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Seminars

Deriving 3D structure of DNA from neighboring data

Hold Date
2017-11-08 15:30〜2017-11-08 16:30
Place
Lecture Room S W1-C-504, West Zone 1, Ito campus, Kyushu University
Object person
 
Speaker
Youichi NAKATA (Graduate School of Mathematical Sciences, University of Tokyo)

Abstract:
It is considered that the spatial structure of DNA is one of the factors which control transcriptional dynamics. However, the structure of DNA in transcription is not directly measured and we can only obtain the neighboring relations by picking up proteins which binding DNA.

We propose a coarse-grained model to estimate the spacial structure of DNA from such binding data. This model is based on bead-spring model in polymer physics.  We also apply this model to experimental data and obtained that spatial localization of DNA sites which play important roles of transcription. This result follows that the idea of the Transcription factory hypothesis, which explains simultaneous transcription between distant DNA sites.

In this talk, we first present a brief introduction of backgrounds and explain the details of our model. Finally, we discuss refinements of this model.