Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler

Abstract

While nuclear compartmentalization is an essential feature of three-dimensional genome organization, no genomic method exists for measuring chromosome distances to defined nuclear structures. In this study, we describe TSA-Seq, a new mapping method capable of providing a "cytological ruler" for estimating mean chromosomal distances from nuclear speckles genome-wide and for predicting several Mbp chromosome trajectories between nuclear compartments without sophisticated computational modeling. Ensemble-averaged results in K562 cells reveal a clear nuclear lamina to speckle axis correlated with a striking spatial gradient in genome activity. This gradient represents a convolution of multiple spatially separated nuclear domains including two types of transcription "hot zones." Transcription hot zones protruding furthest into the nuclear interior and positioning deterministically very close to nuclear speckles have higher numbers of total genes, the most highly expressed genes, housekeeping genes, genes with low transcriptional pausing, and super-enhancers. Our results demonstrate the capability of TSA-Seq for genome-wide mapping of nuclear structure and suggest a new model for spatial organization of transcription and gene expression.

Differential contribution of steady‐state RNA and active transcription in chromatin organization

“…However, it is worth noting that Vian and colleagues have demonstrated that TADs can disappear upon cohesin degradation and reappear after rescue, even in the absence of transcription [32]. Similarly, previous reports suggested that the act of transcription can influence the 3D structure of the nucleus [27,[58][59][60]. Indeed, although the compartmentalization was not markedly altered (Fig 4) we observed a reduction in TAD boundary strength upon transcriptional inhibition ( Fig 5).…”

Joint inference and alignment of genome structures enables characterization of compartment-independent reorganization across cell types

“…One possibility is that the enhancers are differentially associating with nuclear speckles. It has been shown that distance from nuclear speckles in the A compartment is independent of the nuclear lamina compartment axis and is correlated with superenhancers and H3K4me3, H3K9ac, and CTCF peaks (32) . Thus the compartment-independent relocalizations we identified may represent differences in nuclear speckle association.…”

SPIN reveals genome-wide landscape of nuclear compartmentalization

“…1a. Our goal is to identify genome-wide spatial compartmentalization patterns of the chromosomes by integrating TSA-seq (Chen et al, 2018) and DamID (Guelen et al, 2008;Meuleman et al, 2013) data together with Hi-C. TSA-seq and DamID provide complementary information to measure distance and contact frequency between chromosome regions and subnuclear structures. The rationale of including Hi-C is that the pairwise genomic regions spatially interacting with each other more often than expected (from Hi-C) are more likely to share similar spatial compartmentalization patterns.…”

“…In this implementation of SPIN to infer genome-wide nuclear compartmentalization patterns, we used TSA-seq and DamID mapping data in K562 for nuclear speckles (TSA-Seq), lamina (DamID and TSA-Seq), and nucleoli (DamID). Nucleoli DamID data, generated using a Dam methylase fusion with a nucleolar targeting peptide repeat (4xAP3 (Scott et al, 2010)) is new; all remaining data are as published previously (Chen et al, 2018;Leemans et al, 2019). Details of the new nucleolar DamID mapping are described elsewhere (van Schaik et al manuscript in prep.).…”

“…In Fig. 1e, we show three genomic regions (with detailed genomic coordinates) that correspond to different SPIN states with comparisons to DNA FISH data from Chen et al (2018). The probe in the FISH image of the Speckle state has an average distance of 0.16µm from nuclear speckle (SON protein).…”