Chromatin Folding & TAD Loops (2D)

Folding State

Histone acetylation 50%

Nucleosomes in chain 48

Loop Extrusion (cohesin)

Extrusion progress 0%

Chromatin state

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Compaction

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DNA in view

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TAD loop size

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How it works

Every ~147bp of DNA wraps 1.7 turns around a histone octamer to form a nucleosome ("bead"); a short linker (20–80bp) connects each bead to the next. Low histone acetylation lets adjacent nucleosomes stack into a compact 30nm zig-zag fibre (heterochromatin); high acetylation neutralises histone charge and keeps the fibre open ("beads-on-a-string", euchromatin) so transcription machinery can access the DNA.

Nucleosome repeat length (NRL) = 147bp + linker(20-80bp)
Linear compaction: ~6x (open fibre) → ~40x (30nm zig-zag)
Loop extrusion: cohesin reels DNA in from both sides until
  stopped by convergent CTCF sites → a stable TAD loop

Histone acetylation — drives the fibre continuously between open beads-on-a-string and the tightly packed zig-zag.
Nucleosomes in chain — how many beads of this chromatin segment are rendered (view stays framed either way).
Extrusion progress / Auto-extrude — slides the cohesin ring along the fibre, growing a loop anchored at two convergent CTCF sites (flags) until it locks into a topologically associating domain (TAD).
Folding state — switch between a straight fibre segment and the same fibre bent into a cohesin-extruded loop.

Real-world relevance: Hi-C chromosome-conformation maps reveal exactly these TAD loops; disrupting CTCF sites or cohesin can fuse neighbouring TADs and switch on the wrong genes — a mechanism implicated in some cancers and developmental disorders.

Open nucleosome (euchromatin) Condensed nucleosome (heterochromatin) Cohesin ring