Researchers led by Kazuhiro Maeshima at the National Institute of Genetics and SOKENDAI tracked how different transcription systems affect chromatin motion in living human cells. The team combined Repli-Histo labeling, which distinguishes four chromatin classes from active euchromatin to inactive heterochromatin, with single-nucleosome imaging to directly observe individual nucleosome movement.
The study found that transcription does not constrain chromatin uniformly across the nucleus. When RNA polymerase II, which transcribes most protein-coding genes, was inhibited, nucleosome motion increased in euchromatin and in heterochromatin around nucleoli, but showed little change at the nuclear periphery. RNA polymerase I, which produces ribosomal RNAs in nucleoli, had a different effect. Inhibiting Pol I selectively increased nucleosome motion only in late-replicating heterochromatin near nucleoli.
"Different transcription systems appear to impose physical constraints on different chromatin regions, depending on both their chromatin state and where they are located in the nucleus," Maeshima says in the report.
The researchers also developed a machine-learning classifier to objectively identify the four chromatin classes. The work appears in Cell Reports and suggests that nucleolus-associated chromatin is shaped by multiple transcription-dependent mechanisms that act on different chromatin classes.