Biology subjects

Greene, J. E.

Publications and source records attributed to Greene, J. E..

3 recordsLinked to original sources

bioRxiv2026

KAS-CUT&Tag for direct mapping of transcription bubbles

Transcription by RNA Polymerase II (Pol II) generates dynamic transcription bubbles as it moves forward, but existing methods map transcriptional activity in vivo only indirectly. We introduce KAS-CUT&Tag, a method that combines N3-kethoxal labeling of exposed guanines with CUT&Tag to directly map transcription bubbles. We find that bubble density varies across Pol II-bound genes at transcription start sites, gene bodies, and termination sites. Transcription bubbles are enriched at genes marked by the H3K36me3 histone modification and chromatin-bound splicing factor U2AF2, but the highest enrichment is at replication-coupled histone genes throughout the cell cycle. KAS-CUT&Tag also detects colocalization of the histone gene transcription factor NPAT with Pol II at the Histone Locus Body, suggesting NPAT is juxtaposed to transcription bubbles via interaction with Pol II. Together, KAS-CUT&Tag enables direct mapping of Pol II and regulatory interactions at transcription bubbles, providing a powerful tool for precise analysis of transcriptional activity.

genomics↗

bioRxiv2026

Histone H3K27 methylation states are sequentially catalyzed in cycling cells

Polycomb domains form at silenced genes and are marked by histone H3 lysine 27 tri-methylation, but it is unclear how this methylation is maintained following DNA replication in proliferating cells. Here, we use CUT&Tag chromatin profiling to track the dynamics of H3K27 methylation in human cells. We find that tri-methylation in Polycomb domains is maintained by stepwise methylation after DNA replication. Outside of Polycomb domains, thousands of inactive genes gain histone H3K27 di-methylation hours after DNA replication. Acute treatment with small-molecule inhibitors of the Polycomb Repressive Complex 2 (PRC2) histone methyltransferase slows H3K27 methylation during S-phase of the cell cycle and increases acetylation of the residue. This effect is most pronounced at Polycomb domains replicating in early S-phase, suggesting that early replication and slow histone methylation confers plasticity to developmentally silenced genes. Together, our results explain how H3K27 modification patterns are faithfully duplicated in rapidly proliferating cells.

genomics↗

bioRxiv2024

Direct measurement of RNA Polymerase II hypertranscription in cancer FFPE samples

Genome-wide hypertranscription is common in hu-man cancer and predicts poor prognosis. To under-stand how hypertranscription might drive cancer, we applied our FFPE-CUTAC method for mapping RNA Polymerase II (RNAPII) genome-wide in formalin-fixed paraffin-embedded (FFPE) sections. We demonstrate global RNAPII elevations in mouse gliomas and assort-ed human tumors in small clinical samples and discov-er regional elevations corresponding to de novo HER2 amplifications punctuated by likely selective sweeps. RNAPII occupancy at replication-coupled histone genes correlated with WHO grade in meningiomas, ac-curately predicted rapid recurrence, and corresponded to whole-arm chromosome losses. Elevated RNAPII at histone genes in meningiomas and diverse breast cancers is consistent with histone production being rate-limiting for S-phase progression and histone gene hypertranscription driving overproliferation and aneu-ploidy in cancer, with general implications for precision oncology.

cancer biology↗