The residual ethylene sen-sitivity observed in the quadruple-mutantplants is consistent with the fact that theEDF genes represent only one branch of theethylene response
I am very lost with the second half of this paper, were they now using ethylene sensitivity instead of kanamycin resistance as the signature tagged mutagenesis?
We observed no significant corre-lation between the level of gene expressionand the frequency of T-DNA integration.
I think this is an interesting point, but I'm not sure if this result was expected or not. I know that multiple insertions can result in silencing; however, I'm not sure if that logic applies here.
Thus, another plausiblemodel for integration site preference is thatuncoiling of the DNA helix during transcrip-tion initiation and termination at 5 ' and3 'UTRs may allow greater accessibility to theT-DNA integration machinery
This also makes sense to me as a plausible explanation for why integrations favor 5'UTRs and 3'UTRs; those are the exposed regions during transcription that would allow DNA to be integrated
It is conceivable that the bias towardpromoters and UTRs is the result of pref-erential interaction of the Vir proteins withhost proteins involved in initiation or ter-mination of transcription.
I think this is a fancy way of saying what I was thinking; that the bias towards insertion into promoters and UTRs is a defense mechanism (evolved to protect against viral changes to genomic DNA) in order to preserve a favorable phenotype Although, wouldn't an insertion into a promoter region alter the organism's ability to translate and transcribe certain genes?
we found a positivecorrelation between the G + C content andthe number of insertions in promoters,5 'UTRs, exons, and intergenic regions. Sim-ilarly, we detected a negative correlation andno correlation between the G + C contentand insertion frequency in introns and3'UTRs, respectivel
Why would G+C content affect the number of insertions in promoters, 5'UTRs, exons, and intergenic regions? Also, why would G+C content affect the frequency of insertions in introns?
smallbias toward T-DNA insertions in the intergenicregion
Intergenic regions are non-protein coding stretches of DNA between genes, so a bias towards insertions here would mean no change in the phenotype, which would make sense as a defense against changes in the genome that would result in unfavorable mutations
However, a significant bias was seen againstintegration events in introns and coding exonsin favor of 5'UTR, 3'UTRs, and promoters
This is sort of makes sense to me, because integrating into the 5'UTR and 3'UTR would result in no changes to phenotype because these regions don't actually encode functional genes that encode proteins? So it's almost like a defense against changes to the genome?
. In total, a conservative set of 88,122quences were mapped onto the genome se-quence, and a single genomic location wasunambiguously determined.
I think this is saying that 88,122 sequences of nucleotides (unsure how long the sequences are?) were able to be identified and mapped and the location of these sequences in the genome was able to be determined.
heaverage number of T-DNA insertions per linewas found to be 1.5 [a number similar toother T-DNA collections (14)], and there-fore, the entire collection was estimated tocontain 225,000 independent T-DNA integra-tion event
I am confused how they concluded this.
About 150,000transformed plants (T1 plants) expressing aT-DNA-located kanamycin-resistance gene(NPTID
Signature tagged mutagenesis, tag is kanamycin resistance; integrate into genome and then look for unusual phenotypes (kanamycin resistance), when found, this phenotype indicates that the gene relating to the usual phenotype was inactivated