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Genome-wide analysis of Alu editability.

Bazak L, Levanon EY, Eisenberg E - Nucleic Acids Res. (2014)

Bottom Line: We use large RNA-seq data sets to analyze the editing levels in 203 798 Alu repeats residing within human genes.This effect alone accounts for 28% of the total variance in editability.In addition, the number of Alu repeats of the same and reverse strand in the genomic vicinity, the expressed strand of the Alu, Alu's length and subfamily and the occurrence of reversely oriented neighbor in the same intron\exon all contribute, to a lesser extent, to the Alu editability.

View Article: PubMed Central - PubMed

Affiliation: Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel.

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Related in: MedlinePlus

A typical genomic 10k bp neighborhood of an Alu. The UCSC track presents a part of the ATM gene, which shows four of its exons. This part of the gene includes 16 intronic Alus, 9 are in ‘+’ orientation and 7 are in the ‘-’ orientation. Below, appears a figurative representation of the putative paired-Alu dsRNA structures that might form. Alus are shown around the outer ring and are oriented in a clockwise direction with ‘+’ Alu indicated in red and ‘–’ in pale blue. Neighboring inverted non-diverse Alu closer than 3500 bp are connected by a line. Other tracks contain coverage (light-green bars) and editing levels (light-orange bars). Two of the Alus are not editable according to our criteria.
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Figure 9: A typical genomic 10k bp neighborhood of an Alu. The UCSC track presents a part of the ATM gene, which shows four of its exons. This part of the gene includes 16 intronic Alus, 9 are in ‘+’ orientation and 7 are in the ‘-’ orientation. Below, appears a figurative representation of the putative paired-Alu dsRNA structures that might form. Alus are shown around the outer ring and are oriented in a clockwise direction with ‘+’ Alu indicated in red and ‘–’ in pale blue. Neighboring inverted non-diverse Alu closer than 3500 bp are connected by a line. Other tracks contain coverage (light-green bars) and editing levels (light-orange bars). Two of the Alus are not editable according to our criteria.

Mentions: Another important factor that might contribute to editing variability is the structure of the Alu neighborhood. In this work, we have only referred to the nearest reversely oriented Alu repeat. However, the full picture is much more complex. A typical Alu repeat has many neighboring Alu's and the folding of the entire transcript should be considered (see Figure 9). In addition, editing itself might modify the RNA folds, so the relevant paired Alu element might change dynamically.


Genome-wide analysis of Alu editability.

Bazak L, Levanon EY, Eisenberg E - Nucleic Acids Res. (2014)

A typical genomic 10k bp neighborhood of an Alu. The UCSC track presents a part of the ATM gene, which shows four of its exons. This part of the gene includes 16 intronic Alus, 9 are in ‘+’ orientation and 7 are in the ‘-’ orientation. Below, appears a figurative representation of the putative paired-Alu dsRNA structures that might form. Alus are shown around the outer ring and are oriented in a clockwise direction with ‘+’ Alu indicated in red and ‘–’ in pale blue. Neighboring inverted non-diverse Alu closer than 3500 bp are connected by a line. Other tracks contain coverage (light-green bars) and editing levels (light-orange bars). Two of the Alus are not editable according to our criteria.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4066801&req=5

Figure 9: A typical genomic 10k bp neighborhood of an Alu. The UCSC track presents a part of the ATM gene, which shows four of its exons. This part of the gene includes 16 intronic Alus, 9 are in ‘+’ orientation and 7 are in the ‘-’ orientation. Below, appears a figurative representation of the putative paired-Alu dsRNA structures that might form. Alus are shown around the outer ring and are oriented in a clockwise direction with ‘+’ Alu indicated in red and ‘–’ in pale blue. Neighboring inverted non-diverse Alu closer than 3500 bp are connected by a line. Other tracks contain coverage (light-green bars) and editing levels (light-orange bars). Two of the Alus are not editable according to our criteria.
Mentions: Another important factor that might contribute to editing variability is the structure of the Alu neighborhood. In this work, we have only referred to the nearest reversely oriented Alu repeat. However, the full picture is much more complex. A typical Alu repeat has many neighboring Alu's and the folding of the entire transcript should be considered (see Figure 9). In addition, editing itself might modify the RNA folds, so the relevant paired Alu element might change dynamically.

Bottom Line: We use large RNA-seq data sets to analyze the editing levels in 203 798 Alu repeats residing within human genes.This effect alone accounts for 28% of the total variance in editability.In addition, the number of Alu repeats of the same and reverse strand in the genomic vicinity, the expressed strand of the Alu, Alu's length and subfamily and the occurrence of reversely oriented neighbor in the same intron\exon all contribute, to a lesser extent, to the Alu editability.

View Article: PubMed Central - PubMed

Affiliation: Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel.

Show MeSH
Related in: MedlinePlus