KAS-CUT&Tag for direct mapping of transcription bubbles.

KAS-CUT&Tag directly maps RNA polymerase II transcription bubbles by labeling exposed single-stranded DNA, revealing bubble density that tracks nascent transcription across Pol II-bound genes.

• Why it matters: Existing approaches infer transcriptional activity indirectly, leaving transcription bubble dynamics and regulatory contacts hard to measure directly at Pol II loci.
• What they did: The method combines N3-kethoxal labeling with CUT&Tag to map bubbles, then compares bubble density across promoter, gene body, and termination regions and across chromatin marks and factors.
• The result: Bubble density correlates with nascent transcription levels and is enriched at H3K27ac, H3K4me3, H3K36me3 and U2AF2–marked genes, with highest enrichment at replication-coupled histone genes in K562 and GM12878, and it detects NPAT co-occupancy with Pol II at the histone locus body.

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