Single-molecule FRET method to investigate the dynamics of transcription elongation through the nucleosome by RNA polymerase II

Jaehyoun Lee, J. Brooks Crickard, Joseph C. Reese, Tae-hee Lee

Research output: Contribution to journalReview article

3 Citations (Scopus)

Abstract

Transcription elongation through the nucleosome is a precisely coordinated activity to ensure timely production of RNA and accurate regulation of co-transcriptional histone modifications. Nucleosomes actively participate in transcription regulation at various levels and impose physical barriers to RNA polymerase II (RNAPII) during transcription elongation. Despite its high significance, the detailed dynamics of how RNAPII translocates along nucleosomal DNA during transcription elongation and how the nucleosome structure dynamically conforms to the changes necessary for RNAPII progression remain poorly understood. Transcription elongation through the nucleosome is a complex process and investigating the changes of the nucleosome structure during this process by ensemble measurements is daunting. This is because it is nearly impossible to synchronize elongation complexes within a nucleosome or a sub-nucleosome to a designated location at a high enough efficiency for desired sample homogeneity. Here we review our recently developed single-molecule FRET experimental system and method that has fulfilled this deficiency. With our method, one can follow the changes in the structure of individual nucleosomes during transcription elongation. We demonstrated that this method enables the detailed measurements of the kinetics of transcription elongation through the nucleosome and its regulation by a transcription factor, which can be easily extended to investigations of the roles of environmental variables and histone post-translational modifications in regulating transcription elongation.

Original languageEnglish (US)
Pages (from-to)51-58
Number of pages8
JournalMethods
Volume159-160
DOIs
StatePublished - Apr 15 2019

Fingerprint

Nucleosomes
RNA Polymerase II
Transcription
Elongation
Molecules
Histones
Histone Code
Architectural Accessibility
Post Translational Protein Processing
Transcription Factors
RNA
Kinetics
DNA

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

@article{2dcd9dc02f1c44ee8eb4932edbe1f95f,
title = "Single-molecule FRET method to investigate the dynamics of transcription elongation through the nucleosome by RNA polymerase II",
abstract = "Transcription elongation through the nucleosome is a precisely coordinated activity to ensure timely production of RNA and accurate regulation of co-transcriptional histone modifications. Nucleosomes actively participate in transcription regulation at various levels and impose physical barriers to RNA polymerase II (RNAPII) during transcription elongation. Despite its high significance, the detailed dynamics of how RNAPII translocates along nucleosomal DNA during transcription elongation and how the nucleosome structure dynamically conforms to the changes necessary for RNAPII progression remain poorly understood. Transcription elongation through the nucleosome is a complex process and investigating the changes of the nucleosome structure during this process by ensemble measurements is daunting. This is because it is nearly impossible to synchronize elongation complexes within a nucleosome or a sub-nucleosome to a designated location at a high enough efficiency for desired sample homogeneity. Here we review our recently developed single-molecule FRET experimental system and method that has fulfilled this deficiency. With our method, one can follow the changes in the structure of individual nucleosomes during transcription elongation. We demonstrated that this method enables the detailed measurements of the kinetics of transcription elongation through the nucleosome and its regulation by a transcription factor, which can be easily extended to investigations of the roles of environmental variables and histone post-translational modifications in regulating transcription elongation.",
author = "Jaehyoun Lee and Crickard, {J. Brooks} and Reese, {Joseph C.} and Tae-hee Lee",
year = "2019",
month = "4",
day = "15",
doi = "10.1016/j.ymeth.2019.01.009",
language = "English (US)",
volume = "159-160",
pages = "51--58",
journal = "Methods",
issn = "1046-2023",
publisher = "Academic Press Inc.",

}

Single-molecule FRET method to investigate the dynamics of transcription elongation through the nucleosome by RNA polymerase II. / Lee, Jaehyoun; Crickard, J. Brooks; Reese, Joseph C.; Lee, Tae-hee.

In: Methods, Vol. 159-160, 15.04.2019, p. 51-58.

Research output: Contribution to journalReview article

TY - JOUR

T1 - Single-molecule FRET method to investigate the dynamics of transcription elongation through the nucleosome by RNA polymerase II

AU - Lee, Jaehyoun

AU - Crickard, J. Brooks

AU - Reese, Joseph C.

AU - Lee, Tae-hee

PY - 2019/4/15

Y1 - 2019/4/15

N2 - Transcription elongation through the nucleosome is a precisely coordinated activity to ensure timely production of RNA and accurate regulation of co-transcriptional histone modifications. Nucleosomes actively participate in transcription regulation at various levels and impose physical barriers to RNA polymerase II (RNAPII) during transcription elongation. Despite its high significance, the detailed dynamics of how RNAPII translocates along nucleosomal DNA during transcription elongation and how the nucleosome structure dynamically conforms to the changes necessary for RNAPII progression remain poorly understood. Transcription elongation through the nucleosome is a complex process and investigating the changes of the nucleosome structure during this process by ensemble measurements is daunting. This is because it is nearly impossible to synchronize elongation complexes within a nucleosome or a sub-nucleosome to a designated location at a high enough efficiency for desired sample homogeneity. Here we review our recently developed single-molecule FRET experimental system and method that has fulfilled this deficiency. With our method, one can follow the changes in the structure of individual nucleosomes during transcription elongation. We demonstrated that this method enables the detailed measurements of the kinetics of transcription elongation through the nucleosome and its regulation by a transcription factor, which can be easily extended to investigations of the roles of environmental variables and histone post-translational modifications in regulating transcription elongation.

AB - Transcription elongation through the nucleosome is a precisely coordinated activity to ensure timely production of RNA and accurate regulation of co-transcriptional histone modifications. Nucleosomes actively participate in transcription regulation at various levels and impose physical barriers to RNA polymerase II (RNAPII) during transcription elongation. Despite its high significance, the detailed dynamics of how RNAPII translocates along nucleosomal DNA during transcription elongation and how the nucleosome structure dynamically conforms to the changes necessary for RNAPII progression remain poorly understood. Transcription elongation through the nucleosome is a complex process and investigating the changes of the nucleosome structure during this process by ensemble measurements is daunting. This is because it is nearly impossible to synchronize elongation complexes within a nucleosome or a sub-nucleosome to a designated location at a high enough efficiency for desired sample homogeneity. Here we review our recently developed single-molecule FRET experimental system and method that has fulfilled this deficiency. With our method, one can follow the changes in the structure of individual nucleosomes during transcription elongation. We demonstrated that this method enables the detailed measurements of the kinetics of transcription elongation through the nucleosome and its regulation by a transcription factor, which can be easily extended to investigations of the roles of environmental variables and histone post-translational modifications in regulating transcription elongation.

UR - http://www.scopus.com/inward/record.url?scp=85060276414&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85060276414&partnerID=8YFLogxK

U2 - 10.1016/j.ymeth.2019.01.009

DO - 10.1016/j.ymeth.2019.01.009

M3 - Review article

VL - 159-160

SP - 51

EP - 58

JO - Methods

JF - Methods

SN - 1046-2023

ER -