Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae.

Nucleic Acids Research
Michael SeringhausMark B Gerstein

Abstract

Transposons are widely employed as tools for gene disruption. Ideally, they should display unbiased insertion behavior, and incorporate readily into any genomic DNA to which they are exposed. However, many transposons preferentially insert at specific nucleotide sequences. It is unclear to what extent such bias affects their usefulness as mutagenesis tools. Here, we examine insertion site specificity and global insertion behavior of two mini-transposons previously used for large-scale gene disruption in Saccharomyces cerevisiae: Tn3 and Tn7. Using an expanded set of insertion data, we confirm that Tn3 displays marked preference for the AT-rich 5 bp consensus site TA[A/T]TA, whereas Tn7 displays negligible target site preference. On a genome level, both transposons display marked non-uniform insertion behavior: certain sites are targeted far more often than expected, and both distributions depart drastically from Poisson. Thus, to compare their insertion behavior on a genome level, we developed a windowed Kolmogorov-Smirnov (K-S) test to analyze transposon insertion distributions in sequence windows of various sizes. We find that when scored in large windows (>300 bp), both Tn3 and Tn7 distributions appear uniform, whereas in sm...Continue Reading

References

Oct 25, 1990·Nucleic Acids Research·T D Schneider, R M Stephens
Feb 11, 1995·Nucleic Acids Research·C J Davies, C A Hutchison
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Feb 21, 1998·Nucleic Acids Research·J M CherryD Botstein
Jun 26, 2003·Journal of Molecular Biology·Patrick A Pribil, David B Haniford
Jun 3, 2004·Genome Research·Gavin E CrooksSteven E Brenner
Jan 25, 2005·Journal of Molecular Biology·Geyi LiuPerry B Hackett

❮ Previous
Next ❯

Citations

Mar 14, 2007·Journal of Bacteriology·Paula Ann KivistikRita Hõrak
Feb 9, 2012·Mobile DNA·Brian GreenBrendan P Cormack
Oct 28, 2008·Plasmid·Adam R Parks, Joseph E Peters
Mar 10, 2020·F1000Research·Anuj Kumar
Mar 7, 2015·Genetics·Rebecca E ZordanBrendan P Cormack

❮ Previous
Next ❯

Software Mentioned

WebLogo
BLAST
Sequence Logo
Perl

Related Concepts

Related Feeds

CZI Human Cell Atlas Seed Network

The aim of the Human Cell Atlas (HCA) is to build reference maps of all human cells in order to enhance our understanding of health and disease. The Seed Networks for the HCA project aims to bring together collaborators with different areas of expertise in order to facilitate the development of the HCA. Find the latest research from members of the HCA Seed Networks here.