ArticleThe Journal of cell biology2018
Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler.
Article in The Journal of cell biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 261 papers.
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Who cites it
261 citing papers in PubMed.
- Mapping subcellular microenvironments using oligonucleotide-directed proximity labeling.Current opinion in chemical biology · 2026Review
- Nuclear speckle protein SON safeguards efficient splicing of GC-rich genes.Cell research · 2026Article
- LENG8 granule regulates alternative polyadenylation in mammals.Nature communications · 2026Article
- Acidic transcription factors position the genome at nuclear speckles through transcription-dependent and -independent mechanisms.Molecular cell · 2026Article
- Article
- Nuclear speckles: a fundamental layer of gene regulation.Trends in cell biology · 2026Review
- The periphery of nuclear speckles defines a spatially and temporally regulated compartment of long-lived intron-retained RNAs that resolves during mitosis.Nature cell biology · 2026Article
- Epistemological parameters in the recent era of nuclear organization and function.Molecular biology of the cell · 2026Review
- Origins and consequences of oncogenic 3D chromatin remodelling.Nature reviews. Cancer · 2026Review
- Nuclear speckle-associated perispeckle networks partition active chromatin into gene expression niches.Cell reports · 2026Article
- Deep learning enabled prediction of nuclear lamina-associated chromatin.Patterns (New York, N.Y.) · 2026Article
- Genome folding and nuclear speckles converge to orchestrate fibroblast activation.Science advances · 2026Article
- Sequential-GAM constructs the single-cell geometric 3D genome structure.Nucleic acids research · 2026Article
- Capsid stabilization reprograms the nuclear fate of the HIV genome.Science advances · 2026Article
- The cardiac 4D nucleome: nuclear and chromatin dynamics across development, disease and ageing.Nature reviews. Cardiology · 2026Review
- Polycomb-mediated 3D-genome organization controls replication timing.Science advances · 2026Article
- RNA-binding protein transcripts reflect composition of target mRNAs.Nucleic acids research · 2026Article
- Detection of Target Molecules Within One-Millimeter-Thick Mouse Brain Slices by Using Peroxidase-Fused Nanobodies and Fluorochromized Tyramide-Glucose Oxidase Reaction.Bio-protocol · 2026Article
- RYBP regulates selective genomic binding of TrxG and PcG components in embryonic stem cell fate control.The EMBO journal · 2026Article
- Huntingtin (HTT) interactome in regulation of DNA repair/remodeling and RNA processing pathways.Life science alliance · 2026Article
201 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
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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.
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