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We demonstrated how this dynamic behaviour can be exploited to trigger a change in the monomer distributions along the polymer upon binding of a multivalent nucleic acid such as single stranded DNA (ssDNA): the ssDNA acted as a recruiter, binding specific monomers along the polymer and clusters them, which resulted in spatiotemporal control of the monomer distribution.
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This approach allowed us to examine the relationship between Tup1 and possible recruiters, without rigidly selecting bound Tup1 targets, and it determined which possible recruiters' binding pattern changes in a similar manner as Tup1 binding pattern.
The 3D plot shows the FRET ratio for different DNA RNA length (8 to 48mer) and different densities of recruiter-binding monomers (0.5% to 8%) and these results are compared with the FRET ratio in absence of the recruiter (see Fig. S2 and S3, ESI †).
Additionally, the regression between the number of binding recruiters and Tup1 occupancy improves from an R2 of 0.50 to 0.58 when these four proteins are included (same analysis as Figure 2D).
Similarly, accumulation sites for condensin are presumably determined by a combination of pol II-mediated transcription and condensin recruiters at its binding sites.
Nurse recruiters recruited patients between January 14 , 2002and April 13 , 2003
Our multi-recruiter model of Tup1 binding was generated by regression analysis.
A third class of proteins would be represented by PcG/TrxG DNA-binding recruiters or specific co-factors.
To develop our model we initially tested each recruiter to determine if their binding was significantly positively correlated with Tup1 occupancy.
Further, they found that the silenced CMV promoter interacts in vivo with methyl CpG binding protein 2 (MeCP2), a recruiter of HDACs, and histone (H3K9) methyl transferase.
While inclusion of the newly identified Tup1 recruiters does not explain all Tup1 binding, our results do increase the number of Tup1 binding events explained by the presence of a recruiter by 15% or more (depending on cutoff used to define binding events) and explain a significantly greater proportion of the Tup1 occupancy variance.
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