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Modeling the nascent RNA transcriptome with chrTT-seq to extract chromatin dissociation dynamics on newly transcribed RNA.

ABSTRACT: To capture chromatin dissociation dynamics of nascent RNA transcripts we labeled MCF-7 cells with 4-thio-uridine (4-SU) for 8 minutes, then chased with an excess of uridine for 5, 10, 15 and 20 min. At each pulse-chase time point we performed TT-seq from the chromatin-associated and nucleoplasmic fraction. The ratios of spike-in normalized chromatin-associated to chromatin-released nascent RNA read coverage over genomic features (transcripts' last exons) were fitted on an exponential decay function to extract an estimated chromatin association half-live time for each transcript.

ORGANISM(S): Homo sapiens

PROVIDER: GSE218726 | GEO | 2023/09/21

REPOSITORIES: GEO

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