Mission

To uncover how CTCF/CTCFL, cohesin, transcription factors, and nucleosomes generate tunable insulation and state-specific 3D genome folding. We build the tools to see it—from fixed-cell 3D FISH and dual-colour live CRISPR imaging to EpiMethylTag, MethNet, and cluster-based single-molecule nano-NOMe phasing—and apply them to show how drivers like NSD2 reprogram insulated domains and how DNA damage imprints lasting chromatin memory. Our earlier lymphocyte work established the playbook for locus contraction/decontraction, enhancer-guided proximity, recombination centers, and genome-stability checkpoints that still anchor our current cancer and immunity studies.

Summary

Over two decades, the Skok lab has defined how 3D genome architecture, insulation by CTCF/cofactors, and enhancer logic orchestrate antigen-receptor recombination and lineage decisions, built experimental and computational tools to see these processes in living cells and single molecules, and translated these principles to cancer, neuro-oncology, immunology, and epigenetic disease, revealing domain-scale mechanisms and actionable vulnerabilities

Recent Achievements

Chromatin insulation & 3D folding (mechanism-forward)

  • CTCF vs CTCFL (BORIS). Defined overlapping and distinct roles in binding, insulation, and promoter control, explaining when BORIS substitutes for—or antagonizes—CTCF.
  • CTCF DNA-binding domain mutants. A domain-by-domain mutant series separates sequence affinity from organizer function and chromatin engagement, yielding a genotype→insulation/folding map and constraints on nucleosome/TF crosstalk.
  • CTCF–cohesin–TF coordination tunes insulation via nucleosomes. State-specific TF programs reposition nucleosomes and modulate CTCF/cohesin to produce distinct folding states.

Domain-scale dysregulation in disease

  • NSD2 → insulated-domain reprogramming. NSD2 overexpression drives clustered chromatin and transcriptional changes within insulated domains—establishing a domain-level oncogenic mechanism.
  • Damage-imprinted chromatin memory (GBM). Widespread, targeted DSBs induce durable chromatin and expression reprogramming with implications for therapy resistance (preprint).

Technology, analytics & imaging platforms

  • Cluster-based single-molecule nano-NOMe phasing (with molecule stitching). New framework that clusters single molecules and stitches overlapping reads to extend coverage across long regulatory neighborhoods, directly linking CTCF binding states, nucleosome occupancy, and long-range interactions to transcriptional context.
  • Fixed-cell 3D imaging (built & standardized). Extensive 3D DNA-FISH/Immuno-FISH workflows to quantify locus positioning, contraction/decontraction, and higher-order architecture—methods used across our papers.
  • Live-cell CRISPR imaging (dual-colour). CRISPR-dCas9 + sgRNA scaffolds for dual-colour tracking of repeats and individual loci in living cells (Nat Commun).
  • EpiMethylTag (assay + protocol). Simultaneous ATAC-/ChIP-signal with DNA methylation from the same material; full protocol provided.
  • MethNet. Cohort-scale, methylation-anchored graphs that discover distal regulatory hubs and targets across cancers.
  • 4C-ker & multi-contact logic. 4C-ker for reproducible 4C interaction calling and a framework to identify simultaneous interactions in multi-loci hubs.
  • 3D TE→host regulation. Genome-wide 3D analysis nominating host genes under transposable-element control.

Lymphocyte biology

  • First demonstration of looping in individual nuclei & locus contraction → diversity. Using 3D FISH, we were first to show that antigen-receptor loci loop/contract in individual interphase nuclei to bring distal V segments into proximity with DJ, explaining how the genome accesses the full V repertoire and thus creates antigen-receptor diversity—the basis of adaptive immunity (Tcra/Tcrb; building on Pax5-driven Igh contraction).
  • Allelic exclusion mechanics. Decontraction + centromeric tethering enforce monoallelic assembly at Igh.
  • Enhancer-guided proximity. The 3′ Igκ enhancer drives Igκ–Igh association and induces Igh decontraction in pre-B cells.
  • Genome integrity during V(D)J. RAG1 + ATM coordinate monoallelic recombination and nuclear positioning; RAG2 C-terminus/ATM and RAG2-S365 phosphorylation restrict cleavage to individual alleles and loci.
  • Spatial rules for translocations. Proximity to Igh helps explain AID-mediated partner choice.
  • Recombination centers. Higher-order looping concentrates RAG to control cleavage and rearrangement.
  • B-1a ontogeny. B-1a cells bypass pre-BCR selection, explaining their distinctive phenotype and repertoire.