Chromatin Endogenous Cleavage Provides a Global View of Yeast RNA Polymerase II Transcription Kinetics

Overview

Journal bioRxiv

Date 2024 Jul 19

PMID 39026809

Authors

Jake VanBelzen

Bennet Sakelaris

Donna Garvey Brickner

Nikita Marcou

Hermann Riecke

Niall Mangan

Jason H Brickner

Affiliations

Soon will be listed here.

Abstract

Chromatin immunoprecipitation (ChIP-seq) is the most common approach to observe global binding of proteins to DNA . The occupancy of transcription factors (TFs) from ChIP-seq agrees well with an alternative method, chromatin endogenous cleavage (ChEC-seq2). However, ChIP-seq and ChEC-seq2 reveal strikingly different patterns of enrichment of yeast RNA polymerase II. We hypothesized that this reflects distinct populations of RNAPII, some of which are captured by ChIP-seq and some of which are captured by ChEC-seq2. RNAPII association with enhancers and promoters - predicted from biochemical studies - is detected well by ChEC-seq2 but not by ChIP-seq. Enhancer/promoter bound RNAPII correlates with transcription levels and matches predicted occupancy based on published rates of enhancer recruitment, preinitiation assembly, initiation, elongation and termination. The occupancy from ChEC-seq2 allowed us to develop a stochastic model for global kinetics of RNAPII transcription which captured both the ChEC-seq2 data and changes upon chemical-genetic perturbations to transcription. Finally, RNAPII ChEC-seq2 and kinetic modeling suggests that a mutation in the Gcn4 transcription factor that blocks interaction with the NPC destabilizes promoter-associated RNAPII without altering its recruitment to the enhancer.

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