2021
DOI: 10.1128/msystems.00876-21
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Modeling Site-Specific Nucleotide Biases Affecting Himar1 Transposon Insertion Frequencies in TnSeq Data Sets

Abstract: When using the Himar1 transposon to create transposon insertion mutant libraries, it is known that the transposon is restricted to insertions at TA dinucleotide sites throughout the genome, and the absence of insertions is used to infer which genes are essential (or conditionally essential) in a bacterial organism. It is widely assumed that insertions in nonessential regions are otherwise random, and this assumption is used as the basis of several methods for statistical analysis of TnSeq data.

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Cited by 10 publications
(13 citation statements)
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“…Across three libraries, we generated approximately 51,000 unique transposon mutants, as defined by sites of unique transposon insertions across all three libraries. Of note, the Mab libraries shared the same non-permissive ‘TA’ sites for transposon insertion as has been described in other mycobacterial species ( Choudhery et al, 2021 ).…”
Section: Resultsmentioning
confidence: 73%
“…Across three libraries, we generated approximately 51,000 unique transposon mutants, as defined by sites of unique transposon insertions across all three libraries. Of note, the Mab libraries shared the same non-permissive ‘TA’ sites for transposon insertion as has been described in other mycobacterial species ( Choudhery et al, 2021 ).…”
Section: Resultsmentioning
confidence: 73%
“…Across three libraries, we generated approximately 51,000 unique transposon mutants, as defined by sites of unique transposon insertions across all three libraries. Of note, the Mab libraries shared the same non-permissive ‘TA’ sites for transposon insertion as has been described in other mycobacterial species (22).…”
Section: Resultsmentioning
confidence: 73%
“…A widely used approach is the use of transposons that enable the random integration of DNA segments across the genome without the need for homology [ 90 ]. Examples of transposons used for random DNA insertion include Himar1 , which inserts randomly between any TA dinucleotide, and Tn5, which can insert in the genome mostly at random but has a bias towards certain DNA shapes and GC rich or AT rich regions [ 136 , 137 ]; therefore, Tn5 insertion is not uniformly random. The combination of random transposon mutagenesis and high-throughput sequencing for genome-scale analyses is referred to as transposon sequencing (TnSeq).…”
Section: Genetic Design Tools Used To Engineer Probioticsmentioning
confidence: 99%