Table 1 Summary of the advantages and disadvantages of the discussed DNA labeling methods

Fluorescent repressor/operator systems (FROS)

Signal amplification used:

SunTag system [91]

· Sufficient signal with insertion of at least 96 operator repeats

· Simultaneous labeling of several loci possible by insertion of different arrays

· Requires genome editing

· Can lead to genomic instability, heterochromatin formation and gene silencing

· An block transcription when placed in an intron

· Relatively large arrays (several kbs)

Transcription activator-like effectors (TALE)

Signal amplification used: quantum dots [34]

· Highly versatile

· Simultaneous labeling of several loci possible

· No genome editing

· Ideal for repetitive sequences

· Design and generation of multiple TALEs for targeting a locus labor intensive

· Shown to work for single loci only in combination with quantum dots

dCas9 coupled to fluorophores (dCas9)

Signal amplification used:

RNA aptamer signal amplification [48,49,50,51]

SunTag system [42,43,44]

Casilio [50, 53]

ArrayG [47]

· Highly versatile

· Simultaneous labeling of several loci possible

· No genome editing

· Low signal-to-background ratio

· Can block transcription when placed on the wrong DNA strand

ANCHOR

Signal amplification used: none described

· Inserted sequence is relatively small

· Combination of ANCHOR systems can be used simultaneously

· No genomic instability

· Can be inserted close to promoters, enhancers and intragenic

· Requires genome editing

· Not all ANCHOR systems work equally efficiently