Enhancer trapping in zebrafish using the Sleeping Beauty transposon

BMC Genomics

Table 1 pT2/S2 EF1α-GM2 transposon insertion events in analyzed enhancer trap lines.

Trap line	Sequence	Insertion location	Predicted gene
ET1	ATTGTCCtTAGTGTA TGTGTTTGTGTGA	Chr. 4	none
ET2	CAAAAAGACTATATA TAGGAGGCTTCAA	ctg9701	PARG
ET3	AACGCTTACCATGTA TGTTAATAAATGT	Chr. 17	MBIP
ET4	TATATCAAAATTATA TATATGAACGTAT	Chr. 6	Cyt. P450
ET5	GTACATAcACATGTA CAAATCaACATTA	ctg13471	novel
ET6	ATTTTAAACAAACTA AGTtGAACATTAC	ctg13605	Nidogen
ET7	ATCACAGAGCATCTA GCTTGGATGTGCT	ctg12155	novel/mkp3
ET8	TATACAACAAACTTA TCTAACGTGCAAT	Chr. 2	none
ET9	TATTTAATATATATA TTATATTATATTA	Chr. 19	novel

Left column, line designation. Sequence column, the genomic sequence the transposon has inserted into. The target TA dinucleotide is highlighted in bold. The sequences flanking the left inverted repeat are to the left of the target TA, and sequences flanking the right inverted repeat are to the right of the target TA. Lowercase indicates mismatches between an actual sequence read and the current zebrafish genome sequence (Assembly ZV3). Both left and right transposon/genomic DNA junctions were sequenced for ET1, ET2, ET3, ET5 and ET7. Only the left junction was read for ET8, and only the right junction was read for ET4, ET6 and ET9. Insertion location column, predicted insertion chromosome or contig (Zv3 assembly of the zebrafish genome). Predicted gene column, the gene into which the transposon has inserted as annotated in the zebrafish genome assembly Zv3. Novel indicates no significant homologies. Gene name indicates significant homology to denoted genes. The predicted integration into an intron of the PARG locus for line ET2 was experimentally confirmed (see text). For ET7, a comparison of the observed expression pattern in this line with that of a known nearby gene (mkp3) indicates this insertion has most likely trapped an enhancer for this gene (Fig. 7, see text). Actual sequence reads which were used to determine the genomic location of the transposon insertions were longer than shown in this table and are available upon request.

ISSN: 1471-2164