Mesoscale modeling reveals formation of an epigenetically driven HOXC gene hub

Abstract

Gene expression is orchestrated at the structural level by nucleosome positioning, histone tail acetylation, and linker histone (LH) binding. Here, we integrate available data on nucleosome positioning, nucleosome-free regions (NFRs), acetylation islands, and LH binding sites to "fold" in silico the 55-kb HOXC gene cluster and investigate the role of each feature on the gene's folding. The gene cluster spontaneously forms a dynamic connection hub, characterized by hierarchical loops which accommodate multiple contacts simultaneously and decrease the average distance between promoters by ∼100 nm. Contact probability matrices exhibit "stripes" near promoter regions, a feature associated with transcriptional regulation. Interestingly, while LH proteins alone decrease long-range contacts and acetylation alone increases transient contacts, combined LH and acetylation produce long-range contacts. Thus, our work emphasizes how chromatin architecture is coordinated strongly by epigenetic factors and opens the way for nucleosome resolution models incorporating epigenetic modifications to understand and predict gene activity.

Keywords: chromatin folding; chromatin loop domains; chromatin modeling; contact hub; gene structure.

Fig. 1.

Mesoscale model and HOXC system setup. (A) The repeating unit of the mesoscale model consists of a rigid nucleosome core with wrapped DNA represented by 300 point charges and beads for linker DNA, LH, and the flexible histone tails. See details in ref. . NCP, nucleosome core particle. (B) A rendering of the HOXC gene cluster model demonstrates gene positions and epigenetic elements in a 3D model. Acetylated tails are red, and WT tails are blue. Intron DNA is drawn in dark blue, exon DNA is colored light blue, and intergenic DNA is dark red. (C) DNA linker lengths used in the HOXC model are plotted against the nucleosome index, along with annotated gene locations and epigenetic features, with acetylation islands in red, LH in teal, and NFRs in green.

Fig. 2.

Fiber renderings and contact probability matrices for HOXC and reference fibers. Black bars (top and sides) show the positions of HOXC genes. (A) HOXC system. (B) Reference system with life-like nucleosome positions, NFRs, and acetylation marks. (C) Reference system with life-like nucleosome positions and NFRs.

Fig. 3.

Epigenetic factors control fiber morphology and density. (A) Fiber renderings of HOXC, Uniform, Uniform$+$NFR, Life-Like$+$Ac, Life-Like$+$LH, and Life-Like systems. (B) The volume, $R_g^2$, and $S_{w,20}$ measurements as averaged across all 50 trajectories.

Fig. 4.

Analysis of internucleosome interaction contacts for HOXC and reference systems. We annotate structural peaks as follows. Short-range contacts ($>$1 kb) measure next-neighbor interactions common in zigzag fibers. Contacts in the 1- to 2-kb range arise from intraclutch interactions. Chromatin loops between neighboring clutches account for 5- to 10-kb contacts, and hierarchical loops account for 10- to 20-kb contacts.

Fig. 5.

Formation of dynamic contact hub depends on epigenetic features. (A) Number of contacts observed in HOXC fiber system between LH/LH (teal), LH/Ac (pink), Ac/Ac (red), LH/NFR (blue), Ac/NFR (green), and any interaction that involves unmodified regions (WT; gray) as a function of genomic position. (B, Left) Plot of average pairwise distance count between gene promoters in the HOXC system vs. two reference systems. (B, Right) Renderings of chromatin configurations with promoter contacts (green/yellow highlight).

Fig. 6.

Multiple dynamic contacts form within the hub. (A) Hierarchical looping accommodates four simultaneous loops in an individual fiber. One folded HOXC gene cluster fiber is shown with a sketch demonstrating the fiber folding and the genes and fiber-folding pattern and the corresponding contact probability matrix. (B) Cartesian distances between promoter regions of four gene pairs are plotted as a function of simulation length in a single trajectory. Fiber snapshots, with the promoters highlighted in green and yellow, demonstrate the formation of transient connections between promoters. MC, Monte Carlo.