Marcelo A. Carignano

One Chromatin, Many Structures: From Ensemble Contact Maps to Single-Cell 3D Organization

This paper introduces the SR-EV model to interpret chromatin organization as ensemble-level statistical patterns rather than fixed structures, showing how TADs and contact enrichments emerge from geometric rules and heterogeneity.

Gene transcription and chromatin packing domains form a self-organizing system

The paper shows that Pol-II regulates chromatin packing domains through transcriptional loops, linking RNA synthesis to genome organization and gene expression.

Geometrically encoded positioning of introns, intergenic segments, and exons in the human genome

The paper proposes that introns, intergenic segments, and exons are positioned geometrically within chromatin domains to sustain transcriptional memory and reconcile epigenetic patterns and mutation non-randomness.

Chromatin packing domains persist after RAD21 depletion in 3D.

The paper shows that RAD21 depletion reduces but does not eliminate chromatin packing domains in electron microscopy, suggesting non-cohesin mechanisms largely control 3D structure.

Statistical Analysis of Three-Dimensional Chromatin Packing Domains Determined by Chromatin Scanning Transmission Electron Microscopy (ChromSTEM)

The paper introduces ChromSTEM, a method for high-resolution 3D imaging of chromatin structure, and finds that chromatin forms well-defined domains around 100 nm in radius with radially decreasing mass-density.