FB2017_02, released April 18, 2017

A Database of Drosophila Genes & Genomes

New reports for non-transposable element based insertions

FlyBase already produces an Insertion Report for insertions of transposable-element based transgenic constructs, e.g. P{GawB}Dllem212. Starting in the fb_2015_03 release, we now also generate an Insertion Report if exogenous DNA is inserted into the genome via non-transposable element-based means. In this case, since no transposable-element ends are present, the ends of the inserted element are designated using 'TI' (for 'transgene insertion') e.g. TI{GAL4}.

These 'TI' insertions often currently arise through genome engineering techniques (e.g. homologous recombination or CRISPr) which target a desired mutation to a gene of interest, but also insert exogenous DNA as part of the mutagenic event. Examples of the types of DNA that are inserted include a marker to allow easy identification of the chromosome, or a reporter/driver to analyse/utilise the endogenous expression of the targeted gene by enhancer trapping.

As for transposable-element based insertions, in addition to having their own Insertion Report, these 'TI' insertions are used to link related alleles on FlyBase, appearing on the relevant allele reports, and their symbols also appear in the relevant Bloomington Stock genotypes, so that it is easy to see that an insertion is present in a given stock.

For insertions of an open reading frame (ORF) that enhancer traps the targeted gene, the symbol of the inserted element gives an indication of the inserted ORF, e.g. the TI{GAL4} element in the TI{GAL4}mir-1000KO2-GAL4 insertion contains a GAL4 open reading frame.

For insertions of other types of DNA, such as marker alleles, a 'generic' TI{TI} element is usually used, e.g. TI{TI}Hs3st-B6. This is mostly pragmatic, to keep the insertion symbol short and to ensure that curation of these insertions from the literature is time efficient.

In all cases, a detailed description of what has been inserted into the genome for an individual insertion is present in the 'Nature of the lesion' field of any allele reports associated with that insertion. For example, the Hs3st-B6 allele associated with the TI{TI}Hs3st-B6 insertion is described as containing the following lesion:

2595bp deletion in the Hs3st-B locus, starting from 237bp upstream of the ATG start codon and ending 237bp downstream of the stop codon. A w+mW.hs marker flanked by P1\loxP sites has been inserted into the genome in place of the deleted sequence.