Chromatin 3D structure modelling from 2D experimental maps: efforts, grounds and some novel findings

Eukaryotic DNA chain spanning c.a. 2 meters is tightly packed in the nucleus of one cubic micrometer size.  In it, 23 chromosome pairs in human genome are present, which altogether contain the DNA chain and numerous auxiliary proteins (including histons, CTCF and many others).  Genomic techniques like Hi-C or ChIA-PET deliver experimental 2D matrices of interactions between all-against-all genomic fragments, that can serve as a sufficient base for 3D structure determination.  This very approach however has many pitfalls, including the "rigid body" model assumed alone, which tends to be a generalization causing information leaks.

 

In this talk, some basics of structural bioinformatics of the chromatin will be disclosed.  Then, the techniques quoted are to be defined.  Eventually, a research been conducted will be summoned and shown in a form of a novel in-silico technique of determination of 3D chromatin structure from 2D interaction genomic matrices.  In the end, certain crucial ambiguities will be elaborated and some novel initial research hints presented on how to address them, in the subsequent, more mature, proposal attempts.