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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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Number of Alus in the neighborhood affects editability. (a) One finds a positive correlation of editability with the number of reversely oriented repeats in the genomic neighborhood (10 000 bp each side) and a negative correlation with the number of same strand elements. (b) The effect is even stronger when looking at the immediate neighborhood (2000 bp each side). Note that we plot the difference between the observed editing level and the average level for all Alu whose nearest neighbor is at the same distance (formula (1)). This difference could be positive or negative.
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Figure 3: Number of Alus in the neighborhood affects editability. (a) One finds a positive correlation of editability with the number of reversely oriented repeats in the genomic neighborhood (10 000 bp each side) and a negative correlation with the number of same strand elements. (b) The effect is even stronger when looking at the immediate neighborhood (2000 bp each side). Note that we plot the difference between the observed editing level and the average level for all Alu whose nearest neighbor is at the same distance (formula (1)). This difference could be positive or negative.

Mentions: It was already claimed that having many reversely oriented elements nearby increases the probability of an Alu element to be edited (10–13,30,31). In addition, we hypothesized that having many neighbors of the same orientation should reduce editability, as these same-orientation neighbors compete with the Alu of choice and reduce its probability to bind and form a dsRNA. There is a very strong correlation between the density of reversely oriented elements in the vicinity of an Alu to the distance to the closest neighbor—the more neighbors there are, the more likely is one of them to be very close. Thus, in order to properly examine the above two hypotheses one needs to control for the effect of the distance to the nearest neighbor. Given the above functional form (1), one can find the residual (positive or negative) editability of an Alu element beyond what is expected on average based on its distance to the nearest neighbor. This residual editability may then be correlated to the number of reversely oriented, or same strand, elements in the genomic neighborhood (10 000 bp each side). Indeed, one observes a positive correlation of editability with the number of reversely oriented neighbors, and a negative correlation with the number of same strand ones (Figure 3). The effect is even stronger when looking at the immediate neighborhood (2000 bp each side, Figure 3b).


Genome-wide analysis of Alu editability.

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

Number of Alus in the neighborhood affects editability. (a) One finds a positive correlation of editability with the number of reversely oriented repeats in the genomic neighborhood (10 000 bp each side) and a negative correlation with the number of same strand elements. (b) The effect is even stronger when looking at the immediate neighborhood (2000 bp each side). Note that we plot the difference between the observed editing level and the average level for all Alu whose nearest neighbor is at the same distance (formula (1)). This difference could be positive or negative.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 3: Number of Alus in the neighborhood affects editability. (a) One finds a positive correlation of editability with the number of reversely oriented repeats in the genomic neighborhood (10 000 bp each side) and a negative correlation with the number of same strand elements. (b) The effect is even stronger when looking at the immediate neighborhood (2000 bp each side). Note that we plot the difference between the observed editing level and the average level for all Alu whose nearest neighbor is at the same distance (formula (1)). This difference could be positive or negative.
Mentions: It was already claimed that having many reversely oriented elements nearby increases the probability of an Alu element to be edited (10–13,30,31). In addition, we hypothesized that having many neighbors of the same orientation should reduce editability, as these same-orientation neighbors compete with the Alu of choice and reduce its probability to bind and form a dsRNA. There is a very strong correlation between the density of reversely oriented elements in the vicinity of an Alu to the distance to the closest neighbor—the more neighbors there are, the more likely is one of them to be very close. Thus, in order to properly examine the above two hypotheses one needs to control for the effect of the distance to the nearest neighbor. Given the above functional form (1), one can find the residual (positive or negative) editability of an Alu element beyond what is expected on average based on its distance to the nearest neighbor. This residual editability may then be correlated to the number of reversely oriented, or same strand, elements in the genomic neighborhood (10 000 bp each side). Indeed, one observes a positive correlation of editability with the number of reversely oriented neighbors, and a negative correlation with the number of same strand ones (Figure 3). The effect is even stronger when looking at the immediate neighborhood (2000 bp each side, Figure 3b).

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