: 99%

Spliceosomal Introns: Features, Functions, and Evolution

Poverennaya

Roytberg

2020

Biochemistry Moscow

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Spliceosomal introns, which have been found in most eukaryotic genes, are non coding sequences excised from pre mRNAs by a special complex called spliceosome during mRNA splicing. Introns occur in both protein and RNA cod ing genes and can be found in coding and untranslated gene regions. Because intron sequences vary greatly due to a high rate of polymorphism, the functions of intron had been for a long time associated only with alternative splicing, while intron evolution had been viewed not as an evolution of an individual genomic element, but rather considered within a framework of the evolution of the gene intron exon structure. Here, we review the theories of intron origin, evolutionary events in the exon intron structure, such as intron gain, loss, and sliding, intron functions known to date, and mechanisms by which changes in the intron features (length and phase) can affect the regulation of gene mediated processes.

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The evolution mechanism of intron length

Cited by 16 publications

References 33 publications

Predicting gene expression levels from DNA sequences and post-transcriptional information with transformers

Predicting gene expression levels from DNA sequences and post-transcriptional information with transformers

Imaging Intron Evolution

Spliceosomal Introns: Features, Functions, and Evolution

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