Bottom-Up Meets Top-Down: The Crossroads of Multiscale Chromatin Modeling

Moller, Joshua; de Pablo, Juan J.

doi:10.1016/j.bpj.2020.03.014

Title: Bottom-Up Meets Top-Down: The Crossroads of Multiscale Chromatin Modeling

Journal Article · Sat Apr 04 00:00:00 EDT 2020 · Biophysical Journal

DOI:https://doi.org/10.1016/j.bpj.2020.03.014· OSTI ID:1755766

Moller, Joshua ^[1]; de Pablo, Juan J. ^[2]

Univ. of Chicago, IL (United States)
Univ. of Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States)

Chromatin can be viewed as a hierarchically structured fiber that regulates gene expression. It consists of a complex network of DNA and proteins whose characteristic dynamical modes facilitate compaction and rearrangement in the cell nucleus. These modes stem from chromatin's fundamental unit, the nucleosome, and their effects are propagated across length scales. Understanding the effects of nucleosome dynamics on the chromatin fiber, primarily through post-translational modifications that occur on the histones, is of central importance to epigenetics. Within the last decade, imaging and chromosome conformation capture techniques have revealed a number of structural and statistical features of the packaged chromatin fiber at a hitherto unavailable level of resolution. Such experiments have led to increased efforts to develop polymer models that aim to reproduce, explain, and predict the contact probability scaling and density heterogeneity. At nanometer scales, available models have focused on the role of the nucleosome and epigenetic marks on local chromatin structure. At micrometer scales, existing models have sought to explain scaling laws and density heterogeneity. Less work, however, has been done to reconcile these two approaches: bottom-up and top-down models of chromatin. Here, we highlight the multiscale simulation models that are driving toward an understanding of chromatin structure and function, from the nanometer to the micron scale, and we highlight areas of opportunity and some of the prospects for new frameworks that bridge these two scales. Taken together, experimental and modeling advances over the last few years have established a robust platform for the study of chromatin fiber structure and dynamics, which will be of considerable use to the chromatin community in developing an understanding of the interplay between epigenomic regulation and molecular structure.

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Research Organization:: Argonne National Lab. (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE; National Science Foundation (NSF)

Grant/Contract Number:: AC02-06CH11357; EFRI CEE 1830969

OSTI ID:: 1755766

Journal Information:: Biophysical Journal, Vol. 118, Issue 9; ISSN 0006-3495

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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