To investigate how IRF2 regulates the induction of TLR3, we examined the accessibility of the TLR3 promoter to restriction enzyme Hind III, which has a recognition site −39 bp upstream of its TSS.
To circumvent the genome size obstacle (the mouse genome is 2.7 Gb in size), the authors took advantage of the reduced representation generated from DNA digestion with the MspI restriction enzyme, which has a recognition site (CCGG) abundant in CpG islands [ 40].
The junction of Illumina adaptor 1 and the CATG site is the recognition site of MmeI, which has a different recognition and digestion site, i.e., it cuts at 17-bp downstream of the CATG site, producing tags with adaptor 1.
The EcoRII-C endonuclease (which has a CCWGG recognition sequence where W = A or T) is likely to degrade either bacterial DNA to inhibit the host during the KL3 lytic cycle or superinfecting phage DNA [ 81, 82].
In the case of the repeats flanking the 6.1-kb sequence, DNA gel blot hybridizations identified a strong 6.5-kb band in samples digested with EcoRV, which has a single recognition sequence in this region.
To obtain an estimate for the number of gene-disruption constructs integrated in the transformed moss plants, this DNA was digested with PvuII, which has a single recognition site within the nptII coding sequence.
In agreement with our observations, this interaction does not rely on SLP-76, which has a known pTyr recognition motif for the Nck SH2 domain.
Fosmid DNA was subsequently purified and digested with the homing endonuclease PI- SceI, which has a 35-bp recognition site.
Biotinylated linkers are ligated to the DNA molecules and then digested with the fragmenting enzyme NlaIII, which has a 4-bp recognition site.
Briefly, genomic DNA is cleaved with the mapping enzyme SacI, which has a 6-bp recognition sequence that is predicted to cut genomic DNA into several hundred thousand pieces that are on average < 10 kb.
Expression of the Dcm methylase, which has an identical recognition sequence and methylation site as EcoRII methylase, is mutagenic in E. coli because 5-methylcytosines are deaminated to thymines, causing T/G mismatches [ 84, 85].
