Below each phantom dataset is an example of anatomical data that can be obtained in vivo with the same sequence.
Members of subfamily I interact in vitro and in vivo with the pseudo-palindromic sequence CAAT(A/T ATTG [ 13- 16], and have been involved in the adaptive response to abiotic stress [ 4, 11].
In another case, taking advantage of RNA immunoprecipitation and sequencing technology, more than 4,000 Arabidopsis RNAs that directly or indirectly associate in vivo with the SR45 protein were identified46.
To test this, we measured the dynamics of the Pal-mCherry fusion in vivo with time-lapse sequences of Pal-mCherry fluorescence, both before and after photobleaching a small region within cells treated with chloramphenicol to block protein synthesis.
(The amino-terminal methionine residue is removed during protein processing in vivo, so that the sequence begins with Ser-1 and ends with Phe-374).
Although the protein lacks any conventional DNA binding domain, it is shown to interact in vitro and in vivo with a specific 9 bp DNA sequence 5'-AAAGACATG-3' present at the putative promoter of Caspase1 gene and positively regulate its transcription.
37i This comparison as well as the in vitro versus in vivo results with the Widom 601 sequence cited above illustrate that thermodynamically preferred sequences alone cannot predict nucleosome occupancy within living cells.
These algorithms are demonstrated on image sequences acquired in vivo with various imaging devices including a hand-held dual-axes confocal microscope, a miniature two-photon microscope, and a commercially available confocal microendoscope.
Strongly positioned nucleosomes may depend on ATP-dependent chromatin remodelers to be displaced in vivo, perhaps with the assistance of sequence specific DNA binding factors [75], [76] and/or histone chaperones [77].
Scanning of in vivo NFI binding sequences with the NFI weight matrix [ 29] was done using the OPROF software tool from the Signal Search Analysis server (URL: http://ccg.vital-it.ch/ssa/oprof.php).
