Bottom-up data integration in polymer models of chromatin organisation

TL;DR

This paper introduces SEMPER, a stochastic polymer model that integrates sequence-specific biochemical data into 3D chromatin structure modeling, enabling better interpretation of epigenomic data and prediction of chromatin conformations.

Contribution

SEMPER is a novel model that incorporates biochemical processes into chromatin modeling and uses Bayesian inference to assess their influence on chromatin states.

Findings

Model can predict chromatin folding features with reasonable accuracy.

Introduces a new Bayesian inference algorithm for model parameter estimation.

Highlights the importance of physically realistic statistical models in epigenomic analysis.

Abstract

Cellular functions crucially depend on the precise execution of complex biochemical reactions taking place on the chromatin fiber in the tightly packed environment of the cell nucleus. Despite the availability of large data sets probing this process from multiple angles, we still lack a bottom-up framework which can incorporate the sequence-specific nature of biochemistry in a unified model of 3D chromatin dynamics. Here we propose SEMPER (Sequence Enhanced Magnetic PolymER), a novel stochastic polymer model which naturally incorporates observational data about sequence-driven biochemical processes, such as binding of transcription factor proteins, in a 3D model of chromatin structure. By introducing a new algorithm for approximate Bayesian inference, we discuss how to estimate in a robust manner the relative importance of biochemical vs. polymer signals in the determination of the chromatin epigenetic states which is leading to a significant revision of the interpretation of previous models. Furthermore we show that, without additional input from the genome 3D structure, our model can predict with reasonable accuracy some notable and non trivial conformational features of chromatin folding within the nucleus. Our work highlights the importance of introducing physically realistic statistical models for predicting chromatin states from epigenetic data, and opens the way to a new class of more systematic approaches to interpret epigenomic data.