Transcription modulates chromatin dynamics and locus configuration sampling

Abstract

In living cells the 3D structure of gene loci is dynamic, but this is not revealed by 3C and FISH experiments in fixed samples, leaving a significant gap in our understanding. To overcome these limitations we applied the “highly predictive heteromorphic polymer” (HiP-HoP) model, validated by experiments, to determine chromatin fibre mobility at the Pax6 locus in three mouse cell lines with different transcription states. While transcriptional activity minimally affects the movement of 40 kbp regions, we observed that the motion of smaller 1 kbp regions depends strongly on local disruption to chromatin fibre structure marked by H3K27 acetylation. This also significantly influenced locus configuration dynamics by modulating promoter-enhancer loops associated with protein bridging. Importantly these simulations indicate that chromatin dynamics are sufficiently fast to sample all possible conformations of loci within minutes, generating wide dynamic variability of gene loci structure within single cells. Experiments inhibiting transcription change chromatin fibre structure subtly, yet we predict they should substantially affect mobility. This combination of simulation and experimental validation provide a novel insight and mechanistic model to explain how transcriptional activity influences chromatin structure and gene dynamics.

Multiscale Bayesian Simulations Reveal Functional Chromatin Condensation of Gene Loci

“…This nonlinearity has been suggested to originate from a separation of timescales between genomic structural fluctuations and gene activation (17). Indeed, consistently with recent simulations (59), we find that the Sox2, Pou5f1, and Nanog loci of mESCs can rapidly explore their vast space of 3D conformations. Transient contacts between CREs (potentially stimulating gene expression) are formed and broken on a timescale of less than a second, significantly faster than the timescales of gene activation, on the order of several minutes (48).…”

“…For the applications to the genomic organization of mESCs presented here, we integrated Micro-C data (39) into two physics-based models of chromatin, the nucleosome-resolution 1CPN model (30) and a newly parametrized 1kb model, although other models may also be employed (29,59).…”

“…Alternatively, the differences in the conformational ensembles obtained using the physics-based models with and without metainference can guide the modeling of necessary additional factors into the prior model or suggest hypotheses on the underlying mechanism. For the applications to the genomic organization of mESCs presented here, we integrated Micro-C data (39) into two physics-based models of chromatin, the nucleosome-resolution 1CPN model (30) and a newly parametrized 1kb model, although other models may also be employed (29, 59).…”

A Scaffolding Element Rewires Local 3D Chromatin Architecture During Differentiation

“…Local contacts rewiring (under 1 Mb) is often associated with specific gene-expression changes, highlighting the importance of chromatin contacts in regulating transcription 3 . However, even though many studies focused on the causal relationship between chromatin contacts and transcriptional response, they gave conflicting results indicating a context-dependent relationship [8][9][10][11][12][13][14][15][16][17][18][19] . In addition, most of the contacts are not functionally annotated, hence their potential contribution to the transcriptional response is not entirely known.…”

Predicting scale-dependent chromatin polymer properties from systematic coarse-graining

“…In the current models, the heterogeneity of chromatin is often incorporated into additional intra-chromatin interactions—interaction between two far-away beads [10, 22, 66]. Since one does not know the size of a coarse-grained chromatin bead, it is taken as a fitting parameter—a constant number across the filament—to achieve experimentally measured 3D distance values [10, 13, 20, 22, 67, 68]. Fig.…”