Chromatin endogenous cleavage provides a global view of yeast RNA polymerase II transcription kinetics
Chromatin immunoprecipitation (ChIP-seq) is the most common approach to observe global binding of proteins to DNA in vivo. 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 rev...
Saved in:
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
eLife Sciences Publications Ltd
2024-11-01
|
| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/100764 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1846150502511804416 |
|---|---|
| author | Jake VanBelzen Bennet Sakelaris Donna G Brickner Nikita Marcou Hermann Riecke Niall M Mangan Jason H Brickner |
| author_facet | Jake VanBelzen Bennet Sakelaris Donna G Brickner Nikita Marcou Hermann Riecke Niall M Mangan Jason H Brickner |
| author_sort | Jake VanBelzen |
| collection | DOAJ |
| description | Chromatin immunoprecipitation (ChIP-seq) is the most common approach to observe global binding of proteins to DNA in vivo. 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 (RNAPII). 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. |
| format | Article |
| id | doaj-art-f62bc0e3a4cd428c8956e71647aa9493 |
| institution | Kabale University |
| issn | 2050-084X |
| language | English |
| publishDate | 2024-11-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj-art-f62bc0e3a4cd428c8956e71647aa94932024-11-28T17:48:43ZengeLife Sciences Publications LtdeLife2050-084X2024-11-011310.7554/eLife.100764Chromatin endogenous cleavage provides a global view of yeast RNA polymerase II transcription kineticsJake VanBelzen0https://orcid.org/0000-0003-0949-3641Bennet Sakelaris1https://orcid.org/0000-0001-8798-584XDonna G Brickner2Nikita Marcou3https://orcid.org/0000-0003-0232-081XHermann Riecke4https://orcid.org/0000-0002-6070-4742Niall M Mangan5https://orcid.org/0000-0002-3491-8341Jason H Brickner6https://orcid.org/0000-0001-8019-3743Department of Molecular Biosciences, Northwestern University, Evanston, United StatesDepartment of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, United StatesDepartment of Molecular Biosciences, Northwestern University, Evanston, United StatesDepartment of Molecular Biosciences, Northwestern University, Evanston, United StatesDepartment of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, United StatesDepartment of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, United StatesDepartment of Molecular Biosciences, Northwestern University, Evanston, United StatesChromatin immunoprecipitation (ChIP-seq) is the most common approach to observe global binding of proteins to DNA in vivo. 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 (RNAPII). 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.https://elifesciences.org/articles/100764transcriptiongenomicskineticsregulationChIPChEC |
| spellingShingle | Jake VanBelzen Bennet Sakelaris Donna G Brickner Nikita Marcou Hermann Riecke Niall M Mangan Jason H Brickner Chromatin endogenous cleavage provides a global view of yeast RNA polymerase II transcription kinetics eLife transcription genomics kinetics regulation ChIP ChEC |
| title | Chromatin endogenous cleavage provides a global view of yeast RNA polymerase II transcription kinetics |
| title_full | Chromatin endogenous cleavage provides a global view of yeast RNA polymerase II transcription kinetics |
| title_fullStr | Chromatin endogenous cleavage provides a global view of yeast RNA polymerase II transcription kinetics |
| title_full_unstemmed | Chromatin endogenous cleavage provides a global view of yeast RNA polymerase II transcription kinetics |
| title_short | Chromatin endogenous cleavage provides a global view of yeast RNA polymerase II transcription kinetics |
| title_sort | chromatin endogenous cleavage provides a global view of yeast rna polymerase ii transcription kinetics |
| topic | transcription genomics kinetics regulation ChIP ChEC |
| url | https://elifesciences.org/articles/100764 |
| work_keys_str_mv | AT jakevanbelzen chromatinendogenouscleavageprovidesaglobalviewofyeastrnapolymeraseiitranscriptionkinetics AT bennetsakelaris chromatinendogenouscleavageprovidesaglobalviewofyeastrnapolymeraseiitranscriptionkinetics AT donnagbrickner chromatinendogenouscleavageprovidesaglobalviewofyeastrnapolymeraseiitranscriptionkinetics AT nikitamarcou chromatinendogenouscleavageprovidesaglobalviewofyeastrnapolymeraseiitranscriptionkinetics AT hermannriecke chromatinendogenouscleavageprovidesaglobalviewofyeastrnapolymeraseiitranscriptionkinetics AT niallmmangan chromatinendogenouscleavageprovidesaglobalviewofyeastrnapolymeraseiitranscriptionkinetics AT jasonhbrickner chromatinendogenouscleavageprovidesaglobalviewofyeastrnapolymeraseiitranscriptionkinetics |