Limits...
Serial number tagging reveals a prominent sequence preference of retrotransposon integration.

Chatterjee AG, Esnault C, Guo Y, Hung S, McQueen PG, Levin HL - Nucleic Acids Res. (2014)

Bottom Line: To address this problem we developed the serial number system, a TE tagging method that measures the frequency of integration at single nucleotide positions.We sequenced 1 million insertions of retrotransposon Tf1 in the genome of Schizosaccharomyces pombe and obtained the first profile of integration with frequencies for each individual position.Integration levels at individual nucleotides varied over two orders of magnitude and revealed that sequence recognition plays a key role in positioning integration.

View Article: PubMed Central - PubMed

Affiliation: Section on Eukaryotic Transposable Elements, Program in Cellular Regulation and Metabolism, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.

Show MeSH

Related in: MedlinePlus

The integration of WT (Tf1s-neo) and CHD (Tf1s-CHD-neo) have sequence preferences. (A) The 128 386 insertion sites produced by WT2 and WT3 were aligned and the logo pattern of nucleotide preferences was determined. The positions of the 5 nucleotides at the target sites that are duplicated during integration are indicated by target site duplication (TSD). The height of the nucleotide in the logo represents the bit score associated with the bias and the proportional height of a nucleotide relative to the others at a position constitutes the percent of the insertions that have that specific nucleotide. The A at the center of the palindrome is 35.4% of the height indicating that 35.4% of the insertions had an A at that position. (B) The logo pattern was determined for the 123 881 insertion positions generated by CHD1, CHD2 and CHD3.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4117765&req=5

Figure 7: The integration of WT (Tf1s-neo) and CHD (Tf1s-CHD-neo) have sequence preferences. (A) The 128 386 insertion sites produced by WT2 and WT3 were aligned and the logo pattern of nucleotide preferences was determined. The positions of the 5 nucleotides at the target sites that are duplicated during integration are indicated by target site duplication (TSD). The height of the nucleotide in the logo represents the bit score associated with the bias and the proportional height of a nucleotide relative to the others at a position constitutes the percent of the insertions that have that specific nucleotide. The A at the center of the palindrome is 35.4% of the height indicating that 35.4% of the insertions had an A at that position. (B) The logo pattern was determined for the 123 881 insertion positions generated by CHD1, CHD2 and CHD3.

Mentions: The large number of insertion events sequenced with the serial number system allowed us to detect patterns of nucleotide preferences at the insertion sites. We aligned 128 386 integration positions of Tf1s-neo combined from the WT2 and WT3 experiments and examined the nucleotide frequencies of flanking sequence using the logo algorithm (22). The insertion sites possessed a pattern of preferred nucleotides with modest strength that extended 50 bp in either direction (Figure 7A). The preferred nucleotides flanking Tf1s-neo inserts formed a palindrome, a pattern observed with other integrating elements that is thought to be due to stabilizing contacts between the IN and target DNA (4,8,23–26). To determine whether the chromodomain contributed to the overall pattern of nucleotide preference we analyzed the 123 881 insertion sites produced by all three of the Tf1s-CHD-neo experiments. The resulting logo was very similar to that produced by Tf1s-neo indicating that the chromodomain contributed little to the average pattern of nucleotide preference (Figure 7B).


Serial number tagging reveals a prominent sequence preference of retrotransposon integration.

Chatterjee AG, Esnault C, Guo Y, Hung S, McQueen PG, Levin HL - Nucleic Acids Res. (2014)

The integration of WT (Tf1s-neo) and CHD (Tf1s-CHD-neo) have sequence preferences. (A) The 128 386 insertion sites produced by WT2 and WT3 were aligned and the logo pattern of nucleotide preferences was determined. The positions of the 5 nucleotides at the target sites that are duplicated during integration are indicated by target site duplication (TSD). The height of the nucleotide in the logo represents the bit score associated with the bias and the proportional height of a nucleotide relative to the others at a position constitutes the percent of the insertions that have that specific nucleotide. The A at the center of the palindrome is 35.4% of the height indicating that 35.4% of the insertions had an A at that position. (B) The logo pattern was determined for the 123 881 insertion positions generated by CHD1, CHD2 and CHD3.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4117765&req=5

Figure 7: The integration of WT (Tf1s-neo) and CHD (Tf1s-CHD-neo) have sequence preferences. (A) The 128 386 insertion sites produced by WT2 and WT3 were aligned and the logo pattern of nucleotide preferences was determined. The positions of the 5 nucleotides at the target sites that are duplicated during integration are indicated by target site duplication (TSD). The height of the nucleotide in the logo represents the bit score associated with the bias and the proportional height of a nucleotide relative to the others at a position constitutes the percent of the insertions that have that specific nucleotide. The A at the center of the palindrome is 35.4% of the height indicating that 35.4% of the insertions had an A at that position. (B) The logo pattern was determined for the 123 881 insertion positions generated by CHD1, CHD2 and CHD3.
Mentions: The large number of insertion events sequenced with the serial number system allowed us to detect patterns of nucleotide preferences at the insertion sites. We aligned 128 386 integration positions of Tf1s-neo combined from the WT2 and WT3 experiments and examined the nucleotide frequencies of flanking sequence using the logo algorithm (22). The insertion sites possessed a pattern of preferred nucleotides with modest strength that extended 50 bp in either direction (Figure 7A). The preferred nucleotides flanking Tf1s-neo inserts formed a palindrome, a pattern observed with other integrating elements that is thought to be due to stabilizing contacts between the IN and target DNA (4,8,23–26). To determine whether the chromodomain contributed to the overall pattern of nucleotide preference we analyzed the 123 881 insertion sites produced by all three of the Tf1s-CHD-neo experiments. The resulting logo was very similar to that produced by Tf1s-neo indicating that the chromodomain contributed little to the average pattern of nucleotide preference (Figure 7B).

Bottom Line: To address this problem we developed the serial number system, a TE tagging method that measures the frequency of integration at single nucleotide positions.We sequenced 1 million insertions of retrotransposon Tf1 in the genome of Schizosaccharomyces pombe and obtained the first profile of integration with frequencies for each individual position.Integration levels at individual nucleotides varied over two orders of magnitude and revealed that sequence recognition plays a key role in positioning integration.

View Article: PubMed Central - PubMed

Affiliation: Section on Eukaryotic Transposable Elements, Program in Cellular Regulation and Metabolism, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.

Show MeSH
Related in: MedlinePlus